diff --git a/R/graphics_functions.R b/R/graphics_functions.R
index 90b2f08..9db444f 100644
--- a/R/graphics_functions.R
+++ b/R/graphics_functions.R
@@ -850,7 +850,7 @@ plot.setup <- function(newPage) {
label.units <- function(
units = c("ug/kg", "mg/kg", "ng/ml", "pmol/min/mg protein", "ug/ml", "ug/l",
"nmol/min/mg protein", "ng/min/mg protein", "stg", "j/h/g", "mins",
- "d", "%", "nr/1000 cells", "TEQ ug/kg", "ng/l"),
+ "d", "%", "nr/1000 cells", "ng/l"),
basis, html = FALSE, compartment, extra.text = NA) {
units <- match.arg(units)
@@ -873,7 +873,6 @@ label.units <- function(
"ug/ml" = "μg ml-1",
"ug/l" = "μg l-1",
"ng/l" = "ng l-1",
- "TEQ ug/kg" = "TEQ μg kg-1",
"stg" = "stage",
"j/h/g" = "J h -1 g -1",
"pmol/min/mg protein" = "pmol min -1 mg protein -1",
@@ -892,7 +891,6 @@ label.units <- function(
"ug/ml" = 'paste(mu, "g") ~ "ml"^-1',
"ug/l" = 'paste(mu, "g") ~ "l"^-1',
"ng/l" = '"ng l"^-1',
- "TEQ ug/kg" = 'paste("TEQ", mu, "g") ~ "kg"^-1',
"stg" = '"stage"',
"j/h/g" = '"J h"^-1 ~ "g"^-1',
"pmol/min/mg protein" = '"pmol min"^-1 ~ "mg protein"^-1',
diff --git a/R/import_check_functions.R b/R/import_check_functions.R
index 7977148..f428db5 100644
--- a/R/import_check_functions.R
+++ b/R/import_check_functions.R
@@ -516,38 +516,13 @@ ctsm.check.unit.biota <- function(data, info) {
"g/g", "mg/mg", "ug/ug", "ng/ng", "pg/pg", "mg/g", "ug/g", "ng/g", "pg/g",
"g/kg", "mg/kg", "ug/kg", "ng/kg", "pg/kg")
- id <- ctsm_is_contaminant(data$pargroup, exclude = "I-RNC") & data$determinand != "TEQDFP"
+ id <- ctsm_is_contaminant(data$pargroup, exclude = "I-RNC")
if (any(id))
data[id,] <- within(data[id,], {
ok <- unit %in% standard_unit
action <- ifelse(ok, "none", "error")
})
- id <- data$determinand %in% "TEQDFP"
- if (any(id)) {
-
- TEQ_unit <- paste("TEQ", standard_unit)
-
- data[id,] <- within(data[id,], {
- ok <- unit %in% c(standard_unit, TEQ_unit)
- action <- ifelse(ok, "none", "error")
-
- if (any(TEQ_unit %in% unit)) {
- lifecycle::deprecate_warn(
- "1.0.2",
- I("use of units of the form 'TEQ ug/kg' or 'TEQ pg/g'"),
- details = c(
- i = "use e.g. 'ug/kg' instead of 'TEQ ug/kg'",
- i = "you might need to update the determinand reference table"
- ),
- env = rlang::caller_env(),
- user_env = rlang::caller_env(2)
- )
- }
-
- })
- }
-
id <- data$determinand %in% c("LNMEA")
if (any(id))
data[id,] <- within(data[id,], {
diff --git a/R/import_functions.R b/R/import_functions.R
index ea5915a..f86ef67 100644
--- a/R/import_functions.R
+++ b/R/import_functions.R
@@ -3631,145 +3631,6 @@ determinand.link.sum <- function(data, info, keep, drop, weights = NULL) {
-determinand.link.TEQDFP <- function(data, info, keep, drop, weights) {
-
- lifecycle::deprecate_warn(
- "1.0.2",
- "determinand.link.TEQDFP()",
- details = c(
- i = paste(
- "use `determinand.link.sum()` with the TEFs supplied in the weights",
- "argument"
- ),
- i = 'see `vignette("example_HELCOM")` for further details'
- ),
- env = rlang::caller_env(),
- user_env = rlang::caller_env(2)
- )
-
- stopifnot(length(keep) == 1, length(drop) > 1)
-
- if (!any(data$determinand %in% drop))
- return(data)
-
-
- # identify samples with drop and not keep, which are the ones that will be summed
- # if keep already exists, then don't need to do anything
- # don't delete drop data because might want to assess them individually
-
- ID <- with(data, paste(sample, matrix))
-
- dropID <- data$determinand %in% drop
- keepID <- data$determinand %in% keep
-
- sum_ID <- ID %in% setdiff(ID[dropID], ID[keepID])
-
- if (sum(sum_ID) == 0)
- return(data)
-
- dropTxt <- paste(drop, collapse = ", ")
- cat(" Data submitted as", dropTxt, "summed to give", keep, fill = TRUE)
-
-
- # get relevant sample matrix combinations
-
- data <- split(data, with(data, determinand %in% drop))
-
- ID <- with(data[["TRUE"]], paste(sample, matrix))
-
- summed_data <- by(data[["TRUE"]], ID, function(x) {
-
- # check all bases are the same
-
- if (!all(drop %in% x$determinand)) return(NULL)
-
- stopifnot(dplyr::n_distinct(x$basis) == 1)
-
-
- # convert to ug/kg and then to TEQ
-
- id <- c("value", "uncertainty", "limit_detection", "limit_quantification")
-
- x[id] <- lapply(x[id], convert_units, from = x$unit, to = "ug/kg")
-
- TEQ <- weights[as.character(x$determinand)]
-
- x[id] <- lapply(x[id], "*", TEQ)
-
-
- # make output row have all the information from the largest determinand (ad-hoc)
-
- # ensures a sensible qaID, method_analysis, etc.
