Working on #7. Appears to be a functioning patch

NEEDS UNIT TESTS!!!

R/R/REDCap_split.r

@@ -174,11 +174,24 @@ REDCap_split <- function(records, metadata) {
   subtables <- unique(records$redcap_repeat_instrument)
   subtables <- subtables[subtables != ""]
 
-  # Variables to be at the beginning of each repeating instrument
+  # Variables to be present in each output table
-  repeat_instrument_fields <- c(
+  universal_fields <- c(
-    vars_in_data[1:3],
+    vars_in_data[1],
-    grep("redcap_repeat_instrument\\.factor", vars_in_data, value = TRUE)
+    grep(
+      "^redcap_(?!(repeat)).*",
+      vars_in_data,
+      value = TRUE,
+      perl = TRUE
     )
+  )
+
+  # Variables to be at the beginning of each repeating instrument
+  repeat_instrument_fields <- grep(
+    "^redcap_repeat.*",
+    vars_in_data,
+    value = TRUE
+  )
+
 
   # Split the table based on instrument
   out <- split.data.frame(records, records$redcap_repeat_instrument)
@@ -188,12 +201,23 @@ REDCap_split <- function(records, metadata) {
 
     if (i == "") {
 
-      out_fields <- which(vars_in_data %in% fields[!fields[,2] %in% subtables, 1])
+      out_fields <- which(
+        vars_in_data %in% c(
+          universal_fields,
+          fields[!fields[,2] %in% subtables, 1]
+        )
+      )
       out[[which(names(out) == "")]] <- out[[which(names(out) == "")]][out_fields]
 
     } else {
 
-      out_fields <- which(vars_in_data %in% c(repeat_instrument_fields, fields[fields[,2] == i, 1]))
+      out_fields <- which(
+        vars_in_data %in% c(
+          universal_fields,
+          repeat_instrument_fields,
+          fields[fields[,2] == i, 1]
+        )
+      )
       out[[i]] <- out[[i]][out_fields]
 
     }

test-data/test_splitr/WARRIORtestForSoftwa_DATA_2018-06-21_1431.csv

@@ -0,0 +1,11 @@
+record_id,redcap_event_name,redcap_repeat_instrument,redcap_repeat_instance,redcap_data_access_group,redcap_survey_identifier,informed_consent_and_addendum_timestamp,icf_first_name,icf_last_name,icf_date,icf_sign,icf_consenter_name,icf_consentee_info,icf_consentee_sign,icf_consentee_date,informed_consent_and_addendum_complete,signed_consent_1,signed_consent_2,signed_consent_3,signed_addendum1,signed_addendum2,signed_addendum3,upload_of_signed_icfs_complete,demo_date,demo_name_first,demo_name_init,demo_name_last,demo_date_birth,demo_street_ad,demo_city_ad,demo_state_ad,demo_zip,demo_daytime,demo_email,demo_ethnic,demo_racial,demo_racial_oth,demo_military_mrn,demo_ssn,demographics_complete,elig_icf,elig_ischem,elig_signs___1,elig_signs___2,elig_signs___3,elig_signs___4,elig_card_cath,elig_card_cath_details,elig_cath_disease_severity,elig_cath_vessel,elig_ejection_fraction,elig_cath_ffr,elig_ccta,elig_card_cath_details_2,elig_cath_disease_severity_2,elig_ejection_fraction_2,elig_cta_score,elig_nocom_med,elig_ischemia_dilated,elig_doc_acs,elig_lvef,elig_nyha_class,elig_hos_hfref,elig_stroke,elig_carnial_hemo,elig_renal,elig_valvular,elig_life_expect,elig_enroll_clinic,elig_intol_ace,elig_intol_arb,elig_intol_statin,elig_intol_pcsk,elig_preg,elig_liver_dis,elig_hist_rhab,elig_high_dose,elig_study_yes,elig_date,elig_study_no,eligibility_complete
+806-1,baseline_arm_1,,,uf_test,,,,,,,,,,,,[document],,,[document],,,2,2018-05-08,Philip,B,Chase,1964-04-09,"5959 NW 13th Ave",Gainesville,FL,32605,"(352) 555-0760",bobsyouruncle@example.org,2,5,,2,111-22-3333,2,1,1,1,0,0,0,1,1,,,60,1,1,1,,60,24,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,,0,0,0,0,1,2018-05-08,,2
+806-1,followup_month_3_arm_1,,,uf_test,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+806-1,baseline_arm_1,informed_consent,1,uf_test,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+806-1,baseline_arm_1,informed_consent_and_addendum,1,uf_test,,"2018-05-08 21:15:12",Philip,Chase,2018-05-08,[document],"Philip B Chase",UF,[document],2018-05-08,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+806-1,baseline_arm_1,informed_consent_and_addendum,2,uf_test,,,Bobs,Youruncle,2018-06-21,[document],"Yo Mama","Anywhere she wants",[document],2018-06-21,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+806-1,baseline_arm_1,informed_consent_and_addendum,3,uf_test,,,Bobs,Youruncle,2018-06-21,[document],zsdf,DF,[document],2018-06-21,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+806-2,baseline_arm_1,,,uf_test,,,,,,,,,,,,[document],,,[document],,,2,2018-05-08,afadgs,afd,afdsgfd,1977-06-26,24325543,2352453,fwef,32601,"(352) 294-5299",,2,89,,,123-45-6789,2,1,1,0,1,0,0,0,,,,,,0,,,,,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,,0,0,0,0,1,2018-05-08,,2
+806-2,followup_month_3_arm_1,,,uf_test,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+806-2,baseline_arm_1,informed_consent,1,uf_test,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+806-2,baseline_arm_1,informed_consent_and_addendum,1,uf_test,,"2018-05-08 21:02:39",test,test,2018-05-08,[document],taryn,stoffs,[document],2018-05-08,2,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,

