fixed paste

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: REDCapCAST
 Title: REDCap Castellated Data Handling
-Version: 24.3.1
+Version: 24.4.1
 Authors@R: c(
     person("Andreas Gammelgaard", "Damsbo", email = "agdamsbo@clin.au.dk", 
     role = c("aut", "cre"),comment = c(ORCID = "0000-0002-7559-1154")), 
@@ -51,7 +51,8 @@ Imports:
     stats,
     shiny,
     openxlsx2,
-    haven
+    haven,
+    readODS
 Collate: 
     'utils.r'
     'process_user_input.r'

NEWS.md

@@ -1,4 +1,8 @@
-# REDCapCAST 24.3.1 - in development
+# REDCapCAST 24.4.1 - in development
+
+### Functions
+
+* Fix: `read_redcap_tables()`: field names testing allows to include "[form_name]_complete" fields.
 
 ### Documentation and more
 

R/read_redcap_tables.R

@@ -35,7 +35,7 @@ read_redcap_tables <- function(uri,
     REDCapR::redcap_metadata_read(redcap_uri = uri, token = token)[["data"]]
 
   if (!is.null(fields)) {
-    fields_test <- fields %in% unique(m$field_name)
+    fields_test <- fields %in% c(m$field_name,paste0(unique(m$form_name),"_complete"))
 
     if (any(!fields_test)) {
       print(paste0("The following field names are invalid: ",

R/utils.r

@@ -506,6 +506,7 @@ is_repeated_longitudinal <- function(data, generics = c(
 #'
 #' @examples
 #' file_extension(list.files(here::here(""))[[2]])[[1]]
+#' file_extension(c("file.cd..ks","file"))
 file_extension <- function(filenames) {
   sub(pattern = "^(.*\\.|[^.]+)(?=[^.]*)", replacement = "",
       filenames,
@@ -533,8 +534,11 @@ read_input <- function(file, consider.na = c("NA", '""', "")) {
         df <- openxlsx2::read_xlsx(file = file, na.strings = consider.na)
       } else if (ext == "dta") {
         df <- haven::read_dta(file = file)
+      } else if (ext == "ods") {
+        df <- readODS::read_ods(file = file)
       } else {
-        stop("Input file format has to be either '.csv', '.xls' or '.xlsx'")
+        stop("Input file format has to be on of:
+             '.csv', '.xls', '.xlsx', '.dta' or '.ods'")
       }
     },
     error = function(e) {

app/rsconnect/shinyapps.io/agdamsbo/redcapcast.dcf

@@ -5,6 +5,6 @@ account: agdamsbo
 server: shinyapps.io
 hostUrl: https://api.shinyapps.io/v1
 appId: 11351429
-bundleId: 8311272
+bundleId:
 url: https://agdamsbo.shinyapps.io/redcapcast/
 version: 1

man/file_extension.Rd

@@ -17,4 +17,5 @@ Helper to import files correctly
 }
 \examples{
 file_extension(list.files(here::here(""))[[2]])[[1]]
+file_extension(c("file.cd..ks","file"))
 }

