Patient ID [cpr]<\/span><\/h5> <\/td> <\/tr><\/tbody> <\/table> create_html_table(text = paste(\"assessor\", 1:2, sep = \"_\"), variable = c(\"[cpr]\")) #> assessor_1 [cpr]<\/span><\/h5> <\/td> <\/tr> assessor_2 [cpr]<\/span><\/h5> <\/td> <\/tr><\/tbody> <\/table> # create_html_table(text = c(\"CPR nummer\",\"Word\"), variable = c(\"[cpr][1]\", \"[cpr][2]\", \"[test]\"))"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/create_instrument_meta.html","id":null,"dir":"Reference","previous_headings":"","what":"DEPRICATED Create zips file with necessary content based on data set — create_instrument_meta","title":"DEPRICATED Create zips file with necessary content based on data set — create_instrument_meta","text":"Metadata can added editing data dictionary project initial design phase. want later add new instruments, function can used create () instrument(s) add project production.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/create_instrument_meta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"DEPRICATED Create zips file with necessary content based on data set — create_instrument_meta","text":"","code":"create_instrument_meta(data, dir = here::here(\"\"), record.id = TRUE)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/create_instrument_meta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"DEPRICATED Create zips file with necessary content based on data set — create_instrument_meta","text":"data metadata relevant instrument. `ds2dd_detailed()` dir destination dir instrument zip. Default current WD. record.id flag omit first row data dictionary assuming record_id field included instrument. Default TRUE.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/create_instrument_meta.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"DEPRICATED Create zips file with necessary content based on data set — create_instrument_meta","text":"list","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/create_instrument_meta.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"DEPRICATED Create zips file with necessary content based on data set — create_instrument_meta","text":"","code":"if (FALSE) { # \\dontrun{ data <- iris |> ds2dd_detailed( add.auto.id = TRUE, form.name = sample(c(\"b\", \"c\"), size = 6, replace = TRUE, prob = rep(.5, 2) ) ) |> purrr::pluck(\"meta\") # data |> create_instrument_meta() data <- iris |> ds2dd_detailed(add.auto.id = FALSE) |> purrr::pluck(\"data\") iris |> setNames(glue::glue(\"{sample(x = c('a','b'),size = length(ncol(iris)), replace=TRUE,prob = rep(x=.5,2))}__{names(iris)}\")) |> ds2dd_detailed(form.sep = \"__\") data |> purrr::pluck(\"meta\") |> create_instrument_meta(record.id = FALSE) } # }"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/cut_string_length.html","id":null,"dir":"Reference","previous_headings":"","what":"Cut string to desired length — cut_string_length","title":"Cut string to desired length — cut_string_length","text":"Cut string desired length","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/cut_string_length.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cut string to desired length — cut_string_length","text":"","code":"cut_string_length(data, l = 100)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/cut_string_length.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cut string to desired length — cut_string_length","text":"data data l length","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/cut_string_length.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Cut string to desired length — cut_string_length","text":"character string length l","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/cut_string_length.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cut string to desired length — cut_string_length","text":"","code":"\"length\" |> cut_string_length(l=3) #> [1] \"len\""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/d2w.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert single digits to words — d2w","title":"Convert single digits to words — d2w","text":"Convert single digits words","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/d2w.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert single digits to words — d2w","text":"","code":"d2w(x, lang = \"en\", neutrum = FALSE, everything = FALSE)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/d2w.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert single digits to words — d2w","text":"x data. Handle vectors, data.frames lists lang language. Danish (da) English (en), Default \"en\" neutrum numbers depending counted word everything flag also split numbers >9 single digits","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/d2w.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert single digits to words — d2w","text":"returns characters format input","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/d2w.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert single digits to words — d2w","text":"","code":"d2w(c(2:8, 21)) #> [1] \"two\" \"three\" \"four\" \"five\" \"six\" \"seven\" \"eight\" \"21\" d2w(data.frame(2:7, 3:8, 1), lang = \"da\", neutrum = TRUE) #> X2.7 X3.8 X1 #> 1 to tre et #> 2 tre fire et #> 3 fire fem et #> 4 fem seks et #> 5 seks syv et #> 6 syv otte et ## If everything=T, also larger numbers are reduced. ## Elements in the list are same length as input d2w(list(2:8, c(2, 6, 4, 23), 2), everything = TRUE) #> [[1]] #> [1] \"two\" \"three\" \"four\" \"five\" \"six\" \"seven\" \"eight\" #> #> [[2]] #> [1] \"two\" \"six\" \"four\" \"two three\" #> #> [[3]] #> [1] \"two\" #>"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/doc2dd.html","id":null,"dir":"Reference","previous_headings":"","what":"Doc table to data dictionary - EARLY, DOCS MISSING — doc2dd","title":"Doc table to data dictionary - EARLY, DOCS MISSING — doc2dd","text":"Works well `project.aid::docx2list()`. Allows defining database text document (see provided template) easier use data base creation. approach allows easier collaboration defining database. generic case data frame variable names values column. format like REDCap data dictionary, gives options formatting.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/doc2dd.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Doc table to data dictionary - EARLY, DOCS MISSING — doc2dd","text":"","code":"doc2dd( data, instrument.name, col.variables = 1, list.datetime.format = list(date_dmy = \"_dat[eo]$\", time_hh_mm_ss = \"_ti[md]e?$\"), col.description = NULL, col.condition = NULL, col.subheader = NULL, subheader.tag = \"h2\", condition.minor.sep = \",\", condition.major.sep = \";\", col.calculation = NULL, col.choices = NULL, choices.char.sep = \"/\", missing.default = NA )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/doc2dd.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Doc table to data dictionary - EARLY, DOCS MISSING — doc2dd","text":"data tibble data.frame variable names one column instrument.name character vector length one. Instrument name. col.variables variable names column (default = 1), allows dplyr subsetting list.datetime.format formatting date/time detection. See `case_match_regex_list()` col.description descriptions column, allows dplyr subsetting. empty, variable names used. col.condition conditions branching column, allows dplyr subsetting. See `char2cond()`. col.subheader sub-header column, allows dplyr subsetting. See `format_subheader()`. subheader.tag formatting tag. Default \"h2\" condition.minor.sep condition split minor. See `char2cond()`. Default \",\". condition.major.sep condition split major. See `char2cond()`. Default \";\". col.calculation calculations column. written exact. Character vector. col.choices choices column. See `char2choice()`. choices.char.sep choices split. See `char2choice()`. Default \"/\". missing.default value missing fields. Default NA.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/doc2dd.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Doc table to data dictionary - EARLY, DOCS MISSING — doc2dd","text":"tibble data.frame (data)","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/doc2dd.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Doc table to data dictionary - EARLY, DOCS MISSING — doc2dd","text":"","code":"# data <- dd_inst # data |> doc2dd(instrument.name = \"evt\", # col.description = 3, # col.condition = 4, # col.subheader = 2, # col.calculation = 5, # col.choices = 6)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd.html","id":null,"dir":"Reference","previous_headings":"","what":"(DEPRECATED) Data set to data dictionary function — ds2dd","title":"(DEPRECATED) Data set to data dictionary function — ds2dd","text":"Creates basic data dictionary skeleton. Please see `ds2dd_detailed()` advanced function.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"(DEPRECATED) Data set to data dictionary function — ds2dd","text":"","code":"ds2dd( ds, record.id = \"record_id\", form.name = \"basis\", field.type = \"text\", field.label = NULL, include.column.names = FALSE, metadata = names(REDCapCAST::redcapcast_meta) )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"(DEPRECATED) Data set to data dictionary function — ds2dd","text":"ds data set record.id name column number id variable, moved first row data dictionary, character integer. Default \"record_id\". form.name vector form names, character string, length 1 length equal number variables. Default \"basis\". field.type vector field types, character string, length 1 length equal number variables. Default \"text. field.label vector form names, character string, length 1 length equal number variables. Default NULL identical field names. include.column.names Flag give detailed output including new column names original data set upload. metadata Metadata column names. Default included names(REDCapCAST::redcapcast_meta).","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"(DEPRECATED) Data set to data dictionary function — ds2dd","text":"data.frame list data.frame vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"(DEPRECATED) Data set to data dictionary function — ds2dd","text":"Migrated stRoke ds2dd(). Fits better functionality 'REDCapCAST'.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"(DEPRECATED) Data set to data dictionary function — ds2dd","text":"","code":"redcapcast_data$record_id <- seq_len(nrow(redcapcast_data)) ds2dd(redcapcast_data, include.column.names = TRUE) #> $DataDictionary #> field_name form_name section_header field_type #> 1 record_id basis NA text #> 2 redcap_event_name basis NA text #> 3 redcap_repeat_instrument basis NA text #> 4 redcap_repeat_instance basis NA text #> 5 cpr basis NA text #> 6 inclusion basis NA text #> 7 inclusion_time basis NA text #> 8 dob basis NA text #> 9 age basis NA text #> 10 age_integer basis NA text #> 11 sex basis NA text #> 12 cohabitation basis NA text #> 13 hypertension basis NA text #> 14 diabetes basis NA text #> 15 region basis NA text #> 16 baseline_data_start_complete basis NA text #> 17 mrs_assessed basis NA text #> 18 mrs_date basis NA text #> 19 mrs_score basis NA text #> 20 mrs_complete basis NA text #> 21 con_mrs basis NA text #> 22 con_calc basis NA text #> 23 consensus_complete basis NA text #> 24 event_datetime basis NA text #> 25 event_age basis NA text #> 26 event_type basis NA text #> 27 new_event_complete basis NA text #> field_label select_choices_or_calculations field_note #> 1 record_id NA NA #> 2 redcap_event_name NA NA #> 3 redcap_repeat_instrument NA NA #> 4 redcap_repeat_instance NA NA #> 5 cpr NA NA #> 6 inclusion NA NA #> 7 inclusion_time NA NA #> 8 dob NA NA #> 9 age NA NA #> 10 age_integer NA NA #> 11 sex NA NA #> 12 cohabitation NA NA #> 13 hypertension NA NA #> 14 diabetes NA NA #> 15 region NA NA #> 16 baseline_data_start_complete NA NA #> 17 mrs_assessed NA NA #> 18 mrs_date NA NA #> 19 mrs_score NA NA #> 20 mrs_complete NA NA #> 21 con_mrs NA NA #> 22 con_calc NA NA #> 23 consensus_complete NA NA #> 24 event_datetime NA NA #> 25 event_age NA NA #> 26 event_type NA NA #> 27 new_event_complete NA NA #> text_validation_type_or_show_slider_number text_validation_min #> 1 NA NA #> 2 NA NA #> 3 NA NA #> 4 NA NA #> 5 NA NA #> 6 NA NA #> 7 NA NA #> 8 NA NA #> 9 NA NA #> 10 NA NA #> 11 NA NA #> 12 NA NA #> 13 NA NA #> 14 NA NA #> 15 NA NA #> 16 NA NA #> 17 NA NA #> 18 NA NA #> 19 NA NA #> 20 NA NA #> 21 NA NA #> 22 NA NA #> 23 NA NA #> 24 NA NA #> 25 NA NA #> 26 NA NA #> 27 NA NA #> text_validation_max identifier branching_logic required_field #> 1 NA NA NA NA #> 2 NA NA NA NA #> 3 NA NA NA NA #> 4 NA NA NA NA #> 5 NA NA NA NA #> 6 NA NA NA NA #> 7 NA NA NA NA #> 8 NA NA NA NA #> 9 NA NA NA NA #> 10 NA NA NA NA #> 11 NA NA NA NA #> 12 NA NA NA NA #> 13 NA NA NA NA #> 14 NA NA NA NA #> 15 NA NA NA NA #> 16 NA NA NA NA #> 17 NA NA NA NA #> 18 NA NA NA NA #> 19 NA NA NA NA #> 20 NA NA NA NA #> 21 NA NA NA NA #> 22 NA NA NA NA #> 23 NA NA NA NA #> 24 NA NA NA NA #> 25 NA NA NA NA #> 26 NA NA NA NA #> 27 NA NA NA NA #> custom_alignment question_number matrix_group_name matrix_ranking #> 1 NA NA NA NA #> 2 NA NA NA NA #> 3 NA NA NA NA #> 4 NA NA NA NA #> 5 NA NA NA NA #> 6 NA NA NA NA #> 7 NA NA NA NA #> 8 NA NA NA NA #> 9 NA NA NA NA #> 10 NA NA NA NA #> 11 NA NA NA NA #> 12 NA NA NA NA #> 13 NA NA NA NA #> 14 NA NA NA NA #> 15 NA NA NA NA #> 16 NA NA NA NA #> 17 NA NA NA NA #> 18 NA NA NA NA #> 19 NA NA NA NA #> 20 NA NA NA NA #> 21 NA NA NA NA #> 22 NA NA NA NA #> 23 NA NA NA NA #> 24 NA NA NA NA #> 25 NA NA NA NA #> 26 NA NA NA NA #> 27 NA NA NA NA #> field_annotation #> 1 NA #> 2 NA #> 3 NA #> 4 NA #> 5 NA #> 6 NA #> 7 NA #> 8 NA #> 9 NA #> 10 NA #> 11 NA #> 12 NA #> 13 NA #> 14 NA #> 15 NA #> 16 NA #> 17 NA #> 18 NA #> 19 NA #> 20 NA #> 21 NA #> 22 NA #> 23 NA #> 24 NA #> 25 NA #> 26 NA #> 27 NA #> #> $`Column names` #> [1] \"record_id\" \"redcap_event_name\" #> [3] \"redcap_repeat_instrument\" \"redcap_repeat_instance\" #> [5] \"cpr\" \"inclusion\" #> [7] \"inclusion_time\" \"dob\" #> [9] \"age\" \"age_integer\" #> [11] \"sex\" \"cohabitation\" #> [13] \"hypertension\" \"diabetes\" #> [15] \"region\" \"baseline_data_start_complete\" #> [17] \"mrs_assessed\" \"mrs_date\" #> [19] \"mrs_score\" \"mrs_complete\" #> [21] \"con_mrs\" \"con_calc\" #> [23] \"consensus_complete\" \"event_datetime\" #> [25] \"event_age\" \"event_type\" #> [27] \"new_event_complete\" #>"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd_detailed.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract data from stata file for data dictionary — ds2dd_detailed","title":"Extract data from stata file for data dictionary — ds2dd_detailed","text":"Extract data stata file data dictionary","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd_detailed.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract data from stata file for data dictionary — ds2dd_detailed","text":"","code":"ds2dd_detailed( data, add.auto.id = FALSE, date.format = \"dmy\", form.name = NULL, form.sep = NULL, form.prefix = TRUE, field.type = NULL, field.label = NULL, field.label.attr = \"label\", field.validation = NULL, metadata = names(REDCapCAST::redcapcast_meta), convert.logicals = FALSE )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd_detailed.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract data from stata file for data dictionary — ds2dd_detailed","text":"data data frame add.auto.id flag add id column date.format date format, character string. ymd/dmy/mdy. dafault dmy. form.name manually specify form name(s). Vector length 1 ncol(data). Default NULL \"data\" used. form.sep supplied dataset form names suffix prefix column/variable names, seperator can specified. supplied, form.name ignored. Default NULL. form.prefix Flag set form prefix (TRUE) suffix (FALSE) column names. Assumes columns pre- suffix specified. field.type manually specify field type(s). Vector length 1 ncol(data). Default NULL \"text\" used everything factors, wil get \"radio\". field.label manually specify field label(s). Vector length 1 ncol(data). Default NULL colnames(data) used attribute `field.label.attr` haven_labelled data set (imported .dta file `haven::read_dta()`). field.label.attr attribute name named labels haven_labelled data set (imported .dta file `haven::read_dta()`. Default \"label\" field.validation manually specify field validation(s). Vector length 1 ncol(data). Default NULL `levels()` used factors attribute `factor.labels.attr` haven_labelled data set (imported .dta file `haven::read_dta()`). metadata redcap metadata headings. Default names(REDCapCAST::redcapcast_meta). convert.logicals convert logicals factor. Default TRUE.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd_detailed.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract data from stata file for data dictionary — ds2dd_detailed","text":"list length 2","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd_detailed.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Extract data from stata file for data dictionary — ds2dd_detailed","text":"function natural development ds2dd() function. assumes first column ID-column. checks. Please, always inspect data dictionary upload. Ensure, data set formatted much information possible. `field.type` can supplied","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/ds2dd_detailed.