test-data/test_splitr/debug.r

@@ -0,0 +1,61 @@
+# Installing the latest REDCapRITS from GitHub ------------------------------
+#devtools::install_github("SpectrumHealthResearch/REDCapRITS/R@s3methods")
+devtools::install_github("SpectrumHealthResearch/REDCapRITS/R@longitudinal-data")
+
+# Debugging reading in longitudinal datasets ------------------------------
+
+# Reading in the files
+file_paths <- file.path(
+  "../test-data/test_splitr/",
+  c(
+    records = "WARRIORtestForSoftwa_DATA_2018-06-21_1431.csv",
+    metadata = "WARRIORtestForSoftwareUpgrades_DataDictionary_2018-06-21.csv"
+  )
+)
+
+redcap <- lapply(file_paths, read.csv, stringsAsFactors = FALSE)
+
+names(redcap) <- c("records", "metadata")
+str(redcap)
+
+# A bunch of blank rows
+redcap[["metadata"]] <- redcap[["metadata"]][as.logical(nchar(redcap[["metadata"]][,1])),]
+str(redcap, 1)
+
+setdiff(redcap[["metadata"]][,1], names(redcap[["records"]]))
+
+# Viewing the files
+View(redcap[["records"]])
+View(redcap[["metadata"]])
+
+
+# Playing with the names --------------------------------------------------
+
+vars_in_data <- names(redcap$records)
+
+universal_fields <- c(
+  vars_in_data[1],
+  grep("^redcap_(?!(repeat)).*", vars_in_data, value = TRUE, perl = TRUE)
+  )
+
+
+repeat_instrument_fields <- grep("^redcap_repeat.*", vars_in_data, value = TRUE)
+
+
+# Give it a shot ----------------------------------------------------------
+
+testCheck <- with(redcap, REDCap_split(records, metadata))
+
+lapply(testCheck, names)
+
+commonFields <- Reduce(intersect, lapply(testCheck, names))
+
+commonFields
+
+library(dplyr)
+
+lapply(testCheck, glimpse) %>% invisible
+
+testCheck[[1]] %>%
+  left_join(testCheck$informed_consent, by = commonFields) %>%
+  glimpse