renv.lock

@@ -116,13 +116,14 @@
     },
     "bslib": {
       "Package": "bslib",
-      "Version": "0.6.1",
+      "Version": "0.7.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "base64enc",
         "cachem",
+        "fastmap",
         "grDevices",
         "htmltools",
         "jquerylib",
@@ -133,7 +134,7 @@
         "rlang",
         "sass"
       ],
-      "Hash": "c0d8599494bc7fb408cd206bbdd9cab0"
+      "Hash": "8644cc53f43828f19133548195d7e59e"
     },
     "cachem": {
       "Package": "cachem",
@@ -146,6 +147,18 @@
       ],
       "Hash": "c35768291560ce302c0a6589f92e837d"
     },
+    "cellranger": {
+      "Package": "cellranger",
+      "Version": "1.1.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "rematch",
+        "tibble"
+      ],
+      "Hash": "f61dbaec772ccd2e17705c1e872e9e7c"
+    },
     "checkmate": {
       "Package": "checkmate",
       "Version": "2.3.1",
@@ -252,17 +265,6 @@
       ],
       "Hash": "fedd9d00c2944ff00a0e2696ccf048ec"
     },
-    "ellipsis": {
-      "Package": "ellipsis",
-      "Version": "0.3.2",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "rlang"
-      ],
-      "Hash": "bb0eec2fe32e88d9e2836c2f73ea2077"
-    },
     "fansi": {
       "Package": "fansi",
       "Version": "1.0.6",
@@ -390,26 +392,25 @@
     },
     "htmltools": {
       "Package": "htmltools",
-      "Version": "0.5.7",
+      "Version": "0.5.8",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "base64enc",
         "digest",
-        "ellipsis",
         "fastmap",
         "grDevices",
         "rlang",
         "utils"
       ],
-      "Hash": "2d7b3857980e0e0d0a1fd6f11928ab0f"
+      "Hash": "149431ee39aba5bdc264112c8ff94444"
     },
     "httpuv": {
       "Package": "httpuv",
-      "Version": "1.6.14",
+      "Version": "1.6.15",
       "Source": "Repository",
-      "Repository": "RSPM",
+      "Repository": "CRAN",
       "Requirements": [
         "R",
         "R6",
@@ -418,7 +419,7 @@
         "promises",
         "utils"
       ],
-      "Hash": "16abeb167dbf511f8cc0552efaf05bab"
+      "Hash": "d55aa087c47a63ead0f6fc10f8fa1ee0"
     },
     "httr": {
       "Package": "httr",
@@ -542,7 +543,7 @@
     },
     "openxlsx2": {
       "Package": "openxlsx2",
-      "Version": "1.4",
+      "Version": "1.5",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -555,7 +556,7 @@
         "utils",
         "zip"
       ],
-      "Hash": "9fa7cdc5fbdb1c8511fdde72a944db63"
+      "Hash": "60138955e79b56bf75a99f2b04918d48"
     },
     "pillar": {
       "Package": "pillar",
@@ -649,6 +650,24 @@
       ],
       "Hash": "5e3c5dc0b071b21fa128676560dbe94d"
     },
+    "readODS": {
+      "Package": "readODS",
+      "Version": "2.2.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "cellranger",
+        "cpp11",
+        "readr",
+        "stringi",
+        "tibble",
+        "tools",
+        "vctrs",
+        "zip"
+      ],
+      "Hash": "79c0f23a27909659c1a2d62048c15096"
+    },
     "readr": {
       "Package": "readr",
       "Version": "2.1.5",
@@ -672,6 +691,13 @@
       ],
       "Hash": "9de96463d2117f6ac49980577939dfb3"
     },
+    "rematch": {
+      "Package": "rematch",
+      "Version": "2.0.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "cbff1b666c6fa6d21202f07e2318d4f1"
+    },
     "renv": {
       "Package": "renv",
       "Version": "1.0.5",
@@ -695,7 +721,7 @@
     },
     "sass": {
       "Package": "sass",
-      "Version": "0.4.8",
+      "Version": "0.4.9",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -705,11 +731,11 @@
         "rappdirs",
         "rlang"
       ],
-      "Hash": "168f9353c76d4c4b0a0bbf72e2c2d035"
+      "Hash": "d53dbfddf695303ea4ad66f86e99b95d"
     },
     "shiny": {
       "Package": "shiny",
-      "Version": "1.8.0",
+      "Version": "1.8.1.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -719,7 +745,6 @@
         "cachem",
         "commonmark",
         "crayon",
-        "ellipsis",
         "fastmap",
         "fontawesome",
         "glue",
@@ -739,7 +764,7 @@
         "withr",
         "xtable"
       ],
-      "Hash": "3a1f41807d648a908e3c7f0334bf85e6"
+      "Hash": "54b26646816af9960a4c64d8ceec75d6"
     },
     "sodium": {
       "Package": "sodium",