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initial attempt at redcap calc fields/logic #410

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initial attempt at redcap calc fields/logic #410

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122 changes: 122 additions & 0 deletions R/calculationEnvironment.R
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Original file line number Diff line number Diff line change
@@ -0,0 +1,122 @@
#' @keywords internal

.redcapCalculationEnvironment <- function() {
mather <- function(f, na.rm = TRUE, ...) {
args <- list(...)
do.call(f, c(args, na.rm = na.rm))
}

numeric_functions <- list(
round = function(number, digits = 0) round(number, digits),
roundup = function(number, digits = 0) {
base <- 10^digits
ceiling(number * base) / base
},
rounddown = function(number, digits = 0) {
base <- 10^digits
floor(number * base) / base
},
sqrt = function(x) sqrt(x),
abs = function(x) abs(x),
exponential = function(...) mather(exp, na.rm = FALSE, ...),
min = function(...) mather(min, ...),
max = function(...) mather(max, ...),
mean = function(...) mather(mean, ...),
median = function(...) mather(median, ...),
mod = function(dividend, divisor) dividend %% divisor,
sum = function(...) mather(sum, ...),
stdev = function(...) mather(sd, ...),
log = function(number, base) log(number, base),
isnumber = function(x) !is.na(suppressWarnings(as.numeric(x))),
isinteger = function(x) grepl('^[0-9]$', x)
)

dater <- function(date) {
if(inherits(date, 'character')) {
date <- gsub('"|\'', '', date)
useDT <- FALSE
if(any(date %in% 'now')) {
now <- format(Sys.time(), '%Y-%m-%d %H:%M:%S')
date[date == 'now'] <- now
useDT <- TRUE
}
if(any(date %in% 'today')) {
today <- format(Sys.Date(), '%Y-%m-%d')
date[date == 'today'] <- today
}
if(useDT) {
date <- as.POSIXct(date)
} else {
date <- as.Date(date)
}
}
date
}

date_functions <- list(
year = function(date) format(dater(date), '%Y'),
month = function(date) format(dater(date), '%m'),
day = function(date) format(dater(date), '%d')
)

searcher <- function(haystack, needle) {
grepl(needle, haystack, ignore.case = TRUE)
}

text_functions <- list(
contains = function(h, n) searcher(h, n),
not_contain = function(h, n) !searcher(h, n),
starts_with = function(h, n) searcher(h, sprintf('^%s', n)),
ends_with = function(h, n) searcher(h, sprintf('%s$', n)),
left = function(x, n = 1) substr(x, 1, n),
right = function(x, n = 1) substr(x, nchar(x) - n + 1, nchar(x)),
length = function(x) nchar(x),
find = function(needle, haystack) {
m <- c(regexpr(needle, haystack, ignore.case = TRUE)[[1]])[1]
m[m == -1] <- 0
m
},
replace_text = function(h, s, r) gsub(s, r, h, fixed = TRUE),
mid = function(x, start = 1, n = 1) substr(x, start, start + n - 1),
concat = function(...) do.call(paste0, list(...)),
concat_ws = function(sep, ...) do.call(paste0, list(list(...), collapse = sep)),
upper = function(x) toupper(x),
lower = function(x) tolower(x),
trim = function(x) trimws(x)
)

misc_functions <- list(
doif = function(test, yes, no) {
ifelse(test, yes, no)
},
datediff = function(date1, date2, units = 'd', signed = FALSE) {
date1 <- dater(date1)
date2 <- dater(date2)
# "Date" objects will take on 'UTC' timezone by default
# force character conversion
if(inherits(date1, 'Date')) {
date1 <- as.POSIXct(format(date1, '%Y-%m-%d'))
}
if(inherits(date2, 'Date')) {
date2 <- as.POSIXct(format(date2, '%Y-%m-%d'))
}
dt <- as.numeric(difftime(date2, date1, units = 'secs'))
if(!signed) dt <- abs(dt)
den <- switch(units,
s = 1,
m = 60,
h = 3600,
d = 86400,
M = 2630016, # 86400*30.44
y = 31556952 # 86400*365.2425
)
dt / den
},
isblankormissing = function(value, missing_value_code = NULL) {
is.na(value) | is.null(value) | value %in% c('', missing_value_code)
}
)