-
-
- out <- x[which.max(x$value), ]
-
- out$determinand <- keep
-
- target_unit <- ctsm_get_info(info$determinand, keep, "unit", info$compartment, sep="_")
- if (grepl("TEQ", target_unit)) {
- out$unit <- "TEQ ug/kg"
- } else {
- out$unit <- "ug/kg"
- }
- out$group <- "Dioxins"
- out$pargroup <- "OC-DX"
-
- # sum value and limit_detection, make it a less-than if all are less-thans, and take
- # proportional uncertainty from maximum value (for which uncertainty is reported)
- # if no uncertainties reported at all, then have provided value of CB126 in info.unertainty
- # with sdConstant multiplied by 0.1 to reflect TEQ effect on detection limit
-
- out$value <- sum(x$value)
- out$limit_detection <- sum(x$limit_detection)
- out$limit_quantification <- sum(x$limit_quantification)
-
- if ("" %in% x$censoring)
- out$censoring <- ""
- else if (dplyr::n_distinct(x$censoring) == 1)
- out$censoring <- unique(x$censoring)
- else
- out$censoring <- "<"
- out$censoring <- if(all(x$censoring %in% "<")) "<" else ""
-
- if (all(is.na(x$uncertainty)))
- out$uncertainty <- NA
- else {
- wk <- x[!is.na(x$uncertainty), ]
- pos <- which.max(wk$value)
- upct <- with(wk, uncertainty / value)[pos]
- out$uncertainty <- out$value * upct
- }
-
- out
-
- })
-
- summed_data <- do.call(rbind, summed_data)
-
-
- # see how many samples have been lost due to incomplete submissions
-
- nTotal <- length(unique(ID))
- nSummed <- if (is.null(summed_data)) 0 else nrow(summed_data)
- nLost <- nTotal - nSummed
-
- if (nLost > 0)
- message(" ", nLost, " of ", nTotal, " samples lost due to incomplete submissions")
-
-
- # combine data for both drop and keep and then add back into main data set
-
- data[["TRUE"]] <- rbind(data[["TRUE"]], summed_data)
-
- data <- do.call(rbind, data)
-
- data
-}
-
-
-
-
check_censoring <- function(data, info, print_code_warnings) {
# silence non-standard evaluation warnings
diff --git a/R/information_functions.R b/R/information_functions.R
index d8eada7..5ce6449 100644
--- a/R/information_functions.R
+++ b/R/information_functions.R
@@ -647,27 +647,6 @@ ctsm_read_determinand <- function(
})
- # warn about deprecated TEQ units
-
- not_ok <- sapply(compartment, function(id) {
- unit_id <- paste0(id, "_unit")
- any(grepl("^TEQ ", data[[unit_id]]))
- })
-
- if (any(not_ok)) {
- lifecycle::deprecate_warn(
- "1.0.2",
- I("use of units such as 'TEQ ug/kg' and 'TEQ pg/g'"),
- details = c(
- i = "use e.g. 'ug/kg' instead of 'TEQ ug/kg'",
- i = "you might need to update the determinand reference table"
- ),
- env = rlang::caller_env(2),
- user_env = rlang::caller_env(3)
- )
- }
-
-
# tidy up for output
data <- tibble::column_to_rownames(data, "determinand")