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Extract data from stata file for data dictionary — ds2dd_detailed","text":"","code":"## Basic parsing with default options requireNamespace(\"REDCapCAST\") redcapcast_data |> dplyr::select(-dplyr::starts_with(\"redcap_\")) |> ds2dd_detailed() #> $data #> # A tibble: 25 × 24 #> record_id cpr inclusion inclusion_time dob age age_integer sex #> #> 1 1 12034… 2023-03-13 12:38:49 1940-03-12 83.0 83 fema… #> 2 2 01023… 2023-03-01 10:38:57 1934-02-01 89.1 89 male #> 3 2 NA NA NA NA NA NA NA #> 4 2 NA NA NA NA NA NA NA #> 5 3 23015… 2022-03-08 12:01:07 1956-01-23 66.1 66 male #> 6 3 NA NA NA NA NA NA NA #> 7 3 NA NA NA NA NA NA NA #> 8 3 NA NA NA NA NA NA NA #> 9 3 NA NA NA NA NA NA NA #> 10 3 NA NA NA NA NA NA NA #> # ℹ 15 more rows #> # ℹ 16 more variables: cohabitation , hypertension , diabetes , #> # region , baseline_data_start_complete , mrs_assessed , #> # mrs_date , mrs_score , mrs_complete , con_mrs , #> # con_calc , consensus_complete , event_datetime , #> # event_age , event_type , new_event_complete #> #> $meta #> # A tibble: 24 × 18 #> field_name form_name section_header field_type field_label #> #> 1 record_id data NA text record_id #> 2 cpr data NA text cpr #> 3 inclusion data NA text inclusion #> 4 inclusion_time data NA text inclusion_time #> 5 dob data NA text dob #> 6 age data NA text age #> 7 age_integer data NA text age_integer #> 8 sex data NA text sex #> 9 cohabitation data NA text cohabitation #> 10 hypertension data NA text hypertension #> # ℹ 14 more rows #> # ℹ 13 more variables: select_choices_or_calculations , field_note , #> # text_validation_type_or_show_slider_number , #> # text_validation_min , text_validation_max , identifier , #> # branching_logic , required_field , custom_alignment , #> # question_number , matrix_group_name , matrix_ranking , #> # field_annotation #> #> attr(,\"class\") #> [1] \"REDCapCAST\" \"list\" ## Adding a record_id field iris |> ds2dd_detailed(add.auto.id = TRUE) #> $data #> # A tibble: 150 × 6 #> record_id sepallength sepalwidth petallength petalwidth species #> #> 1 1 5.1 3.5 1.4 0.2 1 #> 2 2 4.9 3 1.4 0.2 1 #> 3 3 4.7 3.2 1.3 0.2 1 #> 4 4 4.6 3.1 1.5 0.2 1 #> 5 5 5 3.6 1.4 0.2 1 #> 6 6 5.4 3.9 1.7 0.4 1 #> 7 7 4.6 3.4 1.4 0.3 1 #> 8 8 5 3.4 1.5 0.2 1 #> 9 9 4.4 2.9 1.4 0.2 1 #> 10 10 4.9 3.1 1.5 0.1 1 #> # ℹ 140 more rows #> #> $meta #> # A tibble: 6 × 18 #> field_name form_name section_header field_type field_label #> #> 1 record_id data NA text record_id #> 2 sepallength data NA text Sepal.Length #> 3 sepalwidth data NA text Sepal.Width #> 4 petallength data NA text Petal.Length #> 5 petalwidth data NA text Petal.Width #> 6 species data NA radio Species #> # ℹ 13 more variables: select_choices_or_calculations , field_note , #> # text_validation_type_or_show_slider_number , #> # text_validation_min , text_validation_max , identifier , #> # branching_logic , required_field , custom_alignment , #> # question_number , matrix_group_name , matrix_ranking , #> # field_annotation #> #> attr(,\"class\") #> [1] \"REDCapCAST\" \"list\" ## Passing form name information to function iris |> ds2dd_detailed( add.auto.id = TRUE, form.name = sample(c(\"b\", \"c\"), size = 6, replace = TRUE, prob = rep(.5, 2)) ) |> purrr::pluck(\"meta\") #> # A tibble: 6 × 18 #> field_name form_name section_header field_type field_label #> #> 1 record_id b NA text record_id #> 2 sepallength b NA text Sepal.Length #> 3 sepalwidth c NA text Sepal.Width #> 4 petallength c NA text Petal.Length #> 5 petalwidth b NA text Petal.Width #> 6 species c NA radio Species #> # ℹ 13 more variables: select_choices_or_calculations , field_note , #> # text_validation_type_or_show_slider_number , #> # text_validation_min , text_validation_max , identifier , #> # branching_logic , required_field , custom_alignment , #> # question_number , matrix_group_name , matrix_ranking , #> # field_annotation mtcars |> dplyr::mutate(unknown = NA) |> numchar2fct() |> ds2dd_detailed(add.auto.id = TRUE) #> $data #> # A tibble: 32 × 13 #> record_id mpg cyl disp hp drat wt qsec vs am gear carb #> #> 1 1 21 2 160 110 3.9 2.62 16.5 1 2 2 4 #> 2 2 21 2 160 110 3.9 2.88 17.0 1 2 2 4 #> 3 3 22.8 1 108 93 3.85 2.32 18.6 2 2 2 1 #> 4 4 21.4 2 258 110 3.08 3.22 19.4 2 1 1 1 #> 5 5 18.7 3 360 175 3.15 3.44 17.0 1 1 1 2 #> 6 6 18.1 2 225 105 2.76 3.46 20.2 2 1 1 1 #> 7 7 14.3 3 360 245 3.21 3.57 15.8 1 1 1 4 #> 8 8 24.4 1 147. 62 3.69 3.19 20 2 1 2 2 #> 9 9 22.8 1 141. 95 3.92 3.15 22.9 2 1 2 2 #> 10 10 19.2 2 168. 123 3.92 3.44 18.3 2 1 2 4 #> # ℹ 22 more rows #> # ℹ 1 more variable: unknown #> #> $meta #> # A tibble: 13 × 18 #> field_name form_name section_header field_type field_label #> #> 1 record_id data NA text record_id #> 2 mpg data NA text mpg #> 3 cyl data NA radio cyl #> 4 disp data NA text disp #> 5 hp data NA text hp #> 6 drat data NA text drat #> 7 wt data NA text wt #> 8 qsec data NA text qsec #> 9 vs data NA radio vs #> 10 am data NA radio am #> 11 gear data NA radio gear #> 12 carb data NA radio carb #> 13 unknown data NA truefalse unknown #> # ℹ 13 more variables: select_choices_or_calculations , field_note , #> # text_validation_type_or_show_slider_number , #> # text_validation_min , text_validation_max , identifier , #> # branching_logic , required_field , custom_alignment , #> # question_number , matrix_group_name , matrix_ranking , #> # field_annotation #> #> attr(,\"class\") #> [1] \"REDCapCAST\" \"list\" ## Using column name suffix to carry form name data <- iris |> ds2dd_detailed(add.auto.id = TRUE) |> purrr::pluck(\"data\") names(data) <- glue::glue(\"{sample(x = c('a','b'),size = length(names(data)), replace=TRUE,prob = rep(x=.5,2))}__{names(data)}\") data |> ds2dd_detailed(form.sep = \"__\") #> $data #> # A tibble: 150 × 6 #> record_id sepallength sepalwidth petallength petalwidth species #> #> 1 1 5.1 3.5 1.4 0.2 1 #> 2 2 4.9 3 1.4 0.2 1 #> 3 3 4.7 3.2 1.3 0.2 1 #> 4 4 4.6 3.1 1.5 0.2 1 #> 5 5 5 3.6 1.4 0.2 1 #> 6 6 5.4 3.9 1.7 0.4 1 #> 7 7 4.6 3.4 1.4 0.3 1 #> 8 8 5 3.4 1.5 0.2 1 #> 9 9 4.4 2.9 1.4 0.2 1 #> 10 10 4.9 3.1 1.5 0.1 1 #> # ℹ 140 more rows #> #> $meta #> # A tibble: 6 × 18 #> field_name form_name section_header field_type field_label #> #> 1 record_id a NA text record_id #> 2 sepallength a NA text sepallength #> 3 sepalwidth b NA text sepalwidth #> 4 petallength b NA text petallength #> 5 petalwidth a NA text petalwidth #> 6 species a NA text species #> # ℹ 13 more variables: select_choices_or_calculations , field_note , #> # text_validation_type_or_show_slider_number , #> # text_validation_min , text_validation_max , identifier , #> # branching_logic , required_field , custom_alignment , #> # question_number , matrix_group_name , matrix_ranking , #> # field_annotation #> #> attr(,\"class\") #> [1] \"REDCapCAST\" \"list\""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/easy_redcap.html","id":null,"dir":"Reference","previous_headings":"","what":"Secure API key storage and data acquisition in one — easy_redcap","title":"Secure API key storage and data acquisition in one — easy_redcap","text":"Secure API key storage data acquisition one","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/easy_redcap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Secure API key storage and data acquisition in one — easy_redcap","text":"","code":"easy_redcap( project.name, uri, raw_or_label = \"both\", data_format = c(\"wide\", \"list\", \"redcap\", \"long\"), widen.data = NULL, ... )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/easy_redcap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Secure API key storage and data acquisition in one — easy_redcap","text":"project.name name current project (key storage key_set, using default keyring) uri REDCap database API uri raw_or_label argument passed read_redcap_tables. Default \"\" get labelled data. data_format Choose data widen.data argument widen exported data. [DEPRECATED], use `data_format`instead ... arguments passed read_redcap_tables.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/easy_redcap.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Secure API key storage and data acquisition in one — easy_redcap","text":"data.frame list depending widen.data","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/easy_redcap.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Secure API key storage and data acquisition in one — easy_redcap","text":"","code":"if (FALSE) { # \\dontrun{ easy_redcap(\"My_new_project\", fields = c(\"record_id\", \"age\", \"hypertension\")) } # }"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/export_redcap_instrument.html","id":null,"dir":"Reference","previous_headings":"","what":"Creates zip-file with necessary content to manually add instrument to database — export_redcap_instrument","title":"Creates zip-file with necessary content to manually add instrument to database — export_redcap_instrument","text":"Metadata can added editing data dictionary project initial design phase. want later add new instruments, function can used create () instrument(s) add project production.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/export_redcap_instrument.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Creates zip-file with necessary content to manually add instrument to database — export_redcap_instrument","text":"","code":"export_redcap_instrument(data, file, force = FALSE, record.id = \"record_id\")"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/export_redcap_instrument.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Creates zip-file with necessary content to manually add instrument to database — export_redcap_instrument","text":"data metadata relevant instrument. `ds2dd_detailed()` file destination file name. force force instrument creation ignore different form names just using first. record.id record id variable name. Default 'record_id'.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/export_redcap_instrument.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Creates zip-file with necessary content to manually add instrument to database — export_redcap_instrument","text":"exports zip-file","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/export_redcap_instrument.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Creates zip-file with necessary content to manually add instrument to database — export_redcap_instrument","text":"","code":"# iris |> # ds2dd_detailed( # add.auto.id = TRUE, # form.name = sample(c(\"b\", \"c\"), size = 6, replace = TRUE, prob = rep(.5, 2)) # ) |> # purrr::pluck(\"meta\") |> # (\\(.x){ # split(.x, .x$form_name) # })() |> # purrr::imap(function(.x, .i){ # export_redcap_instrument(.x,file=here::here(paste0(.i,Sys.Date(),\".zip\"))) # }) # iris |> # ds2dd_detailed( # add.auto.id = TRUE # ) |> # purrr::pluck(\"meta\") |> # export_redcap_instrument(file=here::here(paste0(\"instrument\",Sys.Date(),\".zip\")))"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/fct2num.html","id":null,"dir":"Reference","previous_headings":"","what":"Allows conversion of factor to numeric values preserving original levels — fct2num","title":"Allows conversion of factor to numeric values preserving original levels — fct2num","text":"Allows conversion factor numeric values preserving original levels","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/fct2num.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Allows conversion of factor to numeric values preserving original levels — fct2num","text":"","code":"fct2num(data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/fct2num.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Allows conversion of factor to numeric values preserving original levels — fct2num","text":"data vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/fct2num.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Allows conversion of factor to numeric values preserving original levels — fct2num","text":"numeric vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/fct2num.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Allows conversion of factor to numeric values preserving original levels — fct2num","text":"","code":"c(1, 4, 3, \"A\", 7, 8, 1) |> as_factor() |> fct2num() #> [1] 1 2 3 4 5 6 1 structure(c(1, 2, 3, 2, 10, 9), labels = c(Unknown = 9, Refused = 10), class = \"haven_labelled\" ) |> as_factor() |> fct2num() #> [1] 1 2 3 2 10 9 structure(c(1, 2, 3, 2, 10, 9), labels = c(Unknown = 9, Refused = 10), class = \"labelled\" ) |> as_factor() |> fct2num() #> [1] 1 2 3 2 10 9 structure(c(1, 2, 3, 2, 10, 9), labels = c(Unknown = 9, Refused = 10) ) |> as_factor() |> fct2num() #> [1] 1 2 3 2 NA NA"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/fct_drop.html","id":null,"dir":"Reference","previous_headings":"","what":"Drop unused levels preserving label data — fct_drop","title":"Drop unused levels preserving label data — fct_drop","text":"extends [forcats::fct_drop()] natively work across data.frame replaces [base::droplevels()].","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/fct_drop.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Drop unused levels preserving label data — fct_drop","text":"","code":"fct_drop(x, ...) # S3 method for class 'data.frame' fct_drop(x, ...) # S3 method for class 'factor' fct_drop(x, ...)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/fct_drop.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Drop unused levels preserving label data — fct_drop","text":"x Factor drop unused levels ... arguments passed method.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/fct_drop.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Drop unused levels preserving label data — fct_drop","text":"","code":"mtcars |> numchar2fct() |> fct_drop() #> # A tibble: 32 × 11 #> mpg cyl disp hp drat wt qsec vs am gear carb #> #> 1 21 6 160 110 3.9 2.62 16.5 0 1 4 4 #> 2 21 6 160 110 3.9 2.88 17.0 0 1 4 4 #> 3 22.8 4 108 93 3.85 2.32 18.6 1 1 4 1 #> 4 21.4 6 258 110 3.08 3.22 19.4 1 0 3 1 #> 5 18.7 8 360 175 3.15 3.44 17.0 0 0 3 2 #> 6 18.1 6 225 105 2.76 3.46 20.2 1 0 3 1 #> 7 14.3 8 360 245 3.21 3.57 15.8 0 0 3 4 #> 8 24.4 4 147. 62 3.69 3.19 20 1 0 4 2 #> 9 22.8 4 141. 95 3.92 3.15 22.9 1 0 4 2 #> 10 19.2 6 168. 123 3.92 3.44 18.3 1 0 4 4 #> # ℹ 22 more rows mtcars |> numchar2fct() |> dplyr::mutate(vs = fct_drop(vs)) #> mpg cyl disp hp drat wt qsec vs am gear carb #> Mazda RX4 21.0 6 160.0 110 3.90 2.620 16.46 0 1 4 4 #> Mazda RX4 Wag 21.0 6 160.0 110 3.90 2.875 17.02 0 1 4 4 #> Datsun 710 22.8 4 108.0 93 3.85 2.320 18.61 1 1 4 1 #> Hornet 4 Drive 21.4 6 258.0 110 3.08 3.215 19.44 1 0 3 1 #> Hornet Sportabout 18.7 8 360.0 175 3.15 3.440 17.02 0 0 3 2 #> Valiant 18.1 6 225.0 105 2.76 3.460 20.22 1 0 3 1 #> Duster 360 14.3 8 360.0 245 3.21 3.570 15.84 0 0 3 4 #> Merc 240D 24.4 4 146.7 62 3.69 3.190 20.00 1 0 4 2 #> Merc 230 22.8 4 140.8 95 3.92 3.150 22.90 1 0 4 2 #> Merc 280 19.2 6 167.6 123 3.92 3.440 18.30 1 0 4 4 #> Merc 280C 17.8 6 167.6 123 3.92 3.440 18.90 1 0 4 4 #> Merc 450SE 16.4 8 275.8 180 3.07 4.070 17.40 0 0 3 3 #> Merc 450SL 17.3 8 275.8 180 3.07 3.730 17.60 0 0 3 3 #> Merc 450SLC 15.2 8 275.8 180 3.07 3.780 18.00 0 0 3 3 #> Cadillac Fleetwood 10.4 8 472.0 205 2.93 5.250 17.98 0 0 3 4 #> Lincoln Continental 10.4 8 460.0 215 3.00 5.424 17.82 0 0 3 4 #> Chrysler Imperial 14.7 8 440.0 230 3.23 5.345 17.42 0 0 3 4 #> Fiat 128 32.4 4 78.7 66 4.08 2.200 19.47 1 1 4 1 #> Honda Civic 30.4 4 75.7 52 4.93 1.615 18.52 1 1 4 2 #> Toyota Corolla 33.9 4 71.1 65 4.22 1.835 19.90 1 1 4 1 #> Toyota Corona 21.5 4 120.1 97 3.70 2.465 20.01 1 0 3 1 #> Dodge Challenger 15.5 8 318.0 150 2.76 3.520 16.87 0 0 3 2 #> AMC Javelin 15.2 8 304.0 150 3.15 3.435 17.30 0 0 3 2 #> Camaro Z28 13.3 8 350.0 245 3.73 3.840 15.41 0 0 3 4 #> Pontiac Firebird 19.2 8 400.0 175 3.08 3.845 17.05 0 0 3 2 #> Fiat X1-9 27.3 4 79.0 66 4.08 1.935 18.90 1 1 4 1 #> Porsche 914-2 26.0 4 120.3 91 4.43 2.140 16.70 0 1 5 2 #> Lotus Europa 30.4 4 95.1 113 3.77 1.513 16.90 1 1 5 2 #> Ford Pantera L 15.8 8 351.0 264 4.22 3.170 14.50 0 1 5 4 #> Ferrari Dino 19.7 6 145.0 175 3.62 2.770 15.50 0 1 5 6 #> Maserati Bora 15.0 8 301.0 335 3.54 3.570 14.60 0 1 5 8 #> Volvo 142E 21.4 4 121.0 109 4.11 2.780 18.60 1 1 4 2"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/file_extension.html","id":null,"dir":"Reference","previous_headings":"","what":"DEPRECATED Helper to import files correctly — file_extension","title":"DEPRECATED Helper to import files correctly — file_extension","text":"DEPRECATED Helper import files correctly","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/file_extension.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"DEPRECATED Helper to import files correctly — file_extension","text":"","code":"file_extension(filenames)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/file_extension.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"DEPRECATED Helper to import files correctly — file_extension","text":"filenames file names","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/file_extension.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"DEPRECATED Helper to import files correctly — file_extension","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/file_extension.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"DEPRECATED Helper to import files correctly — file_extension","text":"","code":"file_extension(list.files(here::here(\"\"))[[2]])[[1]] #> [1] \"\" file_extension(c(\"file.cd..ks\", \"file\")) #> [1] \"ks\" \"\""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/focused_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"focused_metadata — focused_metadata","title":"focused_metadata — focused_metadata","text":"Extracts limited metadata variables dataset","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/focused_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"focused_metadata — focused_metadata","text":"","code":"focused_metadata(metadata, vars_in_data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/focused_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"focused_metadata — focused_metadata","text":"metadata dataframe containing metadata vars_in_data Vector variable names dataset","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/focused_metadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"focused_metadata — focused_metadata","text":"dataframe containing metadata variables dataset","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/format_redcap_factor.html","id":null,"dir":"Reference","previous_headings":"","what":"Converts REDCap choices to factor levels and stores in labels attribute — format_redcap_factor","title":"Converts REDCap choices to factor levels and stores in labels attribute — format_redcap_factor","text":"Applying as_factor data.frame variable, coerce factor.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/format_redcap_factor.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Converts REDCap choices to factor levels and stores in labels attribute — format_redcap_factor","text":"","code":"format_redcap_factor(data, meta)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/format_redcap_factor.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Converts REDCap choices to factor levels and stores in labels attribute — format_redcap_factor","text":"data vector meta vector REDCap choices","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/format_redcap_factor.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Converts REDCap choices to factor levels and stores in labels attribute — format_redcap_factor","text":"vector class \"labelled\" \"labels\" attribute","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/format_redcap_factor.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Converts REDCap choices to factor levels and stores in labels attribute — format_redcap_factor","text":"","code":"format_redcap_factor(sample(1:3, 20, TRUE), \"1, First. | 2, second | 3, THIRD\") #> [1] 2 2 1 2 1 2 3 1 2 2 2 1 1 3 2 1 2 3 1 1 #> attr(,\"labels\") #> First. second THIRD #> \"1\" \"2\" \"3\" #> attr(,\"class\") #> [1] \"labelled\""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/format_subheader.html","id":null,"dir":"Reference","previous_headings":"","what":"Sub-header formatting wrapper — format_subheader","title":"Sub-header formatting wrapper — format_subheader","text":"Sub-header formatting wrapper","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/format_subheader.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sub-header formatting wrapper — format_subheader","text":"","code":"format_subheader(data, tag = \"h2\")"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/format_subheader.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sub-header formatting wrapper — format_subheader","text":"data character vector tag character vector length 1","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/format_subheader.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sub-header formatting wrapper — format_subheader","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/format_subheader.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sub-header formatting wrapper — format_subheader","text":"","code":"\"Instrument header\" |> format_subheader() #> Instrument header<\/h2><\/div>"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_api_key.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve project API key if stored, if not, set and retrieve — get_api_key","title":"Retrieve project API key if stored, if not, set and retrieve — get_api_key","text":"Attempting make secure API key storage simple, way makes sense. Wrapping key_get key_set using key_list check key storage already.