#' Renames variables in the raw DMS extract to more manageable strings.
#'
#' This function renames the raw DMS extracts to be more consistent and
#' easier to type.
#'
#' This function is only meant to be used internally by \code{\link{clean_to1}}.
#'
#' @param originals The list of data frames generated interally by
#' \code{\link{clean_to1}}
# Rename variables to something actually useful
rename <- function(originals) {
# Keep the originals for comparison
cleaned <- originals
# For whatever reason, StudyID on master has a lower-case last d. Fix it.
names(cleaned$master)[names(cleaned$master) %in% "StudyId"] <- "StudyID"
################################################################################
# Clarify the various VisitDate variables
################################################################################
# I think a good approach is to preserve VisitDate for the event in the table
# so on followupfortb, VisitDate is the date of the follow-up; on skintest,
# it's the date of the TST, and so on. VisitDate.1 and its ilk should be
# renamed to "EnrollDate".
names(cleaned$skintest)[names(cleaned$skintest)
%in% "VisitDate"] <- "EnrollDate"
names(cleaned$qft)[names(cleaned$qft)
%in% "VisitDate"] <- "EnrollDate"
names(cleaned$tspot)[names(cleaned$tspot)
%in% "VisitDate"] <- "EnrollDate"
names(cleaned$ltbi)[names(cleaned$ltbi)
%in% "VisitDate"] <- "EnrollDate"
names(cleaned$ltbifollowup)[names(cleaned$ltbifollowup)
%in% "VisitDate.1"] <- "EnrollDate"
names(cleaned$followupfortb)[names(cleaned$followupfortb)
%in% "VisitDate.1"] <- "EnrollDate"
# One exception: I'm going to call it EnrollDate on master, too,
# since I use that so extensively. It'll get confusing as hell if I don't.
names(cleaned$master)[names(cleaned$master) %in% "VisitDate"] <- "EnrollDate"
################################################################################
# Rename TST variables
################################################################################
names(cleaned$skintest)[names(originals$skintest)
%in% "TstPlacedDateTime"] <- "dt_placed"
names(cleaned$skintest)[names(originals$skintest)
%in% "TstReadDateTime"] <- "dt_read"
names(cleaned$skintest)[names(originals$skintest)
%in% "TstResult"] <- "indur_mm"
names(cleaned$skintest)[names(originals$skintest)
%in% "TstInterpretation"] <- "result"
names(cleaned$skintest)[names(originals$skintest)
%in% "SubmitDateTime"] <- "date_submitted"
# Renaming check
data.frame(old = names(originals$skintest),
new = names(cleaned$skintest))
################################################################################
# Rename QFT variables
################################################################################
names(cleaned$qft)[names(originals$qft)
%in% "BloodDrawDateTime"] <- "dt_placed"
names(cleaned$qft)[names(originals$qft)
%in% "QftResult"] <- "result"
names(cleaned$qft)[names(originals$qft)
%in% "NilControl"] <- "nil"
names(cleaned$qft)[names(originals$qft)
%in% "TbAntigen"] <- "tb"
names(cleaned$qft)[names(originals$qft)
%in% "QFT_8_Mit"] <- "mito"
names(cleaned$qft)[names(originals$qft)
%in% "QFT_8_TBNil"] <- "tbnil"
names(cleaned$qft)[names(originals$qft)
%in% "QFT_8_MitNil"] <- "mitnil"
names(cleaned$qft)[names(originals$qft)
%in% "QftResult2"] <- "rerun_result"
names(cleaned$qft)[names(originals$qft)
%in% "NilControl2"] <- "rerun_nil"
names(cleaned$qft)[names(originals$qft)
%in% "TbAntigen2"] <- "rerun_tb"
names(cleaned$qft)[names(originals$qft)
%in% "Mitogen2"] <- "rerun_mito"
names(cleaned$qft)[names(originals$qft)
%in% "TbAntigenNil2"] <- "rerun_tbnil"
names(cleaned$qft)[names(originals$qft)
%in% "MitogenNil2"] <- "rerun_mitnil"
names(cleaned$qft)[names(originals$qft)
%in% "SubmitDateTime"] <- "date_submitted"
# Renaming check
data.frame(old = names(originals$qft),
new = names(cleaned$qft))
################################################################################
# Rename TSPOT variables
################################################################################
names(cleaned$tspot)[names(originals$tspot)
%in% "CollectDateTime"] <- "dt_placed"
names(cleaned$tspot)[names(originals$tspot)
%in% "TspotResult"] <- "result"
names(cleaned$tspot)[names(originals$tspot)
%in% "NilControl"] <- "nil"
names(cleaned$tspot)[names(originals$tspot)
%in% "PosControl"] <- "mito"
names(cleaned$tspot)[names(originals$tspot)
%in% "PanelA"] <- "panel_a"
names(cleaned$tspot)[names(originals$tspot)
%in% "PanelB"] <- "panel_b"
names(cleaned$tspot)[names(originals$tspot)
%in% "TSPOT_Report_Date"] <- "report_date"
names(cleaned$tspot)[names(originals$tspot)
%in% "SubmitDateTime"] <- "date_submitted"
################################################################################
# Rename TSPOT variables
################################################################################
# Mislabeled drug variables
names(cleaned$ltbi)[names(cleaned$ltbi) %in% "LT_4a_Freq"] <- "IsoniazidFreq"
names(cleaned$ltbi)[names(cleaned$ltbi) %in% "LT_4b_Freq_Other"] <-
"RifampinFreqSpecify"
# Renaming check
# data.frame(old = names(originals$tspot),
# new = names(cleaned$tspot))
cleaned
}
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