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fieldToVar.R
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fieldToVar.R
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#' @name fieldToVar
#'
#' @title Convert a REDCap Data Field to an R Vector
#' @description Converts a field exported from REDCap into a valid R vector
#'
#' @param records A data frame of records returned by `exportRecords`
#' or `exportReports`
#' @param meta_data A data frame giving the data dictionary, as returned
#' by `exportMetaData`
#' @param factors Logical, determines if checkbox, radio button, dropdown and yesno
#' variables are converted to factors
#' @param dates Logical, determines if date variables are converted to POSIXct format
#' @param checkboxLabels Logical, determines if checkbox variables are labeled as
#' "Checked" or using the checkbox label. Only applicable when `factors = TRUE`
#' @param labels Logical. Determines if the variable labels are applied to
#' the data frame.
#' @param handlers List, Specify type conversion overrides for specific REDCap field types.
#' E.g., `handlers=list(date_ = as.Date)`. For datetime specifications the
#' datetime ordering directive from the tail is dropped. The following field
#' types are supported: date_, datetime_, datetime_seconds_, time_mm_ss, time,
#' float, number, calc, int, integer, select, radio, dropdown, yesno, truefalse,
#' checkbox, and form_complete.
#' @param mChoice logical; defaults to TRUE. Convert checkboxes to mChoice if
#' Hmisc is installed.
#' @param ..., additional arguments that are ignored.
#'
#' @details This function is called internally by `exportRecords` and
#' `exportReports`. it is not available to the user.
#'
fieldToVar <- function(records,
meta_data,
factors = TRUE,
dates = TRUE,
checkboxLabels = FALSE,
labels = TRUE,
handlers =list(),
mChoice = NULL,
...)
{
records_raw <- records
# See if mChoice argument is passed, otherwise default to state of Hmisc
if("package:Hmisc" %in% search()) # Hmisc Loaded?
{
if(is.null(mChoice)) mChoice <- TRUE
# Otherwise do what user requests for mChoice
} else # Hmisc not loaded
{
if(is.null(mChoice))
{
mChoice <- FALSE
} else if(mChoice)
{
warning("mChoice=TRUE requires the package Hmisc to be loaded to function properly.")
mChoice <- FALSE
}
}
recordnames <- names(records)
for (i in seq_along(records))
{
# Establish basic info about field/record
field_name <- recordnames[i]
field_base <- sub(REGEX_CHECKBOX_FIELD_NAME, #defined in constants.R
"\\1", field_name, perl = TRUE)
field_text_type <- meta_data$text_validation_type_or_show_slider_number[meta_data$field_name == field_base]
field_type <- meta_data$field_type[meta_data$field_name == field_base]
withCallingHandlers(
warning=function(w) {w$message<-paste(field_name,":", w$message);
warning(w);
invokeRestart("muffleWarning")},
{
#* If the variable is not in the data dictionary (usually it's a field added by REDCap,
#* such as redcap_event_name, instrument_complete, etc), give it a generic name to
#* pass to switch.
if (!length(field_type))
{
if (grepl("_complete$", field_base))
{
field_type <- "form_complete"
}
else
{
field_type <- "unrecognized field type"
}
}
# autocomplete was added to the text_validation... column for
# dropdown menus with the autocomplete feature.
# field_type[is.na(field_type)] <-
# meta_data$field_type[meta_data$field_name == field_base]
field_type[field_type == "text" &
!is.na(field_text_type)] <- field_text_type
field_type <- gsub(pattern = "_(dmy|mdy|ymd)$",
replacement = "_",
x = field_type)
records[[i]] <-
if(field_type %in% names(handlers))
{
handlers[[field_type]](records[[i]])
} else {
switch(field_type,
"date_" =
{
if (dates)
as.POSIXct(records[[i]], format = "%Y-%m-%d")
else
records[[i]]
},
"datetime_" =
{
if (dates)
as.POSIXct(records[[i]], format = "%Y-%m-%d %H:%M")
else
records[[i]]
},
"datetime_seconds_" =
{
if (dates)
as.POSIXct(records[[i]], format = "%Y-%m-%d %H:%M:%S")
else
records[[i]]
},
"time_mm_ss" =
{
if (dates)
chron::times(ifelse(!is.na(records[[i]]),
paste0("00:", records[[i]]),
records[[i]]),
format=c(times="h:m:s"))
else
records[[i]]
},
"time_hh_mm_ss" =
{
if (dates)
chron::times(records[[i]],
format=c(times="h:m:s"))
else
records[[i]]
},
"time" =
{
if (dates)
chron::times(gsub("(^\\d{2}:\\d{2}$)", "\\1:00", records[[i]]),
format=c(times="h:m:s"))
else
records[[i]]
},
"float" = as.numeric(records[[i]]),
"number" = as.numeric(records[[i]]),
"calc" = as.numeric(records[[i]]),
"int" = as.integer(records[[i]]),
"integer"= as.numeric(records[[i]]),
"select" =
makeRedcapFactor(x = records[[i]],
coding = meta_data$select_choices_or_calculations[meta_data$field_name == field_base],
factors = factors,
var_name = meta_data$field_name[meta_data$field_name == field_base]),
"radio" =
makeRedcapFactor(x = records[[i]],
coding = meta_data$select_choices_or_calculations[meta_data$field_name == field_base],
factors = factors,
var_name = meta_data$field_name[meta_data$field_name == field_base]),
"dropdown" =
makeRedcapFactor(x = records[[i]],
coding = meta_data$select_choices_or_calculations[meta_data$field_name == field_base],
factors = factors,
var_name = meta_data$field_name),
"yesno" = makeRedcapYN(records[[i]],
factors),
"truefalse" =
{
if (factors)
as.logical(records[[i]])
else
records[[i]]
},
"checkbox" =
{
makeRedcapCheckbox(x = records[[i]],
suffix = gsub("^.+___", "", names(records)[i]),
coding = meta_data$select_choices_or_calculations[meta_data$field_name == field_base],
factors = factors,
checkboxLabels = checkboxLabels)
},
"form_complete" =
{
makeRedcapFactor(x = records[[i]],
coding = "0, Incomplete | 1, Unverified | 2, Complete",
factors,
var_name = meta_data$field_name[meta_data$field_name == field_base])
},
records[[i]]
) # End switch
} # End of Records[[i]] if
}) # End of withCallingHandlers
} # End for loop
if(mChoice)
{
# Convert checkboxes to mChoice if Hmisc is installed and requested
checkbox_meta <- meta_data[which(meta_data$field_type == 'checkbox'),]
for(i in seq_len(nrow(checkbox_meta)))
{
checkbox_fieldname <- checkbox_meta$field_name[i]
fields <- recordnames[grepl(sprintf("^%s", checkbox_fieldname), recordnames)]
if(length(fields) > 0)
{
opts <- fieldChoiceMapping(checkbox_meta[i,'select_choices_or_calculations'],
fields[i])
levels <- opts[, 1 + labels]
opts <- as.data.frame(matrix(rep(seq_along(fields), nrow(records)), nrow=nrow(records), byrow=TRUE))
checked <- records_raw[,fields] != '1'
opts[which(checked,arr.ind=TRUE)] <- ""
z <- structure(
gsub(";$|^;", "",gsub(";{2,}",";", do.call('paste', c(opts, sep=";")))),
label = checkbox_fieldname,
levels = levels,
class = c("mChoice", "labelled"))
records[[checkbox_fieldname]] <- z
}
}
} # mChoice
records
}