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_api_key.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve project API key if stored, if not, set and retrieve — get_api_key","text":"","code":"get_api_key(key.name, ...)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_api_key.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve project API key if stored, if not, set and retrieve — get_api_key","text":"key.name character vector key name ... passed key_set","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_api_key.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve project API key if stored, if not, set and retrieve — get_api_key","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_attr.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract attribute. Returns NA if none — get_attr","title":"Extract attribute. Returns NA if none — get_attr","text":"Extract attribute. Returns NA none","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_attr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract attribute. Returns NA if none — get_attr","text":"","code":"get_attr(data, attr = NULL)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_attr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract attribute. Returns NA if none — get_attr","text":"data vector attr attribute name","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_attr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract attribute. Returns NA if none — get_attr","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_attr.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Extract attribute. Returns NA if none — get_attr","text":"","code":"attr(mtcars$mpg, \"label\") <- \"testing\" do.call(c, sapply(mtcars, get_attr)) #> $mpg.label #> [1] \"testing\" #> if (FALSE) { # \\dontrun{ mtcars |> numchar2fct(numeric.threshold = 6) |> ds2dd_detailed() } # }"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_id_name.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the id name — get_id_name","title":"Get the id name — get_id_name","text":"Get id name","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_id_name.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the id name — get_id_name","text":"","code":"get_id_name(data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_id_name.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the id name — get_id_name","text":"data data frame list","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/get_id_name.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the id name — get_id_name","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only.html","id":null,"dir":"Reference","previous_headings":"","what":"Guess time variables based on naming pattern — guess_time_only","title":"Guess time variables based on naming pattern — guess_time_only","text":"repairing data time variables appended \"1970-01-01\"","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Guess time variables based on naming pattern — guess_time_only","text":"","code":"guess_time_only( data, validate.time = FALSE, time.var.sel.pos = \"[Tt]i[d(me)]\", time.var.sel.neg = \"[Dd]at[eo]\" )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Guess time variables based on naming pattern — guess_time_only","text":"data data.frame tibble validate.time Flag validate guessed time columns time.var.sel.pos Positive selection regex string passed `gues_time_only_filter()` sel.pos. time.var.sel.neg Negative selection regex string passed `gues_time_only_filter()` sel.neg.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Guess time variables based on naming pattern — guess_time_only","text":"data.frame tibble","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Guess time variables based on naming pattern — guess_time_only","text":"","code":"redcapcast_data |> guess_time_only(validate.time = TRUE) #> $is.POSIX #> # A tibble: 25 × 2 #> inclusion_time event_datetime #> #> 1 12:38:49 NA #> 2 10:38:57 NA #> 3 NA NA #> 4 NA 2024-01-18 12:49:42 #> 5 12:01:07 NA #> 6 NA NA #> 7 NA NA #> 8 NA 2024-01-18 12:49:58 #> 9 NA 2024-01-18 12:50:01 #> 10 NA 2024-01-18 12:50:05 #> # ℹ 15 more rows #> #> $is.datetime #> # A tibble: 25 × 1 #> event_datetime #> #> 1 NA #> 2 NA #> 3 NA #> 4 2024-01-18 12:49:42 #> 5 NA #> 6 NA #> 7 NA #> 8 2024-01-18 12:49:58 #> 9 2024-01-18 12:50:01 #> 10 2024-01-18 12:50:05 #> # ℹ 15 more rows #> #> $is.time_only #> # A tibble: 25 × 1 #> inclusion_time #> #> 1 12:38:49 #> 2 10:38:57 #> 3 NA #> 4 NA #> 5 12:01:07 #> 6 NA #> 7 NA #> 8 NA #> 9 NA #> 10 NA #> # ℹ 15 more rows #>"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only_filter.html","id":null,"dir":"Reference","previous_headings":"","what":"Try at determining which are true time only variables — guess_time_only_filter","title":"Try at determining which are true time only variables — guess_time_only_filter","text":"just try guessing data type based data class column names hoping tiny bit naming consistency. R include time-data format natively, \"hms\" class `readr` used. converted character class REDCap upload.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only_filter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Try at determining which are true time only variables — guess_time_only_filter","text":"","code":"guess_time_only_filter( data, validate = FALSE, sel.pos = \"[Tt]i[d(me)]\", sel.neg = \"[Dd]at[eo]\" )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only_filter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Try at determining which are true time only variables — guess_time_only_filter","text":"data data set validate flag output validation data. output list. sel.pos Positive selection regex string sel.neg Negative selection regex string","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only_filter.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Try at determining which are true time only variables — guess_time_only_filter","text":"character vector list depending `validate` flag.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/guess_time_only_filter.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Try at determining which are true time only variables — guess_time_only_filter","text":"","code":"data <- redcapcast_data data |> guess_time_only_filter() #> [1] \"inclusion_time\" data |> guess_time_only_filter(validate = TRUE) |> lapply(head) #> $is.POSIX #> # A tibble: 6 × 2 #> inclusion_time event_datetime #> #> 1 12:38:49 NA #> 2 10:38:57 NA #> 3 NA NA #> 4 NA 2024-01-18 12:49:42 #> 5 12:01:07 NA #> 6 NA NA #> #> $is.datetime #> # A tibble: 6 × 1 #> event_datetime #> #> 1 NA #> 2 NA #> 3 NA #> 4 2024-01-18 12:49:42 #> 5 NA #> 6 NA #> #> $is.time_only #> # A tibble: 6 × 1 #> inclusion_time #> #> 1 12:38:49 #> 2 10:38:57 #> 3 NA #> 4 NA #> 5 12:01:07 #> 6 NA #>"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/haven_all_levels.html","id":null,"dir":"Reference","previous_headings":"","what":"Finish incomplete haven attributes substituting missings with values — haven_all_levels","title":"Finish incomplete haven attributes substituting missings with values — haven_all_levels","text":"Finish incomplete haven attributes substituting missings values","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/haven_all_levels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Finish incomplete haven attributes substituting missings with values — haven_all_levels","text":"","code":"haven_all_levels(data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/haven_all_levels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Finish incomplete haven attributes substituting missings with values — haven_all_levels","text":"data haven labelled variable","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/haven_all_levels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Finish incomplete haven attributes substituting missings with values — haven_all_levels","text":"named vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/haven_all_levels.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Finish incomplete haven attributes substituting missings with values — haven_all_levels","text":"","code":"ds <- structure(c(1, 2, 3, 2, 10, 9), labels = c(Unknown = 9, Refused = 10), class = \"haven_labelled\" ) haven::is.labelled(ds) #> [1] TRUE attributes(ds) #> $labels #> Unknown Refused #> 9 10 #> #> $class #> [1] \"haven_labelled\" #> ds |> haven_all_levels() #> 1 2 3 Unknown Refused #> 1 2 3 9 10"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/hms2character.html","id":null,"dir":"Reference","previous_headings":"","what":"Change ","title":"Change ","text":"Change \"hms\" \"character\" REDCap upload.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/hms2character.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Change ","text":"","code":"hms2character(data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/hms2character.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Change ","text":"data data set","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/hms2character.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Change ","text":"data.frame tibble","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/hms2character.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Change ","text":"","code":"data <- redcapcast_data ## data |> time_only_correction() |> hms2character()"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/html_tag_wrap.html","id":null,"dir":"Reference","previous_headings":"","what":"Simple html tag wrapping for REDCap text formatting — html_tag_wrap","title":"Simple html tag wrapping for REDCap text formatting — html_tag_wrap","text":"Simple html tag wrapping REDCap text formatting","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/html_tag_wrap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simple html tag wrapping for REDCap text formatting — html_tag_wrap","text":"","code":"html_tag_wrap(data, tag = \"h2\", extra = NULL)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/html_tag_wrap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simple html tag wrapping for REDCap text formatting — html_tag_wrap","text":"data character vector tag character vector length 1 extra character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/html_tag_wrap.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Simple html tag wrapping for REDCap text formatting — html_tag_wrap","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/html_tag_wrap.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Simple html tag wrapping for REDCap text formatting — html_tag_wrap","text":"","code":"html_tag_wrap(\"Titel\", tag = \"div\", extra = 'class=\"rich-text-field-label\"') #> Titel<\/div> html_tag_wrap(\"Titel\", tag = \"h2\") #>
Titel<\/h2>"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is.labelled.html","id":null,"dir":"Reference","previous_headings":"","what":"Tests for multiple label classes — is.labelled","title":"Tests for multiple label classes — is.labelled","text":"Tests multiple label classes","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is.labelled.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tests for multiple label classes — is.labelled","text":"","code":"is.labelled(x, classes = c(\"haven_labelled\", \"labelled\"))"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is.labelled.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tests for multiple label classes — is.labelled","text":"x data classes classes test","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is.labelled.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tests for multiple label classes — is.labelled","text":"logical","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is.labelled.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Tests for multiple label classes — is.labelled","text":"","code":"structure(c(1, 2, 3, 2, 10, 9), labels = c(Unknown = 9, Refused = 10), class = \"haven_labelled\" ) |> is.labelled() #> [1] TRUE"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is_missing.html","id":null,"dir":"Reference","previous_headings":"","what":"Multi missing check — is_missing","title":"Multi missing check — is_missing","text":"Multi missing check","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is_missing.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Multi missing check — is_missing","text":"","code":"is_missing(data, nas = c(\"\", \"NA\"))"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is_missing.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Multi missing check — is_missing","text":"data character vector nas character vector strings considered NA","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is_missing.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Multi missing check — is_missing","text":"logical vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is_repeated_longitudinal.html","id":null,"dir":"Reference","previous_headings":"","what":"Test if repeatable or longitudinal — is_repeated_longitudinal","title":"Test if repeatable or longitudinal — is_repeated_longitudinal","text":"Test repeatable longitudinal","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is_repeated_longitudinal.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Test if repeatable or longitudinal — is_repeated_longitudinal","text":"","code":"is_repeated_longitudinal( data, generics = c(\"redcap_event_name\", \"redcap_repeat_instrument\", \"redcap_repeat_instance\") )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is_repeated_longitudinal.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Test if repeatable or longitudinal — is_repeated_longitudinal","text":"data data set generics default \"redcap_event_name\", \"redcap_repeat_instrument\" \"redcap_repeat_instance\"","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is_repeated_longitudinal.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Test if repeatable or longitudinal — is_repeated_longitudinal","text":"logical","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/is_repeated_longitudinal.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Test if repeatable or longitudinal — is_repeated_longitudinal","text":"","code":"is_repeated_longitudinal(c(\"record_id\", \"age\", \"record_id\", \"gender\")) #> [1] FALSE is_repeated_longitudinal(redcapcast_data) #> [1] TRUE is_repeated_longitudinal(list(redcapcast_data)) #> [1] TRUE"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/mark_complete.html","id":null,"dir":"Reference","previous_headings":"","what":"Completion marking based on completed upload — mark_complete","title":"Completion marking based on completed upload — mark_complete","text":"Completion marking based completed upload","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/mark_complete.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Completion marking based on completed upload — mark_complete","text":"","code":"mark_complete(upload, ls)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/mark_complete.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Completion marking based on completed upload — mark_complete","text":"upload output list `REDCapR::redcap_write()` ls output list `ds2dd_detailed()`","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/mark_complete.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Completion marking based on completed upload — mark_complete","text":"list `REDCapR::redcap_write()` results","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/match_fields_to_form.html","id":null,"dir":"Reference","previous_headings":"","what":"Match fields to forms — match_fields_to_form","title":"Match fields to forms — match_fields_to_form","text":"Match fields forms","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/match_fields_to_form.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Match fields to forms — match_fields_to_form","text":"","code":"match_fields_to_form(metadata, vars_in_data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/match_fields_to_form.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Match fields to forms — match_fields_to_form","text":"metadata data frame containing field names form names vars_in_data character vector variable names","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/match_fields_to_form.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Match fields to forms — match_fields_to_form","text":"data frame containing field names form names","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/mtcars_redcap.html","id":null,"dir":"Reference","previous_headings":"","what":"mtcars dataset slightly modified to use for Shiny app upload demonstration — mtcars_redcap","title":"mtcars dataset slightly modified to use for Shiny app upload demonstration — mtcars_redcap","text":"mtcars dataset slightly modified use Shiny app upload demonstration","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/mtcars_redcap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"mtcars dataset slightly modified to use for Shiny app upload demonstration — mtcars_redcap","text":"","code":"data(mtcars_redcap)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/mtcars_redcap.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"mtcars dataset slightly modified to use for Shiny app upload demonstration — mtcars_redcap","text":"data frame 13 variables: record_id ID, numeric mpg ID, numeric cyl ID, numeric disp ID, numeric hp ID, numeric drat ID, numeric wt ID, numeric qsec ID, numeric vs ID, numeric ID, numeric gear ID, numeric carb ID, numeric name original rownames, charater","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/named_levels.html","id":null,"dir":"Reference","previous_headings":"","what":"Get named vector of factor levels and values — named_levels","title":"Get named vector of factor levels and values — named_levels","text":"Get named vector factor levels values","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/named_levels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get named vector of factor levels and values — named_levels","text":"","code":"named_levels( data, label = \"labels\", na.label = NULL, na.value = 99, sort.numeric = TRUE )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/named_levels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get named vector of factor levels and values — named_levels","text":"data factor label character string attribute named vector factor labels na.label character string refactor NA values. Default NULL. na.value new value NA strings. Ignored na.label NULL. Default 99. sort.numeric sort factor levels levels numeric. Default TRUE","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/named_levels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get named vector of factor levels and values — named_levels","text":"named vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/named_levels.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get named vector of factor levels and values — named_levels","text":"","code":"structure(c(1, 2, 3, 2, 10, 9), labels = c(Unknown = 9, Refused = 10), class = \"haven_labelled\" ) |> as_factor() |> named_levels() #> 1 2 3 Refused Unknown #> 1 2 3 10 9 structure(c(1, 2, 3, 2, 10, 9), labels = c(Unknown = 9, Refused = 10), class = \"labelled\" ) |> as_factor() |> named_levels() #> 1 2 3 Refused Unknown #> 1 2 3 10 9"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/nav_bar_page.html","id":null,"dir":"Reference","previous_headings":"","what":"Nav_bar defining function for shiny ui — nav_bar_page","title":"Nav_bar defining function for shiny ui — nav_bar_page","text":"Nav_bar defining function shiny ui","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/nav_bar_page.