redcap_functions <- c(numeric_functions, date_functions, text_functions, misc_functions)
list2env(redcap_functions)
}
33 changes: 28 additions & 5 deletions R/fieldCastingFunctions.R
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Original file line number Diff line number Diff line change
Expand Up @@ -547,14 +547,31 @@ mChoiceCast <- function(data,
###################################################################
# Derive field information ####
MetaData <- rcon$metadata()
field_names <- names(Raw)

field_names <- names(Raw)

field_bases <- sub(REGEX_CHECKBOX_FIELD_NAME, #defined in constants.R
"\\1", field_names, perl = TRUE)
field_text_types <- MetaData$text_validation_type_or_show_slider_number[match(field_bases, MetaData$field_name)]
field_map <- match(field_bases, MetaData$field_name)

field_text_types <- MetaData$text_validation_type_or_show_slider_number[field_map]

###################################################################
# Recalculate Values from "calc" fields ####
calc_data <- NULL
calc_fields <- MetaData[MetaData[,'field_type'] == 'calc',]
nr <- nrow(calc_fields)
if(nr > 0L) {
calc_data <- Raw[,'record_id', drop = FALSE]
raw_name <- field_names[match(calc_fields[,'field_name'], field_bases)]
calc_data[,paste0(raw_name, '_recalc')] <- NA
for(i in seq_len(nr)) {
expr_i <- calc_fields[i,'select_choices_or_calculations']
calc_i <- .redcapCalculation(expr_i, Raw)
calc_data[,i+1] <- calc_i
}
calc_data <- calc_data[, -1, drop = FALSE]
}

field_types <- .castRecords_getFieldTypes(rcon = rcon,
field_map = field_map,
field_bases = field_bases,
Expand Down Expand Up @@ -628,6 +645,12 @@ mChoiceCast <- function(data,
field_names = field_names,
field_types = field_types)

###################################################################
# Recalculated Values ####
if(!is.null(calc_data)) {
Records <- cbind(Records, calc_data)
}

###################################################################
# Return Results ####
Records
Expand Down
50 changes: 50 additions & 0 deletions R/redcapCalculations.R
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@@ -0,0 +1,50 @@
#' @keywords internal
.calculationToLanguage <- function(x) {
if(grepl('(^|\\b)if\\(', x, ignore.case = TRUE)) {
x <- gsub('(^|\\b)if\\(', 'doif(', x, ignore.case = TRUE)
x <- gsub('(?<![!=])=(?!=)', '==', x, perl = TRUE)
x <- gsub('<>', '!=', x)
}
y <- gregexpr('\\[[^[]+\\]', x)[[1]]
if(length(y) > 1 || y[[1]] != -1) {
ytxt <- mapply(substr, x, y + 1, y + attr(y, 'match.length') - 2, USE.NAMES = FALSE)
yseq <- mapply(seq, y, length.out = attr(y, 'match.length'), USE.NAMES = FALSE, SIMPLIFY = FALSE)
xseq <- setdiff(seq(nchar(x)), unlist(yseq))
xbrk <- cumsum(c(FALSE, diff(xseq) > 1))
xgrp <- split(strsplit(x, '')[[1]][xseq], xbrk)
xstr <- vapply(xgrp, paste, character(1), collapse = '', USE.NAMES = FALSE)
nn <- length(xstr) * 2 - 1
x1 <- character(nn)
x1[seq(1, nn, by = 2)] <- xstr
x1[seq(2, nn, by = 2)] <- ytxt
x2 <- paste(x1, collapse = '')
str2lang(x2)
} else {
str2lang(x)
}
}

#' @keywords internal
.calculationEval <- function(x, env, call_string) {
tryCatch(eval(x, envir = env), error = function(e) {
stop(sprintf('Error in %s: %s', call_string, e[[1]]))
})
}

#' @keywords internal
.redcapCalculation <- function(expr, dat = NULL) {
x <- .calculationToLanguage(expr)
xstr <- as.character(as.expression(x))
e <- new.env(parent = .redcapCalculationEnvironment())
if(!is.null(dat)) {
nr <- nrow(dat)
res <- lapply(seq_len(nr), function(i) {
list2env(dat[i,], envir = e)
.calculationEval(x, e, xstr)
})
res <- unlist(res)
} else {
res <- .calculationEval(x, e, xstr)
}
res
}
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