Merge pull request #90 from fishR-Core-Team/88-alkindivage-fails-ungr…

…acefully-if-na-in-length-variable-of-length-sample

Added check for NA with error message in alkIndivAge(). This closes #88

NEWS.md

@@ -2,6 +2,7 @@
 * Updated sticker.
 * Updated `pkgdown.yaml` GitHub action to [v2](https://github.com/r-lib/actions/tree/v2-branch/examples#build-pkgdown-site). Changed action to only run on a release (rather than a push) but it can be [run manually](https://docs.github.com/en/actions/managing-workflow-runs/manually-running-a-workflow) as well.
 * Updated `R-CMD-check.yaml` GitHub action to [v2](https://github.com/r-lib/actions/tree/v2-branch/examples#standard-ci-workflow). Note that I had to add the [extra code for dealing with graphics on the Mac version](https://github.com/r-lib/actions#common-questions).
+* `alkIndivAge()`: Modified. Added a catch for `NA`s in the length sample. Also added a test. This addresses [#88](https://github.com/fishR-Core-Team/FSA/issues/88)).
 
 # FSA 0.9.3 15-Feb-21
 * Moved `dplyr` from `imports` to `suggests` (needed because functions were removed in last version; however it is still used in some examples; partially addresses [#87](https://github.com/fishR-Core-Team/FSA/issues/87)).

R/ageComparisons.R

@@ -1,6 +1,6 @@
 #' @title Compute measures of precision among sets of ages.
 #'
-#' @description Computes overall measures of precision for multiple age estimates made on the same individuals. Ages may be from two or more readers of the same structure, one reader at two or more times, or two or more structures (e.g., scales, spines, otoliths). Measures of precision include ACV (Average Coefficient of Variation), APE (Average Percent Error), AAD (Average Absolute Deviation), and ASD (Average Standard Devation), and various percentage difference values.
+#' @description Computes overall measures of precision for multiple age estimates made on the same individuals. Ages may be from two or more readers of the same structure, one reader at two or more times, or two or more structures (e.g., scales, spines, otoliths). Measures of precision include ACV (Average Coefficient of Variation), APE (Average Percent Error), AAD (Average Absolute Deviation), and ASD (Average Standard Deviation), and various percentage difference values.
 #'
 #' @param formula A formula of the form \code{~var1+var2+var3+...} or, alternatively, \code{var1~var2+var3+...}, where the \code{varX} generically represent the variables that contain the age estimates. The alternative formula allows for similar code as used in \code{\link{ageBias}} and can have only one variable on the left-hand side.
 #' @param data A data.frame that minimally contains the variables in \code{formula}.

R/alkIndivAge.R

@@ -108,7 +108,7 @@ alkIndivAge <- function(key,formula,data,type=c("SR","CR"),
   # handle differently depending on how many variables were in the formula
   if (tmp$vnum==1) {
     if (!tmp$vclass %in% c("numeric","integer"))
-      STOP("RHS ariable must be numeric.")
+      STOP("RHS variable must be numeric.")
     ca <- "age"
     cl <- tmp$vname
   } else if (tmp$vnum==2) {
@@ -121,6 +121,9 @@ alkIndivAge <- function(key,formula,data,type=c("SR","CR"),
     cl <- tmp$Enames
     ca <- tmp$Rname
   } else STOP("'formula' must have only one variable on LHS and RHS.")
+  #Check for NA's
+  if (any(is.na(data[,cl]))) 
+    STOP("Length variable contains 'NA's;\n  Please remove these fish from the length sample before using 'alkIndivAge()'.")
   ## Set the random seed if asked to do so
   if (!is.null(seed)) set.seed(seed)
   ## Begin process

tests/testthat/testthat_AgeLengthKey.R

@@ -98,6 +98,10 @@ test_that("alkIndivAge() messages",{
                  "will be treated as all-inclusive")
   expect_error(alkIndivAge(WR1.key[-c(1:5),],age~len,data=WR1.len),
                "minimum observed length in the length")
+  ## Length sample has some NAs
+  WR1.len.problem <- rbind(WR1.len,c(ID=999,len=NA,age=NA,LCat=NA))
+  expect_error(alkIndivAge(WR1.key,age~len,data=WR1.len.problem),
+               "Length variable contains 'NA's")
 })
 
 test_that("alkMeanVar() errors and warnings",{