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Nav_bar defining function for shiny ui — nav_bar_page","text":"","code":"nav_bar_page()"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/nav_bar_page.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Nav_bar defining function for shiny ui — nav_bar_page","text":"shiny object","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/numchar2fct.html","id":null,"dir":"Reference","previous_headings":"","what":"Applying var2fct across data set — numchar2fct","title":"Applying var2fct across data set — numchar2fct","text":"Individual thresholds character numeric columns","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/numchar2fct.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Applying var2fct across data set — numchar2fct","text":"","code":"numchar2fct(data, numeric.threshold = 6, character.throshold = 6)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/numchar2fct.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Applying var2fct across data set — numchar2fct","text":"data dataset. data.frame tibble numeric.threshold threshold var2fct numeric columns. Default 6. character.throshold threshold var2fct character columns. Default 6.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/numchar2fct.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Applying var2fct across data set — numchar2fct","text":"data.frame tibble","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/numchar2fct.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Applying var2fct across data set — numchar2fct","text":"","code":"mtcars |> str() #> 'data.frame':\t32 obs. of 11 variables: #> $ mpg : num 21 21 22.8 21.4 18.7 18.1 14.3 24.4 22.8 19.2 ... #> $ cyl : num 6 6 4 6 8 6 8 4 4 6 ... #> $ disp: num 160 160 108 258 360 ... #> $ hp : num 110 110 93 110 175 105 245 62 95 123 ... #> $ drat: num 3.9 3.9 3.85 3.08 3.15 2.76 3.21 3.69 3.92 3.92 ... #> $ wt : num 2.62 2.88 2.32 3.21 3.44 ... #> $ qsec: num 16.5 17 18.6 19.4 17 ... #> $ vs : num 0 0 1 1 0 1 0 1 1 1 ... #> $ am : num 1 1 1 0 0 0 0 0 0 0 ... #> $ gear: num 4 4 4 3 3 3 3 4 4 4 ... #> $ carb: num 4 4 1 1 2 1 4 2 2 4 ... if (FALSE) { # \\dontrun{ mtcars |> numchar2fct(numeric.threshold = 6) |> str() } # }"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/parse_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper to auto-parse un-formatted data with haven and readr — parse_data","title":"Helper to auto-parse un-formatted data with haven and readr — parse_data","text":"Helper auto-parse un-formatted data haven readr","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/parse_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper to auto-parse un-formatted data with haven and readr — parse_data","text":"","code":"parse_data( data, guess_type = TRUE, col_types = NULL, locale = readr::default_locale(), ignore.vars = \"cpr\", ... )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/parse_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper to auto-parse un-formatted data with haven and readr — parse_data","text":"data data.frame tibble guess_type logical guess type readr col_types specify col_types using readr semantics. Ignored guess_type TRUE locale option specify locale. Defaults readr::default_locale(). ignore.vars specify column names columns ignore parsing ... ignored","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/parse_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper to auto-parse un-formatted data with haven and readr — parse_data","text":"data.frame tibble","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/parse_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper to auto-parse un-formatted data with haven and readr — parse_data","text":"","code":"mtcars |> parse_data() |> str() #> 'data.frame':\t32 obs. of 11 variables: #> $ mpg : num 21 21 22.8 21.4 18.7 18.1 14.3 24.4 22.8 19.2 ... #> $ cyl : num 6 6 4 6 8 6 8 4 4 6 ... #> $ disp: num 160 160 108 258 360 ... #> $ hp : num 110 110 93 110 175 105 245 62 95 123 ... #> $ drat: num 3.9 3.9 3.85 3.08 3.15 2.76 3.21 3.69 3.92 3.92 ... #> $ wt : num 2.62 2.88 2.32 3.21 3.44 ... #> $ qsec: num 16.5 17 18.6 19.4 17 ... #> $ vs : num 0 0 1 1 0 1 0 1 1 1 ... #> $ am : num 1 1 1 0 0 0 0 0 0 0 ... #> $ gear: num 4 4 4 3 3 3 3 4 4 4 ... #> $ carb: num 4 4 1 1 2 1 4 2 2 4 ..."},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/possibly_numeric.html","id":null,"dir":"Reference","previous_headings":"","what":"Tests if vector can be interpreted as numeric without introducing NAs by coercion — possibly_numeric","title":"Tests if vector can be interpreted as numeric without introducing NAs by coercion — possibly_numeric","text":"Tests vector can interpreted numeric without introducing NAs coercion","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/possibly_numeric.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tests if vector can be interpreted as numeric without introducing NAs by coercion — possibly_numeric","text":"","code":"possibly_numeric(data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/possibly_numeric.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tests if vector can be interpreted as numeric without introducing NAs by coercion — possibly_numeric","text":"data vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/possibly_numeric.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tests if vector can be interpreted as numeric without introducing NAs by coercion — possibly_numeric","text":"logical","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/possibly_numeric.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Tests if vector can be interpreted as numeric without introducing NAs by coercion — possibly_numeric","text":"","code":"c(\"1\",\"5\") |> possibly_numeric() #> [1] TRUE c(\"1\",\"5\",\"e\") |> possibly_numeric() #> [1] FALSE"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/possibly_roman.html","id":null,"dir":"Reference","previous_headings":"","what":"Test if vector can be interpreted as roman numerals — possibly_roman","title":"Test if vector can be interpreted as roman numerals — possibly_roman","text":"Test vector can interpreted roman numerals","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/possibly_roman.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Test if vector can be interpreted as roman numerals — possibly_roman","text":"","code":"possibly_roman(data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/possibly_roman.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Test if vector can be interpreted as roman numerals — possibly_roman","text":"data character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/possibly_roman.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Test if vector can be interpreted as roman numerals — possibly_roman","text":"logical","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/possibly_roman.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Test if vector can be interpreted as roman numerals — possibly_roman","text":"","code":"sample(1:100, 10) |> as.roman() |> possibly_roman() #> [1] TRUE sample(c(TRUE, FALSE), 10, TRUE) |> possibly_roman() #> [1] FALSE rep(NA, 10) |> possibly_roman() #> [1] FALSE"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.character.html","id":null,"dir":"Reference","previous_headings":"","what":"User input processing character — process_user_input.character","title":"User input processing character — process_user_input.character","text":"User input processing character","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.character.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"User input processing character — process_user_input.character","text":"","code":"# S3 method for class 'character' process_user_input(x, ...)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.character.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"User input processing character — process_user_input.character","text":"x input ... ignored","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.character.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"User input processing character — process_user_input.character","text":"processed input","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.data.frame.html","id":null,"dir":"Reference","previous_headings":"","what":"User input processing data.frame — process_user_input.data.frame","title":"User input processing data.frame — process_user_input.data.frame","text":"User input processing data.frame","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.data.frame.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"User input processing data.frame — process_user_input.data.frame","text":"","code":"# S3 method for class 'data.frame' process_user_input(x, ...)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.data.frame.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"User input processing data.frame — process_user_input.data.frame","text":"x input ... ignored","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.data.frame.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"User input processing data.frame — process_user_input.data.frame","text":"processed input","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.default.html","id":null,"dir":"Reference","previous_headings":"","what":"User input processing default — process_user_input.default","title":"User input processing default — process_user_input.default","text":"User input processing default","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.default.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"User input processing default — process_user_input.default","text":"","code":"# Default S3 method process_user_input(x, ...)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.default.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"User input processing default — process_user_input.default","text":"x input ... ignored","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.default.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"User input processing default — process_user_input.default","text":"processed input","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.html","id":null,"dir":"Reference","previous_headings":"","what":"User input processing — process_user_input","title":"User input processing — process_user_input","text":"User input processing","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"User input processing — process_user_input","text":"","code":"process_user_input(x)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"User input processing — process_user_input","text":"x input","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"User input processing — process_user_input","text":"processed input","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.response.html","id":null,"dir":"Reference","previous_headings":"","what":"User input processing response — process_user_input.response","title":"User input processing response — process_user_input.response","text":"User input processing response","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.response.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"User input processing response — process_user_input.response","text":"","code":"# S3 method for class 'response' process_user_input(x, ...)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.response.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"User input processing response — process_user_input.response","text":"x input ... ignored","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/process_user_input.response.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"User input processing response — process_user_input.response","text":"processed input","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_input.html","id":null,"dir":"Reference","previous_headings":"","what":"Flexible file import based on extension — read_input","title":"Flexible file import based on extension — read_input","text":"Flexible file import based extension","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_input.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Flexible file import based on extension — read_input","text":"","code":"read_input(file, consider.na = c(\"NA\", \"\\\"\\\"\", \"\"))"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_input.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Flexible file import based on extension — read_input","text":"file file name consider.na character vector strings consider NAs","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_input.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Flexible file import based on extension — read_input","text":"tibble","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_input.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Flexible file import based on extension — read_input","text":"","code":"read_input(\"https://raw.githubusercontent.com/agdamsbo/cognitive.index.lookup/main/data/sample.csv\") #> Rows: 28 Columns: 8 #> ── Column specification ──────────────────────────────────────────────────────── #> Delimiter: \",\" #> dbl (8): id, ab, age, imm, vis, ver, att, del #> #> ℹ Use `spec()` to retrieve the full column specification for this data. #> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message. #> # A tibble: 28 × 8 #> id ab age imm vis ver att del #> #> 1 1 1 74 38 35 30 29 35 #> 2 1 2 69 36 36 21 27 37 #> 3 2 1 63 32 31 26 34 38 #> 4 2 2 64 37 34 26 36 46 #> 5 3 1 69 39 33 31 47 29 #> 6 3 2 70 40 36 31 46 25 #> 7 4 1 79 44 37 20 37 36 #> 8 4 2 81 35 36 31 37 40 #> 9 5 1 77 35 26 17 20 36 #> 10 5 2 80 29 34 18 23 36 #> # ℹ 18 more rows"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_instrument.html","id":null,"dir":"Reference","previous_headings":"","what":"Convenience function to download complete instrument, using token storage in keyring. — read_redcap_instrument","title":"Convenience function to download complete instrument, using token storage in keyring. — read_redcap_instrument","text":"Convenience function download complete instrument, using token storage keyring.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_instrument.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convenience function to download complete instrument, using token storage in keyring. — read_redcap_instrument","text":"","code":"read_redcap_instrument( key, uri, instrument, raw_or_label = \"raw\", id_name = \"record_id\", records = NULL )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_instrument.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convenience function to download complete instrument, using token storage in keyring. — read_redcap_instrument","text":"key key name standard keyring token retrieval. uri REDCap database API uri instrument instrument name raw_or_label raw label passed `REDCapR::redcap_read()` id_name id variable name. Default \"record_id\". records specify records download. Index numbers. Numeric vector.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_instrument.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convenience function to download complete instrument, using token storage in keyring. — read_redcap_instrument","text":"data.frame","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_tables.html","id":null,"dir":"Reference","previous_headings":"","what":"Download REDCap data — read_redcap_tables","title":"Download REDCap data — read_redcap_tables","text":"Implementation passed REDCap_split focused data acquisition approach using passed redcap_read downloading specified fields, forms /events using built-focused_metadata including clean-. Works classical longitudinal projects without repeating instruments. preserve metadata data.frames labels.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_tables.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Download REDCap data — read_redcap_tables","text":"","code":"read_redcap_tables( uri, token, records = NULL, fields = NULL, events = NULL, forms = NULL, raw_or_label = c(\"raw\", \"label\", \"both\"), split_forms = c(\"all\", \"repeating\", \"none\"), ... )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_tables.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Download REDCap data — read_redcap_tables","text":"uri REDCap database API uri token API token records records download fields fields download events events download forms forms download raw_or_label raw label tags. Can \"raw\", \"label\" \"\". * \"raw\": Standard redcap_read method get raw values. * \"label\": Standard redcap_read method get label values. * \"\": Get raw values REDCap labels applied labels. Use as_factor format factors original labels use `gtsummary` package functions like tbl_summary easily get beautiful tables original labels REDCap. Use fct_drop drop empty levels. split_forms Whether split \"repeating\" \"\" forms, default . Give \"none\" export native semi-long REDCap format ... passed redcap_read","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_tables.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Download REDCap data — read_redcap_tables","text":"list instruments","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/read_redcap_tables.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Download REDCap data — read_redcap_tables","text":"","code":"# Examples will be provided later"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcap_wider.html","id":null,"dir":"Reference","previous_headings":"","what":"Transforms list of REDCap data.frames to a single wide data.frame — redcap_wider","title":"Transforms list of REDCap data.frames to a single wide data.frame — redcap_wider","text":"Converts list REDCap data.frames long wide format. essence wrapper pivot_wider function applied REDCap output (read_redcap_tables) manually split REDCap_split.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcap_wider.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Transforms list of REDCap data.frames to a single wide data.frame — redcap_wider","text":"","code":"redcap_wider( data, event.glue = \"{.value}____{redcap_event_name}\", inst.glue = \"{.value}____{redcap_repeat_instance}\" )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcap_wider.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Transforms list of REDCap data.frames to a single wide data.frame — redcap_wider","text":"data list data frames event.glue glue string repeated events naming inst.glue glue string repeated instruments naming","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcap_wider.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Transforms list of REDCap data.frames to a single wide data.frame — redcap_wider","text":"data.frame wide format","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcap_wider.