From ced5f70764de7263a0de857ede64b4749d22a3e0 Mon Sep 17 00:00:00 2001
From: fawda123 <mbafs2012@gmail.com>
Date: Sun, 28 Jan 2024 14:11:59 -0500
Subject: [PATCH] added check in checkMWRresults if non-numeric in Quantitation
 Limit, excludes NA

---
 R/checkMWRresults.R                   | 12 ++++++++++++
 man/checkMWRresults.Rd                |  1 +
 tests/testthat/test-checkMWRresults.R |  8 ++++++++
 vignettes/inputs.Rmd                  |  1 +
 4 files changed, 22 insertions(+)

diff --git a/R/checkMWRresults.R b/R/checkMWRresults.R
index e0482566..2a4249e6 100644
--- a/R/checkMWRresults.R
+++ b/R/checkMWRresults.R
@@ -18,6 +18,7 @@
 #'  \item Activity Depth/Height Measure out of range: All depth values should be less than or equal to 1 meter / 3.3 feet or entered as Surface in the Activity Relative Depth Name column (warning only)
 #'  \item Characteristic Name: Should match parameter names in the \code{Simple Parameter} or \code{WQX Parameter} columns of the \code{\link{paramsMWR}} data (warning only)
 #'  \item Result Value: Should be a numeric value or a text value as AQL or BDL
+#'  \item Non-numeric Quantitation Limit: All values should be numbers, excluding missing values
 #'  \item QC Reference Value: Should be a numeric value or a text value as AQL or BDL
 #'  \item Result Unit: No missing entries in \code{Result Unit}, except pH which can be blank
 #'  \item Single Result Unit: Each unique parameter in \code{Characteristic Name} should have only one entry in \code{Result Unit} (excludes entries for lab spikes reported as \code{\%} or \code{\% recovery})
@@ -197,6 +198,17 @@ checkMWRresults <- function(resdat, warn = TRUE){
     stop(msg, '\n\tIncorrect entries in Result Value found: ', paste(tochk, collapse = ', '), ' in rows ', paste(rws, collapse = ', '), call. = FALSE)
   }
   message(paste(msg, 'OK'))
+
+  # check Quantitation Limit for non-numeric (allows NA/missing)
+  msg <- '\tChecking for non-numeric values in Quantitation Limit...'
+  typ <- resdat$`Quantitation Limit`
+  chk <- !is.na(suppressWarnings(as.numeric(typ))) | is.na(typ)
+  if(any(!chk)){
+    rws <- which(!chk)
+    tochk <- unique(typ[!chk])
+    stop(msg, '\n\tNon-numeric entries in Quantitation Limit found: ', paste(tochk, collapse = ', '), ' in rows ', paste(rws, collapse = ', '), call. = FALSE)
+  }
+  message(paste(msg, 'OK'))
   
   # check QC Reference Values 
   msg <- '\tChecking QC Reference Values...'
diff --git a/man/checkMWRresults.Rd b/man/checkMWRresults.Rd
index 187a7ea4..e45c0e93 100644
--- a/man/checkMWRresults.Rd
+++ b/man/checkMWRresults.Rd
@@ -33,6 +33,7 @@ The following checks are made:
 \item Activity Depth/Height Measure out of range: All depth values should be less than or equal to 1 meter / 3.3 feet or entered as Surface in the Activity Relative Depth Name column (warning only)
 \item Characteristic Name: Should match parameter names in the \code{Simple Parameter} or \code{WQX Parameter} columns of the \code{\link{paramsMWR}} data (warning only)
 \item Result Value: Should be a numeric value or a text value as AQL or BDL
+\item Non-numeric Quantitation Limit: All values should be numbers, excluding missing values
 \item QC Reference Value: Should be a numeric value or a text value as AQL or BDL
 \item Result Unit: No missing entries in \code{Result Unit}, except pH which can be blank
 \item Single Result Unit: Each unique parameter in \code{Characteristic Name} should have only one entry in \code{Result Unit} (excludes entries for lab spikes reported as \code{\%} or \code{\% recovery})
diff --git a/tests/testthat/test-checkMWRresults.R b/tests/testthat/test-checkMWRresults.R
index 02496545..c4558f73 100644
--- a/tests/testthat/test-checkMWRresults.R
+++ b/tests/testthat/test-checkMWRresults.R
@@ -73,6 +73,14 @@ test_that("Checking correct Characteristic Names", {
 })
 
 test_that("Checking entries in Result Value", {
+  chk <- resdatchk
+  chk[23, 11] <- '<1'
+  chk[200, 11] <- 'a'
+  chk[250, 11] <- NA # does not trigger
+  expect_error(checkMWRresults(chk), 'Non-numeric entries in Quantitation Limit found: <1, a in rows 23, 200') 
+})
+
+test_that("Checking entries in Quantitation Limit", {
   chk <- resdatchk
   chk[23, 9] <- '1.a09'
   chk[200, 9] <- 'MDL'
diff --git a/vignettes/inputs.Rmd b/vignettes/inputs.Rmd
index b250b1e0..badfbb0a 100644
--- a/vignettes/inputs.Rmd
+++ b/vignettes/inputs.Rmd
@@ -108,6 +108,7 @@ Several checks are run automatically when the data are imported. These file chec
 -   **Activity Depth/Height Measure out of range**: All depth values should be less than or equal to 1 meter / 3.3 feet or entered as Surface in the Activity Relative Depth Name column (warning only)
 -   **Characteristic Name**: Should match parameter names in the `Simple Parameter` or `WQX Parameter` column of the `paramsMWR` data (warning only)
 -   **Result Value**: Should be a numeric value or a text value as AQL or BDL
+-   **Non-numeric Quantitation Limit**: All values should be numbers, excluding missing values
 -   **QC Reference Value**: Any entered values should be numeric or a text value as AQL or BDL
 -   **Result Unit**: No missing entries in `Result Unit`, except pH which can be blank
 -   **Single Result Unit**: Each unique parameter in `Characteristic Name` should have only one entry in `Result Unit` (excludes entries for lab spikes reported as `%` or `% recovery`)