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Transforms list of REDCap data.frames to a single wide data.frame — redcap_wider","text":"","code":"# Longitudinal list1 <- list( data.frame( record_id = c(1, 2, 1, 2), redcap_event_name = c(\"baseline\", \"baseline\", \"followup\", \"followup\"), age = c(25, 26, 27, 28) ), data.frame( record_id = c(1, 2), redcap_event_name = c(\"baseline\", \"baseline\"), gender = c(\"male\", \"female\") ) ) redcap_wider(list1) #> Joining with `by = join_by(record_id)` #> # A tibble: 2 × 4 #> record_id age____baseline age____followup gender #> #> 1 1 25 27 male #> 2 2 26 28 female # Simpel with two instruments list2 <- list( data.frame( record_id = c(1, 2), age = c(25, 26) ), data.frame( record_id = c(1, 2), gender = c(\"male\", \"female\") ) ) redcap_wider(list2) #> Joining with `by = join_by(record_id)` #> record_id age gender #> 1 1 25 male #> 2 2 26 female # Simple with single instrument list3 <- list(data.frame( record_id = c(1, 2), age = c(25, 26) )) redcap_wider(list3) #> record_id age #> 1 1 25 #> 2 2 26 # Longitudinal with repeatable instruments list4 <- list( data.frame( record_id = c(1, 2, 1, 2), redcap_event_name = c(\"baseline\", \"baseline\", \"followup\", \"followup\"), age = c(25, 26, 27, 28) ), data.frame( record_id = c(1, 1, 1, 1, 2, 2, 2, 2), redcap_event_name = c( \"baseline\", \"baseline\", \"followup\", \"followup\", \"baseline\", \"baseline\", \"followup\", \"followup\" ), redcap_repeat_instrument = \"walk\", redcap_repeat_instance = c(1, 2, 1, 2, 1, 2, 1, 2), dist = c(40, 32, 25, 33, 28, 24, 23, 36) ), data.frame( record_id = c(1, 2), redcap_event_name = c(\"baseline\", \"baseline\"), gender = c(\"male\", \"female\") ) ) redcap_wider(list4) #> Joining with `by = join_by(record_id)` #> Joining with `by = join_by(record_id)` #> # A tibble: 2 × 8 #> record_id age____baseline age____followup dist____1____baseline #> #> 1 1 25 27 40 #> 2 2 26 28 28 #> # ℹ 4 more variables: dist____1____followup , dist____2____baseline , #> # dist____2____followup , gender "},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcapcast_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Data set for demonstration — redcapcast_data","title":"Data set for demonstration — redcapcast_data","text":"small dataset REDCap database demonstrational purposes. Contains synthetic data.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcapcast_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data set for demonstration — redcapcast_data","text":"","code":"data(redcapcast_data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcapcast_data.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Data set for demonstration — redcapcast_data","text":"data frame 22 variables: record_id ID, numeric redcap_event_name Event name, character redcap_repeat_instrument Repeat instrument, character redcap_repeat_instance Repeat instance, numeric cpr CPR number, character inclusion Inclusion date, Date inclusion_time Inclusion time, hms dob Date birth, Date age Age decimal, numeric age_integer Age integer, numeric sex Legal sex, character cohabitation Cohabitation status, character con_calc con_calc con_mrs con_mrs consensus_complete consensus_complete hypertension Hypertension, character diabetes diabetes, character region region, character baseline_data_start_complete Completed, character mrs_assessed mRS Assessed, character mrs_date Assesment date, Date mrs_score Categorical score, numeric mrs_complete Complete, numeric event_datetime Event datetime, POSIXct event_age Age time event, numeric event_type Event type, character new_event_complete Completed, character","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcapcast_meta.html","id":null,"dir":"Reference","previous_headings":"","what":"REDCap metadata from data base — redcapcast_meta","title":"REDCap metadata from data base — redcapcast_meta","text":"metadata dataset REDCap database demonstration purposes.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcapcast_meta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"REDCap metadata from data base — redcapcast_meta","text":"","code":"data(redcapcast_meta)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/redcapcast_meta.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"REDCap metadata from data base — redcapcast_meta","text":"data frame 22 variables: field_name field_name, character form_name form_name, character section_header section_header, character field_type field_type, character field_label field_label, character select_choices_or_calculations select_choices_or_calculations, character field_note field_note, character text_validation_type_or_show_slider_number text_validation_type_or_show_slider_number, character text_validation_min text_validation_min, character text_validation_max text_validation_max, character identifier identifier, character branching_logic branching_logic, character required_field required_field, character custom_alignment custom_alignment, character question_number question_number, character matrix_group_name matrix_group_name, character matrix_ranking matrix_ranking, character field_annotation field_annotation, character","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/replace_curly_quote.html","id":null,"dir":"Reference","previous_headings":"","what":"Replace curly apostrophes and quotes from word — replace_curly_quote","title":"Replace curly apostrophes and quotes from word — replace_curly_quote","text":"Copied textclean, updated since 2018 CRAN. Github:https://github.com/trinker/textclean","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/replace_curly_quote.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Replace curly apostrophes and quotes from word — replace_curly_quote","text":"","code":"replace_curly_quote(x)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/replace_curly_quote.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Replace curly apostrophes and quotes from word — replace_curly_quote","text":"x character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/replace_curly_quote.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Replace curly apostrophes and quotes from word — replace_curly_quote","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/sanitize_split.html","id":null,"dir":"Reference","previous_headings":"","what":"Sanitize list of data frames — sanitize_split","title":"Sanitize list of data frames — sanitize_split","text":"Removing empty rows","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/sanitize_split.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sanitize list of data frames — sanitize_split","text":"","code":"sanitize_split( l, generic.names = c(\"redcap_event_name\", \"redcap_repeat_instrument\", \"redcap_repeat_instance\"), drop.complete = TRUE, drop.empty = TRUE )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/sanitize_split.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sanitize list of data frames — sanitize_split","text":"l list data frames. generic.names vector generic names excluded. drop.complete logical remove generic REDCap variables indicating instrument completion. Default TRUE. drop.empty logical remove variables NAs Default TRUE.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/sanitize_split.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sanitize list of data frames — sanitize_split","text":"list data frames generic names excluded.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/set_attr.html","id":null,"dir":"Reference","previous_headings":"","what":"Set attributes for named attribute. Appends if attr is NULL — set_attr","title":"Set attributes for named attribute. Appends if attr is NULL — set_attr","text":"Set attributes named attribute. Appends attr NULL","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/set_attr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set attributes for named attribute. Appends if attr is NULL — set_attr","text":"","code":"set_attr(data, label, attr = NULL, overwrite = FALSE)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/set_attr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set attributes for named attribute. Appends if attr is NULL — set_attr","text":"data vector label label attr attribute name overwrite overwrite existing attributes. Default FALSE.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/set_attr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set attributes for named attribute. Appends if attr is NULL — set_attr","text":"vector attribute","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/shiny_cast.html","id":null,"dir":"Reference","previous_headings":"","what":"Launch the included Shiny-app for database casting and upload — shiny_cast","title":"Launch the included Shiny-app for database casting and upload — shiny_cast","text":"Wraps shiny::runApp()","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/shiny_cast.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Launch the included Shiny-app for database casting and upload — shiny_cast","text":"","code":"shiny_cast(...)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/shiny_cast.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Launch the included Shiny-app for database casting and upload — shiny_cast","text":"... Arguments passed shiny::runApp()","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/shiny_cast.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Launch the included Shiny-app for database casting and upload — shiny_cast","text":"shiny app","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/shiny_cast.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Launch the included Shiny-app for database casting and upload — shiny_cast","text":"","code":"# shiny_cast()"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/split_non_repeating_forms.html","id":null,"dir":"Reference","previous_headings":"","what":"Split a data frame into separate tables for each form — split_non_repeating_forms","title":"Split a data frame into separate tables for each form — split_non_repeating_forms","text":"Split data frame separate tables form","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/split_non_repeating_forms.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split a data frame into separate tables for each form — split_non_repeating_forms","text":"","code":"split_non_repeating_forms(table, universal_fields, fields)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/split_non_repeating_forms.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split a data frame into separate tables for each form — split_non_repeating_forms","text":"table data frame universal_fields character vector fields included every table fields two-column matrix containing names fields included form","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/split_non_repeating_forms.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split a data frame into separate tables for each form — split_non_repeating_forms","text":"list data frames, one non-repeating form","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/split_non_repeating_forms.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split a data frame into separate tables for each form — split_non_repeating_forms","text":"","code":"# Create a table table <- data.frame( id = c(1, 2, 3, 4, 5), form_a_name = c(\"John\", \"Alice\", \"Bob\", \"Eve\", \"Mallory\"), form_a_age = c(25, 30, 25, 15, 20), form_b_name = c(\"John\", \"Alice\", \"Bob\", \"Eve\", \"Mallory\"), form_b_gender = c(\"M\", \"F\", \"M\", \"F\", \"F\") ) # Create the universal fields universal_fields <- c(\"id\") # Create the fields fields <- matrix( c( \"form_a_name\", \"form_a\", \"form_a_age\", \"form_a\", \"form_b_name\", \"form_b\", \"form_b_gender\", \"form_b\" ), ncol = 2, byrow = TRUE ) # Split the table split_non_repeating_forms(table, universal_fields, fields) #> $form_a_age #> id #> 1 1 #> 2 2 #> 3 3 #> 4 4 #> 5 5 #>"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/strsplitx.html","id":null,"dir":"Reference","previous_headings":"","what":"Extended string splitting — strsplitx","title":"Extended string splitting — strsplitx","text":"Can used substitute base function. Main claim fame easing split around defined delimiter, see example.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/strsplitx.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extended string splitting — strsplitx","text":"","code":"strsplitx(x, split, type = \"classic\", perl = FALSE, ...)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/strsplitx.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extended string splitting — strsplitx","text":"x data split delimiter type Split type. Can c(\"classic\", \"\", \"\", \"around\") perl perl param strsplit() ... additional parameters passed base strsplit handling splits","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/strsplitx.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extended string splitting — strsplitx","text":"list","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/strsplitx.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Extended string splitting — strsplitx","text":"","code":"test <- c(\"12 months follow-up\", \"3 steps\", \"mRS 6 weeks\", \"Counting to 231 now\") strsplitx(test, \"[0-9]\", type = \"around\") #> [[1]] #> [1] \"1\" \"2\" \" months follow-up\" #> #> [[2]] #> [1] \"3\" \" steps\" #> #> [[3]] #> [1] \"mRS \" \"6\" \" weeks\" #> #> [[4]] #> [1] \"Counting to \" \"2\" \"3\" \"1\" \" now\" #>"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/suffix2label.html","id":null,"dir":"Reference","previous_headings":"","what":"Transfer variable name suffix to label in widened data — suffix2label","title":"Transfer variable name suffix to label in widened data — suffix2label","text":"Transfer variable name suffix label widened data","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/suffix2label.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Transfer variable name suffix to label in widened data — suffix2label","text":"","code":"suffix2label( data, suffix.sep = \"____\", attr = \"label\", glue.str = \"{label} ({paste(suffixes,collapse=', ')})\" )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/suffix2label.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Transfer variable name suffix to label in widened data — suffix2label","text":"data data.frame suffix.sep string split suffix(es). Passed strsplit attr label attribute. Default \"label\" glue.str glue string new label. Available variables \"label\" \"suffixes\"","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/suffix2label.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Transfer variable name suffix to label in widened data — suffix2label","text":"data.frame","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/time_only_correction.html","id":null,"dir":"Reference","previous_headings":"","what":"Correction based on time_only_filter function — time_only_correction","title":"Correction based on time_only_filter function — time_only_correction","text":"Correction based time_only_filter function","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/time_only_correction.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Correction based on time_only_filter function — time_only_correction","text":"","code":"time_only_correction(data, ...)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/time_only_correction.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Correction based on time_only_filter function — time_only_correction","text":"data data set ... arguments passed `guess_time_only_filter()`","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/time_only_correction.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Correction based on time_only_filter function — time_only_correction","text":"tibble","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/time_only_correction.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Correction based on time_only_filter function — time_only_correction","text":"","code":"data <- redcapcast_data ## data |> time_only_correction()"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/var2fct.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert vector to factor based on threshold of number of unique levels — var2fct","title":"Convert vector to factor based on threshold of number of unique levels — var2fct","text":"wrapper forcats::as_factor, sorts numeric vectors factoring, levels character vectors order appearance.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/var2fct.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert vector to factor based on threshold of number of unique levels — var2fct","text":"","code":"var2fct(data, unique.n)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/var2fct.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert vector to factor based on threshold of number of unique levels — var2fct","text":"data vector data.frame column unique.n threshold convert class factor","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/var2fct.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert vector to factor based on threshold of number of unique levels — var2fct","text":"vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/var2fct.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert vector to factor based on threshold of number of unique levels — var2fct","text":"","code":"sample(seq_len(4), 20, TRUE) |> var2fct(6) |> summary() #> 1 2 3 4 #> 2 1 7 10 sample(letters, 20) |> var2fct(6) |> summary() #> Length Class Mode #> 20 character character sample(letters[1:4], 20, TRUE) |> var2fct(6) #> [1] c c d b c d b c b c b b b b b a c d b b #> Levels: c d b a"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/vec2choice.html","id":null,"dir":"Reference","previous_headings":"","what":"Named vector to REDCap choices (`wrapping compact_vec()`) — vec2choice","title":"Named vector to REDCap choices (`wrapping compact_vec()`) — vec2choice","text":"Named vector REDCap choices (`wrapping compact_vec()`)","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/vec2choice.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Named vector to REDCap choices (`wrapping compact_vec()`) — vec2choice","text":"","code":"vec2choice(data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/vec2choice.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Named vector to REDCap choices (`wrapping compact_vec()`) — vec2choice","text":"data named vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/vec2choice.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Named vector to REDCap choices (`wrapping compact_vec()`) — vec2choice","text":"character string","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/vec2choice.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Named vector to REDCap choices (`wrapping compact_vec()`) — vec2choice","text":"","code":"sample(seq_len(4), 20, TRUE) |> as_factor() |> named_levels() |> sort() |> vec2choice() #> [1] \"1, 1 | 2, 2 | 3, 3 | 4, 4\""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-2531","dir":"Changelog","previous_headings":"","what":"REDCapCAST 25.3.1","title":"REDCapCAST 25.3.1","text":"CRAN release: 2025-03-05 FIX: as_factor() now interprets empty variables empty levels attribute logicals avoid returning factors empty levels. NEW: as_logical(): interprets vectors two levels logical values matches supplied list logical pairs like “TRUE”/“FALSE”, “Yes”/“” 1/2. Eases interpretation data databases minimal metadata. Works vectors data.frames. Interprets vectors single value also matching supplied levels (Chooses first match pair several matches). NEW: easy_redcap(): new parameter data_format specify data format c(“wide”, “list”, “redcap”, “long”). now “redcap” “long” treated equally. added ease MMRM analyses. case, missing baseline values can carried forward “last observation carried forward” using tidyr::fill() function specifying variables fill. Interesting discussion filling data Stackoverflow. redcap_read_tables() now option “none” split_forms parameter allow splitting data. FIX: ds2dd_detailed(): convert_logicals parameter turned default logicals now interpreted field type “truefalse”. Converting logicals factors result numeric values 1 FALSE 2 TRUE, opposite traditional notation lead serous problems handled correctly. solve .","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-2511","dir":"Changelog","previous_headings":"","what":"REDCapCAST 25.1.1","title":"REDCapCAST 25.1.1","text":"CRAN release: 2025-01-29 newly introduced extension forcats::fct_drop() corrected work intended method. Conversion column names field_names aligning better REDCap naming. Shorten variable names 100 characters (REDCap criteria; note recommended variable name length <26) Fixed params conflict easy_redcap() specifying raw_or_label.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-24121","dir":"Changelog","previous_headings":"","what":"REDCapCAST 24.12.1","title":"REDCapCAST 24.12.1","text":"CRAN release: 2024-12-02 release attempts solve problems hosting shiny_cast app, also implementing functions preserve much meta data possible REDCap database exporting data. hosting shinyapps.io given lot trouble recently. Modified package structure little around shiny_cast(), accommodate alternative hosting approach package functions included script instead requiring package. NEW: new option raw_or_label read_redcap_tables() added: “”. Get raw values REDCap labels applied labels. Use as_factor() format factors original labels use gtsummary package easily get beautiful tables original labels REDCap. Use fct_drop() drop empty levels. NEW: fct_drop() added extension forcats::fct_drop(), works across data.frames. Use fct_drop(). CHANGE: default data export method easy_redcap() changed use new labelled data export read_redcap_tables().","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-24113","dir":"Changelog","previous_headings":"","what":"REDCapCAST 24.11.3","title":"REDCapCAST 24.11.3","text":"BUG: shiny_cast() fails load missed loading REDCapCAST library ui.r. Fixed. Tests great.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-24112","dir":"Changelog","previous_headings":"","what":"REDCapCAST 24.11.2","title":"REDCapCAST 24.11.2","text":"CRAN release: 2024-11-22 24.11.1 rejected CRAN based wrong title capitalisation. opportunity extend package overhaul. actually turned major step towards usable shiny app received focus. implemented option specify categorical variables factorize, modified version {forcats} {haven}’s as_factor(), preserve attributes applied data able upload cast REDCap meta data richly formatted data (use .rds). matter input type, input parsed using default options {readr} package. Also avoid mis-labelling, logicals converted factors REDCap truefalse class follows different naming conversion compared R. Also correct support variable labels field labels (use .rds formatted data label labelled::var_label()) Vignettes documentation restructured. package detached REDCapRITS, originally forked . data split function kept, testing rewritten. projects evolved away original fork.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-24111","dir":"Changelog","previous_headings":"","what":"REDCapCAST 24.11.1","title":"REDCapCAST 24.11.1","text":"Revised tests. Documentation slightly updated highlight shiny app casting REDCap metadata. working hosting Shiny Server.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"functions-24-11-1","dir":"Changelog","previous_headings":"","what":"Functions:","title":"REDCapCAST 24.11.1","text":"Bug: ‘form.name’ specified ‘ds2dd_detailed()’ ignored. Corrected ignored ‘form.sep’ specified. Added handling re-occurring form.sep pattern. New: export_redcap_instrument() new version create_instrument_meta(), export single instrument. Multiple instrument export can done lapply() purrr::map(). allows inclusion functionality Shiny implementation easier handle. create_instrument_meta() deprecated. Improved: shiny_cast() app updated actually work install package clones whole repository.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"shiny-24-11-1","dir":"Changelog","previous_headings":"","what":"Shiny:","title":"REDCapCAST 24.11.1","text":"New: Major overhaul app interface introduction bslib building page. Also Detailed documentation added app workflow. New: Export REDCap instrument ready add database based uploaded spreadsheet. thanks export_redcap_instrument() function. functionality intended projects production adding instruments handled manually API upload. Bug: Export datadictionary “” instead “NA” NAs. Upload REDCap failed. anymore. shiny implementation included package. Implementing shinylive may looked later.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-24103","dir":"Changelog","previous_headings":"","what":"REDCapCAST 24.10.3","title":"REDCapCAST 24.10.3","text":"CRAN release: 2024-10-03 Updated links spelling.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-24101","dir":"Changelog","previous_headings":"","what":"REDCapCAST 24.10.1","title":"REDCapCAST 24.10.1","text":"Minor changes pass tests renv . rhub really running smooth previously.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-2461","dir":"Changelog","previous_headings":"","what":"REDCapCAST 24.6.1","title":"REDCapCAST 24.6.1","text":"CRAN release: 2024-06-07","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"functions-24-6-1","dir":"Changelog","previous_headings":"","what":"Functions","title":"REDCapCAST 24.6.1","text":"Fix: read_redcap_tables(): field names testing allows include “[form_name]_complete” fields. Fix: ds2dd_detailed(): default record ID name now “record_id”, REDCap default. Default still use first column name. Support added interpret column name prefix suffix instrument names. See examples. New: create_instrument_meta(): creates zip instrument files allow adding new instruments project production. Takes data dictionary input creates zip instrument specified form_name column. New: doc2dd(): function convert document table data dictionary. allows specify instrument whole data dictionary text document, easier work easily modifiable. generic case data frame variable names values column. format like REDCap data dictionary, gives options formatting. related functions data handling formatting. One interesting function case_match_regex_list(), allows dynamic dplyr::case_when()-like approach regex-matching. think neat least.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"documentation-and-more-24-6-1","dir":"Changelog","previous_headings":"","what":"Documentation and more","title":"REDCapCAST 24.6.1","text":"Dependencies: order deploy shiny_cast() shinylive, need remove curl dependency. accomplish , shiny_deploy() helper functions moved package project.aid. realising REDCapR curl dependency, culprit. REDCapCAST going shinylive web-app without removing REDCapR dependency REDCap database interaction, defy purpose. ’ll stick hosted Shiny app instead.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-2421","dir":"Changelog","previous_headings":"","what":"REDCapCAST 24.2.1","title":"REDCapCAST 24.2.1","text":"CRAN release: 2024-02-28","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"functions-24-2-1","dir":"Changelog","previous_headings":"","what":"Functions","title":"REDCapCAST 24.2.1","text":"Fix: ds2dd(): uses correct default dd column names. deprecated. Fix: easy_redcap(): fixed actually allow project naming. also specifically asks uri. widening updated work. Fix: redcap_wider(): updated accept formats allow handling simple projects without repeating instruments longitudinal. Fix: read_redcap_tables(): now handles non-longitudinal project without repeatable instruments. NEW: ds2dd_detailed(): extension ds2dd(), serves preserve much metadata possible automatically. Depends group helper functions also introduced. special note guess_time_only_filter(), try guess columns/variables formatted time formats. Supports hms time format. DETAILED INSTRUCTION VIGNETTE PENDING. NEW: read_redcap_instrument(): convenience function retrieve complete instrument. Goes little focused approach. REDCapR::redcap_read() can specify form download. also specify record id variable though. done read_redcap_instrument(). Nothing fancy. NEW: shiny_cast(): Shiny application ease process converting spreadsheet/data set REDCap database. app runs locally data transferred securely. can just create upload data dictionary, can also transfer given data process. plan host app shinyapps.io, now can run locally.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"other-24-2-1","dir":"Changelog","previous_headings":"","what":"Other","title":"REDCapCAST 24.2.1","text":"believe renv now added runs correctly. clone, renv::restore() install necessary package modify package. seems always back forth. renv may way . Added Code Conduct.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-2411","dir":"Changelog","previous_headings":"","what":"REDCapCAST 24.1.1","title":"REDCapCAST 24.1.1","text":"CRAN release: 2024-01-09","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"functions-24-1-1","dir":"Changelog","previous_headings":"","what":"Functions","title":"REDCapCAST 24.1.1","text":"Fix: read_redcap_tables(): checking form names based data dictionary allow handling non-longitudinal projects. Prints invalid form names invalid event names. invalid form names supplied REDCapR::redcap_read() (backbone), forms exported, want focused approach. Invalid event names give output rather peculiar formatting. Checking field names validity also added.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-23121","dir":"Changelog","previous_headings":"","what":"REDCapCAST 23.12.1","title":"REDCapCAST 23.12.1","text":"CRAN release: 2023-12-20 One new function ease secure dataset retrieval bug fixes.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"functions-23-12-1","dir":"Changelog","previous_headings":"","what":"Functions","title":"REDCapCAST 23.12.1","text":"New: easy_redcap() function ease retrieval dataset read_redcap_tables() keyring-package based key storage, handles secure API set, storage retrieval. Relies small helper function, get_api_key(), wraps relevant keyring-functions. Includes option cast data wide format flag widen.data. Fix: REDCap_split(): using function , supplying data set check boxes fail metadata supplied tibble. Metadata now converted data.frame. Fixed. Fix: read_redcap_tables(): fixed bug supplying events.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-2362","dir":"Changelog","previous_headings":"","what":"REDCapCAST 23.6.2","title":"REDCapCAST 23.6.2","text":"CRAN release: 2023-07-04 version marks introduction helper functions handle database creation.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"functions-23-6-2","dir":"Changelog","previous_headings":"","what":"Functions","title":"REDCapCAST 23.6.2","text":"New: ds2dd() function migrating stRoke-package. Assists building data dictionary REDCap dataset. New: strsplitx() function ease string splitting extension base::strsplit(). Inspiration https://stackoverflow.com//11014253/21019325 https://www.r-bloggers.com/2018/04/strsplit--keeping--delimiter/. New: d2n() function converts single digits written numbers. Used sanitize variable form names REDCap database creation. universal number word suggest english::word() xfun::numbers_to_words(), though testing .","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"redcapcast-2361","dir":"Changelog","previous_headings":"","what":"REDCapCAST 23.6.1","title":"REDCapCAST 23.6.1","text":"CRAN release: 2023-06-06","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"documentation-23-6-1","dir":"Changelog","previous_headings":"","what":"Documentation:","title":"REDCapCAST 23.6.1","text":"Updated description. Look! hex icon! Heading CRAN.","code":""},{"path":[]},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"documentation-23-4-1","dir":"Changelog","previous_headings":"","what":"Documentation:","title":"REDCapCAST 23.4.1","text":"Aiming CRAN","code":""},{"path":[]},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"documentation-23-3-2","dir":"Changelog","previous_headings":"","what":"Documentation:","title":"REDCapCAST 23.3.2","text":"Page added. Vignettes follow. GithubActions tests added code coverage assessed. Badge galore..","code":""},{"path":[]},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"new-name-redcapcast-23-3-1","dir":"Changelog","previous_headings":"","what":"New name: REDCapCAST","title":"REDCapCAST 23.3.1","text":"reflect new functions limitation working R, changed naming fork, still, course, maintaining status fork. versioning moved monthly naming convention. main goal package keep option export defined subset whole dataset REDCap server made possible REDCapR::redcap_read() function, combine work put REDCapRITS package handling longitudinal projects /projects repeated instruments.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"functions-23-3-1","dir":"Changelog","previous_headings":"","what":"Functions:","title":"REDCapCAST 23.3.1","text":"read_redcap_tables() NEW: function mainly implementation combined use REDCapR::redcap_read() REDCap_split() maintain focused nature REDCapR::redcap_read(), download specified data. Also implements tests valid form names event names. usual fall-back solution get data. redcap_wider() NEW: function pivots long data frames read_redcap_tables() using tidyr::pivot_wider(). focused_metadata() NEW: hidden helper function enable focused data acquisition approach handle subset metadata corresponding focused dataset.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/news/index.html","id":"notes-23-3-1","dir":"Changelog","previous_headings":"","what":"Notes:","title":"REDCapCAST 23.3.1","text":"metadata handling IMPROVED: improved handling different column names matadata (DataDictionary) REDCap dependent whether acquired thorugh api og downloaded server.","code":""}]
+[{"path":[]},{"path":"https://agdamsbo.github.io/REDCapCAST/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement andreas@gdamsbo.dk. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.1, available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc. .","code":" Copyright (C) This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see Copyright (C) This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Database-creation.html","id":"two-different-ways-to-create-a-data-base","dir":"Articles","previous_headings":"","what":"Two different ways to create a data base","title":"Database-creation","text":"REDCapCAST provides two approaches creating data dictionary aimed helping two different cases: Easily create REDCap data base existing data set. Create table Word describing variables data base use create data base. following try come suggestions use approaches.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Database-creation.html","id":"easy-data-set-to-data-base-workflow","dir":"Articles","previous_headings":"Two different ways to create a data base","what":"Easy data set to data base workflow","title":"Database-creation","text":"first iteration dataset data dictionary function ds2dd(), creates basic data dictionary variables stored text. sufficient just storing old datasets/spreadsheets securely REDCap. advanced ds2dd_detailed() natural development. try apply common data classes data validation assume first column id number. outputs list dataset modified variable names comply REDCap naming conventions data dictionary. dataset correctly formatted data dictionary preserve much information possible. Additional specifications DataDictionary can made manually, can uploaded modified manually graphical user interface REDCap server.","code":"d1 <- mtcars |> dplyr::mutate(record_id = seq_len(dplyr::n())) |> ds2dd() d1 |> gt::gt() d2 <- REDCapCAST::redcapcast_data |> dplyr::mutate(record_id = seq_len(dplyr::n()), region=factor(region)) |> dplyr::select(record_id, dplyr::everything()) |> (\\(.x){ .x[!grepl(\"_complete$\",names(.x))] })() |> (\\(.x){ .x[!grepl(\"^redcap\",names(.x))] })() |> ds2dd_detailed() |> purrr::pluck(\"meta\") d2 |> gt::gt()"},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Database-creation.html","id":"data-base-from-table","dir":"Articles","previous_headings":"Two different ways to create a data base","what":"Data base from table","title":"Database-creation","text":"…instructions examples coming…","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Database-creation.html","id":"meta-data-and-data-upload","dir":"Articles","previous_headings":"Two different ways to create a data base","what":"Meta data and data upload","title":"Database-creation","text":"Now DataDictionary can exported spreadsheet uploaded can uploaded using REDCapR package (projects “Development” status). Use one two approaches :","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Database-creation.html","id":"manual-upload","dir":"Articles","previous_headings":"Two different ways to create a data base > Meta data and data upload","what":"Manual upload","title":"Database-creation","text":"","code":"write.csv(dd_ls$meta, \"datadictionary.csv\")"},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Database-creation.html","id":"upload-with-redcapr","dir":"Articles","previous_headings":"Two different ways to create a data base > Meta data and data upload","what":"Upload with REDCapR","title":"Database-creation","text":"“REDCap R Handbook” written interfacing REDCap R using library(keyring)store credentials chapter 1.1.","code":"REDCapR::redcap_metadata_write( dd_ls$meta, redcap_uri = keyring::key_get(\"DB_URI\"), token = keyring::key_get(\"DB_TOKEN\") )"},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/Database-creation.html","id":"step-4---data-upload","dir":"Articles","previous_headings":"Two different ways to create a data base","what":"Step 4 - Data upload","title":"Database-creation","text":"two options available data upload meta data upload: manual REDCapR. latter shown .","code":"REDCapR::redcap_write( dd_ls$data, redcap_uri = keyring::key_get(\"DB_URI\"), token = keyring::key_get(\"DB_TOKEN\") )"},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/REDCapCAST.html","id":"casting-meta-data","dir":"Articles","previous_headings":"","what":"Casting meta data","title":"REDCapCAST","text":"easiest way use shiny_cast(). can access hosted version launch locally like :","code":"shiny_cast()"},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/REDCapCAST.html","id":"reading-data-from-redcap","dir":"Articles","previous_headings":"","what":"Reading data from REDCap","title":"REDCapCAST","text":"get started, easiest way possible, can use easy_redcap() function (example ). need API-key REDCap server, uri/URL/address API connection (usually address used accessing institutions REDCap server, appended “/api/”). function includes convenience features ease work. project uses repeating instruments possible longitudinal project, can choose widen data. , result list instrument chosen extract data . Make sure specify fields instruments need, avoid save data locally, always source REDCap avoid possibly insecure local storage sensitive data.","code":"easy_redcap( uri = \"YOUR URI\", project.name = \"MY_PROJECT\", widen.data = TRUE, fields = c(\"record_id\", \"OTHER FIELDS\") )"},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/REDCapCAST.html","id":"splitting-the-dataset","dir":"Articles","previous_headings":"","what":"Splitting the dataset","title":"REDCapCAST","text":"easy_redcap() function things hood. examples show nicely formatted output achieved. sample dataset Data Dictionary/metadata provided demonstration: save metadata labels dataset, can save field labels choices radio buttons dropdown features: REDCap_split function splits data set list data.frames. easy_redcap() (optionally) continue widen data, transforming list data.frames single data.frame one row subject/record_id (wide data format): Transfer suffixes labels:","code":"redcapcast_data |> gt::gt() redcapcast_meta |> gt::gt() labelled_data <- apply_field_label( data = redcapcast_data, meta = redcapcast_meta ) |> apply_factor_labels(meta = redcapcast_meta) list <- REDCap_split( records = labelled_data, metadata = redcapcast_meta, forms = \"all\" ) |> # Next steps cleans up and removes generic columns sanitize_split() str(list) #> List of 3 #> $ baseline_data_start: tibble [6 × 14] (S3: tbl_df/tbl/data.frame) #> ..$ record_id : num [1:6] 1 2 3 4 5 6 #> .. ..- attr(*, \"label\")= chr \"ID\" #> ..$ redcap_event_name : chr [1:6] \"inclusion\" \"inclusion\" \"inclusion\" \"inclusion\" ... #> ..$ cpr : chr [1:6] \"1203401OB4\" \"0102342303\" \"2301569823\" \"0204051342\" ... #> .. ..- attr(*, \"label\")= chr \"CPR (Danish civil registration number)\" #> ..$ inclusion : Date[1:6], format: \"2023-03-13\" \"2023-03-01\" ... #> ..$ inclusion_time : 'hms' num [1:6] 12:38:49 10:38:57 12:01:07 20:39:19 ... #> .. ..- attr(*, \"units\")= chr \"secs\" #> ..$ dob : Date[1:6], format: \"1940-03-12\" \"1934-02-01\" ... #> ..$ age : num [1:6] 83 89.1 66.1 117.9 126.2 ... #> .. ..- attr(*, \"label\")= chr \"Age\\r\\nNote: Apparently, the build in datediff() function does not handle counting whole years. This results in\"| __truncated__ #> ..$ age_integer : num [1:6] 83 89 66 117 126 91 #> .. ..- attr(*, \"label\")= chr \"Age integer\\r\\nNote: as opposed to the build in datediff() this handles counting years as integers very well. C\"| __truncated__ #> ..$ sex : chr [1:6] \"female\" \"male\" \"male\" \"female\" ... #> .. ..- attr(*, \"label\")= chr \"Legal sex\" #> ..$ cohabitation : 'labelled' chr [1:6] \"Yes\" \"Yes\" \"No\" NA ... #> .. ..- attr(*, \"label\")= chr \"Cohabitation\" #> .. ..- attr(*, \"labels\")= Named chr [1:2] \"1\" \"2\" #> .. .. ..- attr(*, \"names\")= chr [1:2] \"Yes\" \"No\" #> ..$ hypertension : 'labelled' chr [1:6] \"No\" \"No\" \"Yes\" NA ... #> .. ..- attr(*, \"label\")= chr \"Hypertension\" #> .. ..- attr(*, \"labels\")= Named chr [1:2] \"1\" \"2\" #> .. .. ..- attr(*, \"names\")= chr [1:2] \"Yes\" \"No\" #> ..$ diabetes : 'labelled' chr [1:6] \"Yes\" \"No\" \"Yes\" NA ... #> .. ..- attr(*, \"label\")= chr \"Diabetes\" #> .. ..- attr(*, \"labels\")= Named chr [1:2] \"1\" \"2\" #> .. .. ..- attr(*, \"names\")= chr [1:2] \"Yes\" \"No\" #> ..$ region : 'labelled' chr [1:6] \"East\" \"South\" \"North\" NA ... #> .. ..- attr(*, \"label\")= chr \"Region\" #> .. ..- attr(*, \"labels\")= Named chr [1:4] \"1\" \"2\" \"3\" \"4\" #> .. .. ..- attr(*, \"names\")= chr [1:4] \"North\" \"East\" \"South\" \"West\" #> ..$ baseline_data_start_complete: chr [1:6] \"Incomplete\" \"Incomplete\" \"Incomplete\" \"Incomplete\" ... #> $ mrs : tibble [5 × 6] (S3: tbl_df/tbl/data.frame) #> ..$ record_id : num [1:5] 1 2 2 3 3 #> .. ..- attr(*, \"label\")= chr \"ID\" #> ..$ redcap_event_name: chr [1:5] \"inclusion\" \"inclusion\" \"follow1\" \"follow1\" ... #> ..$ mrs_assessed : 'labelled' chr [1:5] \"Yes\" \"Yes\" \"Yes\" \"Yes\" ... #> .. ..- attr(*, \"label\")= chr \"Assesed\" #> .. ..- attr(*, \"labels\")= Named chr [1:2] \"1\" \"2\" #> .. .. ..- attr(*, \"names\")= chr [1:2] \"Yes\" \"No\" #> ..$ mrs_date : Date[1:5], format: \"2023-03-13\" \"2023-03-07\" ... #> ..$ mrs_score : 'labelled' num [1:5] 1 1 3 2 1 #> .. ..- attr(*, \"label\")= chr \"mRS score\" #> .. ..- attr(*, \"labels\")= Named chr [1:6] \"0\" \"1\" \"2\" \"3\" ... #> .. .. ..- attr(*, \"names\")= chr [1:6] \"0\" \"1\" \"2\" \"3\" ... #> ..$ mrs_complete : chr [1:5] \"Incomplete\" \"Incomplete\" \"Incomplete\" \"Incomplete\" ... #> $ new_event : tibble [13 × 8] (S3: tbl_df/tbl/data.frame) #> ..$ record_id : num [1:13] 2 3 3 3 3 3 4 4 4 4 ... #> .. ..- attr(*, \"label\")= chr \"ID\" #> ..$ redcap_event_name : chr [1:13] \"follow1\" \"follow1\" \"follow1\" \"follow2\" ... #> ..$ redcap_repeat_instrument: chr [1:13] \"new_event\" \"new_event\" \"new_event\" \"new_event\" ... #> ..$ redcap_repeat_instance : num [1:13] 1 1 2 1 2 3 1 2 1 2 ... #> ..$ event_datetime : POSIXct[1:13], format: \"2024-01-18 12:49:42\" \"2024-01-18 12:49:58\" ... #> ..$ event_age : num [1:13] NA NA NA NA NA NA 96 105 118 118 ... #> .. ..- attr(*, \"label\")= chr \"Age at event\" #> ..$ event_type : 'labelled' chr [1:13] \"TIA\" \"AIS\" \"ICH\" \"ICH\" ... #> .. ..- attr(*, \"label\")= chr \"Neurovascular event\" #> .. ..- attr(*, \"labels\")= Named chr [1:5] \"1\" \"2\" \"3\" \"4\" ... #> .. .. ..- attr(*, \"names\")= chr [1:5] \"TIA\" \"AIS\" \"ICH\" \"SAH\" ... #> ..$ new_event_complete : chr [1:13] \"Incomplete\" \"Incomplete\" \"Incomplete\" \"Incomplete\" ... wide_data <- redcap_wider(list, event.glue = \"{.value}____{redcap_event_name}\", inst.glue = \"{.value}____{redcap_repeat_instance}\" ) #> Joining with `by = join_by(record_id)` #> Joining with `by = join_by(record_id)` wide_data |> str() #> tibble [6 × 49] (S3: tbl_df/tbl/data.frame) #> $ record_id : num [1:6] 1 2 3 4 5 6 #> ..- attr(*, \"label\")= chr \"ID\" #> $ cpr : chr [1:6] \"1203401OB4\" \"0102342303\" \"2301569823\" \"0204051342\" ... #> ..- attr(*, \"label\")= chr \"CPR (Danish civil registration number)\" #> $ inclusion : Date[1:6], format: \"2023-03-13\" \"2023-03-01\" ... #> $ inclusion_time : 'hms' num [1:6] 12:38:49 10:38:57 12:01:07 20:39:19 ... #> ..- attr(*, \"units\")= chr \"secs\" #> $ dob : Date[1:6], format: \"1940-03-12\" \"1934-02-01\" ... #> $ age : num [1:6] 83 89.1 66.1 117.9 126.2 ... #> ..- attr(*, \"label\")= chr \"Age\\r\\nNote: Apparently, the build in datediff() function does not handle counting whole years. This results in\"| __truncated__ #> $ age_integer : num [1:6] 83 89 66 117 126 91 #> ..- attr(*, \"label\")= chr \"Age integer\\r\\nNote: as opposed to the build in datediff() this handles counting years as integers very well. C\"| __truncated__ #> $ sex : chr [1:6] \"female\" \"male\" \"male\" \"female\" ... #> ..- attr(*, \"label\")= chr \"Legal sex\" #> $ cohabitation : 'labelled' chr [1:6] \"Yes\" \"Yes\" \"No\" NA ... #> ..- attr(*, \"label\")= chr \"Cohabitation\" #> ..- attr(*, \"labels\")= Named chr [1:2] \"1\" \"2\" #> .. ..- attr(*, \"names\")= chr [1:2] \"Yes\" \"No\" #> $ hypertension : 'labelled' chr [1:6] \"No\" \"No\" \"Yes\" NA ... #> ..- attr(*, \"label\")= chr \"Hypertension\" #> ..- attr(*, \"labels\")= Named chr [1:2] \"1\" \"2\" #> .. ..- attr(*, \"names\")= chr [1:2] \"Yes\" \"No\" #> $ diabetes : 'labelled' chr [1:6] \"Yes\" \"No\" \"Yes\" NA ... #> ..- attr(*, \"label\")= chr \"Diabetes\" #> ..- attr(*, \"labels\")= Named chr [1:2] \"1\" \"2\" #> .. ..- attr(*, \"names\")= chr [1:2] \"Yes\" \"No\" #> $ region : 'labelled' chr [1:6] \"East\" \"South\" \"North\" NA ... #> ..- attr(*, \"label\")= chr \"Region\" #> ..- attr(*, \"labels\")= Named chr [1:4] \"1\" \"2\" \"3\" \"4\" #> .. ..- attr(*, \"names\")= chr [1:4] \"North\" \"East\" \"South\" \"West\" #> $ baseline_data_start_complete : chr [1:6] \"Incomplete\" \"Incomplete\" \"Incomplete\" \"Incomplete\" ... #> $ mrs_assessed____inclusion : 'labelled' chr [1:6] \"Yes\" \"Yes\" NA NA ... #> ..- attr(*, \"label\")= chr \"Assesed\" #> ..- attr(*, \"labels\")= Named chr [1:2] \"1\" \"2\" #> .. ..- attr(*, \"names\")= chr [1:2] \"Yes\" \"No\" #> $ mrs_assessed____follow1 : 'labelled' chr [1:6] NA \"Yes\" \"Yes\" NA ... #> ..- attr(*, \"label\")= chr \"Assesed\" #> ..- attr(*, \"labels\")= Named chr [1:2] \"1\" \"2\" #> .. ..- attr(*, \"names\")= chr [1:2] \"Yes\" \"No\" #> $ mrs_assessed____follow2 : 'labelled' chr [1:6] NA NA \"Yes\" NA ... #> ..- attr(*, \"label\")= chr \"Assesed\" #> ..- attr(*, \"labels\")= Named chr [1:2] \"1\" \"2\" #> .. ..- attr(*, \"names\")= chr [1:2] \"Yes\" \"No\" #> $ mrs_date____inclusion : Date[1:6], format: \"2023-03-13\" \"2023-03-07\" ... #> $ mrs_date____follow1 : Date[1:6], format: NA \"2023-03-09\" ... #> $ mrs_date____follow2 : Date[1:6], format: NA NA ... #> $ mrs_score____inclusion : 'labelled' num [1:6] 1 1 NA NA NA NA #> ..- attr(*, \"label\")= chr \"mRS score\" #> ..- attr(*, \"labels\")= Named chr [1:6] \"0\" \"1\" \"2\" \"3\" ... #> .. ..- attr(*, \"names\")= chr [1:6] \"0\" \"1\" \"2\" \"3\" ... #> $ mrs_score____follow1 : 'labelled' num [1:6] NA 3 2 NA NA NA #> ..- attr(*, \"label\")= chr \"mRS score\" #> ..- attr(*, \"labels\")= Named chr [1:6] \"0\" \"1\" \"2\" \"3\" ... #> .. ..- attr(*, \"names\")= chr [1:6] \"0\" \"1\" \"2\" \"3\" ... #> $ mrs_score____follow2 : 'labelled' num [1:6] NA NA 1 NA NA NA #> ..- attr(*, \"label\")= chr \"mRS score\" #> ..- attr(*, \"labels\")= Named chr [1:6] \"0\" \"1\" \"2\" \"3\" ... #> .. ..- attr(*, \"names\")= chr [1:6] \"0\" \"1\" \"2\" \"3\" ... #> $ mrs_complete____inclusion : chr [1:6] \"Incomplete\" \"Incomplete\" NA NA ... #> $ mrs_complete____follow1 : chr [1:6] NA \"Incomplete\" \"Incomplete\" NA ... #> $ mrs_complete____follow2 : chr [1:6] NA NA \"Incomplete\" NA ... #> $ event_datetime____1____follow1 : POSIXct[1:6], format: NA \"2024-01-18 12:49:42\" ... #> $ event_datetime____1____follow2 : POSIXct[1:6], format: NA NA ... #> $ event_age____1____follow1 : num [1:6] NA NA NA 96 127 NA #> ..- attr(*, \"label\")= chr \"Age at event\" #> $ event_age____1____follow2 : num [1:6] NA NA NA 118 NA NA #> ..- attr(*, \"label\")= chr \"Age at event\" #> $ event_type____1____follow1 : 'labelled' chr [1:6] NA \"TIA\" \"AIS\" \"TIA\" ... #> ..- attr(*, \"label\")= chr \"Neurovascular event\" #> ..- attr(*, \"labels\")= Named chr [1:5] \"1\" \"2\" \"3\" \"4\" ... #> .. ..- attr(*, \"names\")= chr [1:5] \"TIA\" \"AIS\" \"ICH\" \"SAH\" ... #> $ event_type____1____follow2 : 'labelled' chr [1:6] NA NA \"ICH\" \"AIS\" ... #> ..- attr(*, \"label\")= chr \"Neurovascular event\" #> ..- attr(*, \"labels\")= Named chr [1:5] \"1\" \"2\" \"3\" \"4\" ... #> .. ..- attr(*, \"names\")= chr [1:5] \"TIA\" \"AIS\" \"ICH\" \"SAH\" ... #> $ new_event_complete____1____follow1: chr [1:6] NA \"Incomplete\" \"Incomplete\" \"Complete\" ... #> $ new_event_complete____1____follow2: chr [1:6] NA NA \"Incomplete\" \"Complete\" ... #> $ event_datetime____2____follow1 : POSIXct[1:6], format: NA NA ... #> $ event_datetime____2____follow2 : POSIXct[1:6], format: NA NA ... #> $ event_datetime____3____follow1 : POSIXct[1:6], format: NA NA ... #> $ event_datetime____3____follow2 : POSIXct[1:6], format: NA NA ... #> $ event_age____2____follow1 : num [1:6] NA NA NA 105 127 NA #> ..- attr(*, \"label\")= chr \"Age at event\" #> $ event_age____2____follow2 : num [1:6] NA NA NA 118 NA NA #> ..- attr(*, \"label\")= chr \"Age at event\" #> $ event_age____3____follow1 : num [1:6] NA NA NA NA NA NA #> ..- attr(*, \"label\")= chr \"Age at event\" #> $ event_age____3____follow2 : num [1:6] NA NA NA 118 NA NA #> ..- attr(*, \"label\")= chr \"Age at event\" #> $ event_type____2____follow1 : 'labelled' chr [1:6] NA NA \"ICH\" \"TIA\" ... #> ..- attr(*, \"label\")= chr \"Neurovascular event\" #> ..- attr(*, \"labels\")= Named chr [1:5] \"1\" \"2\" \"3\" \"4\" ... #> .. ..- attr(*, \"names\")= chr [1:5] \"TIA\" \"AIS\" \"ICH\" \"SAH\" ... #> $ event_type____2____follow2 : 'labelled' chr [1:6] NA NA \"TIA\" \"ICH\" ... #> ..- attr(*, \"label\")= chr \"Neurovascular event\" #> ..- attr(*, \"labels\")= Named chr [1:5] \"1\" \"2\" \"3\" \"4\" ... #> .. ..- attr(*, \"names\")= chr [1:5] \"TIA\" \"AIS\" \"ICH\" \"SAH\" ... #> $ event_type____3____follow1 : 'labelled' chr [1:6] NA NA NA NA ... #> ..- attr(*, \"label\")= chr \"Neurovascular event\" #> ..- attr(*, \"labels\")= Named chr [1:5] \"1\" \"2\" \"3\" \"4\" ... #> .. ..- attr(*, \"names\")= chr [1:5] \"TIA\" \"AIS\" \"ICH\" \"SAH\" ... #> $ event_type____3____follow2 : 'labelled' chr [1:6] NA NA \"AIS\" \"Unknown\" ... #> ..- attr(*, \"label\")= chr \"Neurovascular event\" #> ..- attr(*, \"labels\")= Named chr [1:5] \"1\" \"2\" \"3\" \"4\" ... #> .. ..- attr(*, \"names\")= chr [1:5] \"TIA\" \"AIS\" \"ICH\" \"SAH\" ... #> $ new_event_complete____2____follow1: chr [1:6] NA NA \"Incomplete\" \"Complete\" ... #> $ new_event_complete____2____follow2: chr [1:6] NA NA \"Incomplete\" \"Incomplete\" ... #> $ new_event_complete____3____follow1: chr [1:6] NA NA NA NA ... #> $ new_event_complete____3____follow2: chr [1:6] NA NA \"Incomplete\" \"Complete\" ... wide_data_suffixes <- wide_data |> suffix2label()"},{"path":"https://agdamsbo.github.io/REDCapCAST/articles/REDCapCAST.html","id":"creating-a-nice-table","dir":"Articles","previous_headings":"","what":"Creating a nice table","title":"REDCapCAST","text":"","code":"wide_data_suffixes |> as_factor()|> dplyr::select(sex, hypertension, diabetes,mrs_score____follow2) |> gtsummary::tbl_summary(type = gtsummary::all_dichotomous() ~ \"categorical\")"},{"path":"https://agdamsbo.github.io/REDCapCAST/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Andreas Gammelgaard Damsbo. Author, maintainer. Paul Egeler. Author.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Damsbo , Egeler P (2025). REDCapCAST: REDCap Metadata Casting Castellated Data Handling. R package version 25.3.1, https://agdamsbo.github.io/REDCapCAST/, https://github.com/agdamsbo/REDCapCAST.","code":"@Manual{, title = {REDCapCAST: REDCap Metadata Casting and Castellated Data Handling}, author = {Andreas Gammelgaard Damsbo and Paul Egeler}, year = {2025}, note = {R package version 25.3.1, https://agdamsbo.github.io/REDCapCAST/}, url = {https://github.com/agdamsbo/REDCapCAST}, }"},{"path":"https://agdamsbo.github.io/REDCapCAST/index.html","id":"redcapcast-package-","dir":"","previous_headings":"","what":"REDCap Metadata Casting and Castellated Data Handling","title":"REDCap Metadata Casting and Castellated Data Handling","text":"Casting metadata REDCap database creation handling castellated data using repeated instruments longitudinal projects REDCap. implemented app-interface easy database creation accessible available run locally shiny_cast() allowing easily create REDCap database based existing spreadsheet. Export data REDCap different formats handling castellated data, default export requested data, mainly read_redcap_tables(). REDCapCAST initially build , still includes code pegeler/REDCapRITS, relies functions REDCapR-project","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/index.html","id":"history","dir":"","previous_headings":"","what":"History","title":"REDCap Metadata Casting and Castellated Data Handling","text":"package originally forked pegeler/REDCapRITS. REDCapRITS represents great extensive work handle castellated REDCap data different programming languages. REDCapCAST evolved much just handling castellated data detatched original project still relying main REDCap_split function. access REDCap database build outstanding work REDCapR. package really started frustration PhD health science hearing colleagues complaining “castellated” data formatting REDCap exports longitudinal projects used wide data. led bad decisions building databases avoiding repeated instruments. package solves challenges, solutions also implemented else like redcapAPI REDCapTidieR packages, bigger project. help new PhD students researchers, also worked creating helper/wrapper-functions ease data access. Documentation ’s way. advanced uses, consider using redcapAPI REDCapR packages.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/index.html","id":"future","dir":"","previous_headings":"","what":"Future","title":"REDCap Metadata Casting and Castellated Data Handling","text":"plan package bundled Handbook working REDCap R. work progress limited time available. Please feel free contact create issue ideas future additions.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/index.html","id":"installation-and-use","dir":"","previous_headings":"","what":"Installation and use","title":"REDCap Metadata Casting and Castellated Data Handling","text":"package available CRAN. Install latest version: Install latest version directly GitHub: Launch REDCapCAST app interface directly machine:","code":"install.packages(\"REDCapCAST\") require(\"remotes\") remotes::install_github(\"agdamsbo/REDCapCAST\") REDCapCAST::shiny_cast()"},{"path":"https://agdamsbo.github.io/REDCapCAST/index.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"REDCap Metadata Casting and Castellated Data Handling","text":"Please note REDCapCAST project released Contributor Code Conduct. contributing project, agree abide terms.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCapCAST-package.html","id":null,"dir":"Reference","previous_headings":"","what":"REDCapCAST: REDCap Metadata Casting and Castellated Data Handling — REDCapCAST-package","title":"REDCapCAST: REDCap Metadata Casting and Castellated Data Handling — REDCapCAST-package","text":"Casting metadata REDCap database creation handling castellated data using repeated instruments longitudinal projects 'REDCap'. Keeps focused data export approach, allowing export required data database. Also casting new REDCap databases based datasets sources. Originally forked R part 'REDCapRITS' Paul Egeler. See https://github.com/pegeler/REDCapRITS. 'REDCap' (Research Electronic Data Capture) secure, web-based software platform designed support data capture research studies, providing 1) intuitive interface validated data capture; 2) audit trails tracking data manipulation export procedures; 3) automated export procedures seamless data downloads common statistical packages; 4) procedures data integration interoperability external sources (Harris et al (2009) doi:10.1016/j.jbi.2008.08.010 ; Harris et al (2019) doi:10.1016/j.jbi.2019.103208 ).","code":""},{"path":[]},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCapCAST-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"REDCapCAST: REDCap Metadata Casting and Castellated Data Handling — REDCapCAST-package","text":"Maintainer: Andreas Gammelgaard Damsbo agdamsbo@clin.au.dk (ORCID) Authors: Paul Egeler paulegeler@gmail.com (ORCID)","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCap_split.html","id":null,"dir":"Reference","previous_headings":"","what":"Split REDCap repeating instruments table into multiple tables — REDCap_split","title":"Split REDCap repeating instruments table into multiple tables — REDCap_split","text":"take output REDCap export split base table child tables repeating instrument. Metadata used determine fields included resultant table.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCap_split.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split REDCap repeating instruments table into multiple tables — REDCap_split","text":"","code":"REDCap_split( records, metadata, primary_table_name = \"\", forms = c(\"repeating\", \"all\") )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCap_split.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split REDCap repeating instruments table into multiple tables — REDCap_split","text":"records Exported project records. May data.frame, response, character vector containing JSON API call. metadata Project metadata (data dictionary). May data.frame, response, character vector containing JSON API call. primary_table_name Name given list element primary output table. Ignored forms = ''. forms Indicate whether create separate tables repeating instruments forms.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCap_split.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split REDCap repeating instruments table into multiple tables — REDCap_split","text":"list \"data.frame\"s. number tables differ depending forms option selected. 'repeating': one base table one tables repeating instrument. '': data.frame instrument, regardless whether repeating instrument .","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCap_split.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Split REDCap repeating instruments table into multiple tables — REDCap_split","text":"Paul W. Egeler","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/REDCap_split.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split REDCap repeating instruments table into multiple tables — REDCap_split","text":"","code":"if (FALSE) { # \\dontrun{ # Using an API call ------------------------------------------------------- library(RCurl) # Get the records records <- postForm( uri = api_url, # Supply your site-specific URI token = api_token, # Supply your own API token content = \"record\", format = \"json\", returnFormat = \"json\" ) # Get the metadata metadata <- postForm( uri = api_url, # Supply your site-specific URI token = api_token, # Supply your own API token content = \"metadata\", format = \"json\" ) # Convert exported JSON strings into a list of data.frames REDCapCAST::REDCap_split(records, metadata) # Using a raw data export ------------------------------------------------- # Get the records records <- read.csv(\"/path/to/data/ExampleProject_DATA_2018-06-03_1700.csv\") # Get the metadata metadata <- read.csv( \"/path/to/data/ExampleProject_DataDictionary_2018-06-03.csv\" ) # Split the tables REDCapCAST::REDCap_split(records, metadata) # In conjunction with the R export script --------------------------------- # You must set the working directory first since the REDCap data export # script contains relative file references. old <- getwd() setwd(\"/path/to/data/\") # Run the data export script supplied by REDCap. # This will create a data.frame of your records called 'data' source(\"ExampleProject_R_2018-06-03_1700.r\") # Get the metadatan metadata <- read.csv(\"ExampleProject_DataDictionary_2018-06-03.csv\") # Split the tables REDCapCAST::REDCap_split(data, metadata) setwd(old) } # }"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/all_na.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if vector is all NA — all_na","title":"Check if vector is all NA — all_na","text":"Check vector NA","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/all_na.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if vector is all NA — all_na","text":"","code":"all_na(data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/all_na.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if vector is all NA — all_na","text":"data vector data.frame","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/all_na.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if vector is all NA — all_na","text":"logical","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/all_na.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check if vector is all NA — all_na","text":"","code":"rep(NA, 4) |> all_na() #> [1] TRUE"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/apply_factor_labels.html","id":null,"dir":"Reference","previous_headings":"","what":"Preserve all factor levels from REDCap data dictionary in data export — apply_factor_labels","title":"Preserve all factor levels from REDCap data dictionary in data export — apply_factor_labels","text":"Preserve factor levels REDCap data dictionary data export","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/apply_factor_labels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Preserve all factor levels from REDCap data dictionary in data export — apply_factor_labels","text":"","code":"apply_factor_labels(data, meta = NULL)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/apply_factor_labels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Preserve all factor levels from REDCap data dictionary in data export — apply_factor_labels","text":"data REDCap exported data set meta REDCap data dictionary","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/apply_factor_labels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Preserve all factor levels from REDCap data dictionary in data export — apply_factor_labels","text":"data.frame","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/apply_field_label.html","id":null,"dir":"Reference","previous_headings":"","what":"Apply REDCap filed labels to data frame — apply_field_label","title":"Apply REDCap filed labels to data frame — apply_field_label","text":"Apply REDCap filed labels data frame","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/apply_field_label.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Apply REDCap filed labels to data frame — apply_field_label","text":"","code":"apply_field_label(data, meta)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/apply_field_label.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Apply REDCap filed labels to data frame — apply_field_label","text":"data REDCap exported data set meta REDCap data dictionary","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/apply_field_label.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Apply REDCap filed labels to data frame — apply_field_label","text":"data.frame","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/as_factor.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert labelled vectors to factors while preserving attributes — as_factor","title":"Convert labelled vectors to factors while preserving attributes — as_factor","text":"extends as_factor well as_factor, appending original attributes except \"class\" converting factor avoid ta loss case rich formatted labelled data.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/as_factor.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert labelled vectors to factors while preserving attributes — as_factor","text":"","code":"as_factor(x, ...) # S3 method for class 'factor' as_factor(x, ...) # S3 method for class 'logical' as_factor(x, ...) # S3 method for class 'numeric' as_factor(x, ...) # S3 method for class 'character' as_factor(x, ...) # S3 method for class 'haven_labelled' as_factor( x, levels = c(\"default\", \"labels\", \"values\", \"both\"), ordered = FALSE, ... ) # S3 method for class 'labelled' as_factor( x, levels = c(\"default\", \"labels\", \"values\", \"both\"), ordered = FALSE, ... ) # S3 method for class 'data.frame' as_factor(x, ..., only_labelled = TRUE)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/as_factor.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert labelled vectors to factors while preserving attributes — as_factor","text":"x Object coerce factor. ... arguments passed method. levels create levels generated factor: * \"default\": uses labels available, otherwise values. Labels sorted value. * \"\": like \"default\", pastes together level value * \"label\": use labels; unlabelled values become `NA` * \"values\": use values ordered `TRUE` create ordered (ordinal) factor, `FALSE` (default) create regular (nominal) factor. only_labelled apply labelled columns?","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/as_factor.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Convert labelled vectors to factors while preserving attributes — as_factor","text":"Please refer parent functions extended documentation. avoid redundancy calls errors, functions copy-pasted Empty variables empty levels attribute interpreted logicals","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/as_factor.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert labelled vectors to factors while preserving attributes — as_factor","text":"","code":"# will preserve all attributes c(1, 4, 3, \"A\", 7, 8, 1) |> as_factor() #> [1] 1 4 3 A 7 8 1 #> Levels: 1 4 3 A 7 8 structure(c(1, 2, 3, 2, 10, 9), labels = c(Unknown = 9, Refused = 10) ) |> as_factor() |> dput() #> structure(c(1L, 2L, 3L, 2L, 5L, 4L), levels = c(\"1\", \"2\", \"3\", #> \"9\", \"10\"), class = \"factor\", labels = c(Unknown = 9, Refused = 10 #> )) structure(c(1, 2, 3, 2, 10, 9), labels = c(Unknown = 9, Refused = 10), class = \"haven_labelled\" ) |> as_factor() |> class() #> [1] \"factor\" structure(rep(NA,10), class = c(\"labelled\") ) |> as_factor() |> summary() #> FALSE TRUE NA's #> 0 0 10 rep(NA,10) |> as_factor() #> [1] #> Levels: FALSE TRUE"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/as_logical.html","id":null,"dir":"Reference","previous_headings":"","what":"Interpret specific binary values as logicals — as_logical","title":"Interpret specific binary values as logicals — as_logical","text":"Interpret specific binary values logicals","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/as_logical.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Interpret specific binary values as logicals — as_logical","text":"","code":"as_logical( x, values = list(c(\"TRUE\", \"FALSE\"), c(\"Yes\", \"No\"), c(1, 0), c(1, 2)), ... ) # S3 method for class 'data.frame' as_logical( x, values = list(c(\"TRUE\", \"FALSE\"), c(\"Yes\", \"No\"), c(1, 0), c(1, 2)), ... ) # Default S3 method as_logical( x, values = list(c(\"TRUE\", \"FALSE\"), c(\"Yes\", \"No\"), c(1, 0), c(1, 2)), ... )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/as_logical.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Interpret specific binary values as logicals — as_logical","text":"x vector data.frame values list values interpret logicals. First value ... ignored interpreted TRUE.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/as_logical.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Interpret specific binary values as logicals — as_logical","text":"vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/as_logical.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Interpret specific binary values as logicals — as_logical","text":"","code":"c(sample(c(\"TRUE\", \"FALSE\"), 20, TRUE), NA) |> as_logical() |> class() #> [1] \"logical\" ds <- dplyr::tibble( B = factor(sample(c(1, 2), 20, TRUE)), A = factor(sample(c(\"TRUE\", \"FALSE\"), 20, TRUE)), C = sample(c(3, 4), 20, TRUE), D = factor(sample(c(\"In\", \"Out\"), 20, TRUE)) ) ds |> as_logical() |> sapply(class) #> B A C D #> \"logical\" \"logical\" \"numeric\" \"factor\" ds$A |> class() #> [1] \"factor\" sample(c(\"TRUE\",NA), 20, TRUE) |> as_logical() #> [1] NA NA TRUE NA NA NA NA NA TRUE TRUE TRUE NA TRUE TRUE TRUE #> [16] TRUE NA TRUE TRUE TRUE as_logical(0) #> [1] FALSE"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/case_match_regex_list.html","id":null,"dir":"Reference","previous_headings":"","what":"List-base regex case_when — case_match_regex_list","title":"List-base regex case_when — case_match_regex_list","text":"Mimics case_when list regex patterns values. Used date/time validation generation name vector. Like case_when, matches order priority. Primarily used REDCapCAST data type coding systematic variable naming.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/case_match_regex_list.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List-base regex case_when — case_match_regex_list","text":"","code":"case_match_regex_list(data, match.list, .default = NA)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/case_match_regex_list.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"List-base regex case_when — case_match_regex_list","text":"data vector match.list list case matches .default Default value non-matches. Default NA.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/case_match_regex_list.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List-base regex case_when — case_match_regex_list","text":"vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/case_match_regex_list.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List-base regex case_when — case_match_regex_list","text":"","code":"case_match_regex_list( c(\"test_date\", \"test_time\", \"test_tida\", \"test_tid\"), list(date_dmy = \"_dat[eo]$\", time_hh_mm_ss = \"_ti[md]e?$\") ) #> [1] \"date_dmy\" \"time_hh_mm_ss\" NA \"time_hh_mm_ss\""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/cast_data_overview.html","id":null,"dir":"Reference","previous_headings":"","what":"Overview of REDCapCAST data for shiny — cast_data_overview","title":"Overview of REDCapCAST data for shiny — cast_data_overview","text":"Overview REDCapCAST data shiny","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/cast_data_overview.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Overview of REDCapCAST data for shiny — cast_data_overview","text":"","code":"cast_data_overview(data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/cast_data_overview.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Overview of REDCapCAST data for shiny — cast_data_overview","text":"data list class 'REDCapCAST'","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/cast_data_overview.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Overview of REDCapCAST data for shiny — cast_data_overview","text":"gt object","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/cast_meta_overview.html","id":null,"dir":"Reference","previous_headings":"","what":"Overview of REDCapCAST meta data for shiny — cast_meta_overview","title":"Overview of REDCapCAST meta data for shiny — cast_meta_overview","text":"Overview REDCapCAST meta data shiny","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/cast_meta_overview.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Overview of REDCapCAST meta data for shiny — cast_meta_overview","text":"","code":"cast_meta_overview(data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/cast_meta_overview.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Overview of REDCapCAST meta data for shiny — cast_meta_overview","text":"data list class 'REDCapCAST'","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/cast_meta_overview.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Overview of REDCapCAST meta data for shiny — cast_meta_overview","text":"gt object","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/char2choice.html","id":null,"dir":"Reference","previous_headings":"","what":"Simple function to generate REDCap choices from character vector — char2choice","title":"Simple function to generate REDCap choices from character vector — char2choice","text":"Simple function generate REDCap choices character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/char2choice.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simple function to generate REDCap choices from character vector — char2choice","text":"","code":"char2choice(data, char.split = \"/\", raw = NULL, .default = NA)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/char2choice.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simple function to generate REDCap choices from character vector — char2choice","text":"data vector char.split splitting character(s) raw specific values. Can used options length. .default default value missing. Default NA.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/char2choice.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Simple function to generate REDCap choices from character vector — char2choice","text":"vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/char2choice.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Simple function to generate REDCap choices from character vector — char2choice","text":"","code":"char2choice(c(\"yes/no\",\" yep. / nope \",\"\",NA,\"what\"),.default=NA) #> [1] \"1, yes | 2, no\" \"1, yep. | 2, nope\" NA #> [4] NA \"1, what\""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/char2cond.html","id":null,"dir":"Reference","previous_headings":"","what":"Simple function to generate REDCap branching logic from character vector — char2cond","title":"Simple function to generate REDCap branching logic from character vector — char2cond","text":"Simple function generate REDCap branching logic character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/char2cond.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Simple function to generate REDCap branching logic from character vector — char2cond","text":"","code":"char2cond( data, minor.split = \",\", major.split = \";\", major.sep = \" or \", .default = NA )"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/char2cond.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Simple function to generate REDCap branching logic from character vector — char2cond","text":"data vector minor.split minor split major.split major split major.sep argument separation. Default \" \". .default default value missing. Default NA.","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/char2cond.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Simple function to generate REDCap branching logic from character vector — char2cond","text":"vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/char2cond.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Simple function to generate REDCap branching logic from character vector — char2cond","text":"","code":"#data <- dd_inst$betingelse #c(\"Extubation_novent, 2; Pacu_delay, 1\") |> char2cond()"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/clean_field_label.html","id":null,"dir":"Reference","previous_headings":"","what":"Very simple function to remove rich text formatting from field label and save the first paragraph ('...<\/p>'). — clean_field_label","title":"Very simple function to remove rich text formatting from field label and save the first paragraph ('
...<\/p>'). — clean_field_label","text":"simple function remove rich text formatting field label save first paragraph ('
...<\/p>').","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/clean_field_label.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Very simple function to remove rich text formatting from field label and save the first paragraph ('
...<\/p>'). — clean_field_label","text":"","code":"clean_field_label(data)"},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/clean_field_label.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Very simple function to remove rich text formatting from field label and save the first paragraph ('
...<\/p>'). — clean_field_label","text":"data field label","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/clean_field_label.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Very simple function to remove rich text formatting from field label and save the first paragraph ('
...<\/p>'). — clean_field_label","text":"character vector","code":""},{"path":"https://agdamsbo.github.io/REDCapCAST/reference/clean_field_label.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Very simple function to remove rich text formatting from field label and save the first paragraph ('
...<\/p>'). — clean_field_label","text":"","code":"clean_field_label(\"