v3.5 issue #56 switch to "none" approach for incorp NA problem

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: ALFAM2
 Type: Package
 Title: Model on Ammonia Emission from Field-Applied Manure
-Version: 3.4
+Version: 3.5
 Date: 2023-06-07
 Authors@R: c(person("Sasha D.", "Hafner", role = c("aut", "cre"), email = "sasha.hafner@bce.au.dk"),
              person("Christoph", "Haeni", role = "aut"),

R/prepDat.R

@@ -40,6 +40,12 @@ prepDat <- function(dat, app.mthd.name = 'app.mthd', incorp.name = 'incorp', sou
   if (incorp.name %in% names(dat)) {
     dat[, incorp.name] <- tolower(dat[, incorp.name])
 
+    # Replace NA values with 'none'
+    if (any(is.na(dat[, incorp.name]))) {
+      warning(paste0('Some NA values in incorporation column ', incorp.name, '.\nReplacing all with "none".'))
+      dat[is.na(dat[, incorp.name]), incorp.name] <- 'none'
+    }
+
     # Convert incorporation values to standards
     for (i in 1:length(incorp.levels)) {
       dat[dat[, incorp.name] %in% incorp.levels[[i]], incorp.name] <- names(incorp.levels)[i] 

R/prepIncorp.R

@@ -9,10 +9,6 @@ prepIncorp <- function(dat, pars, time.name, time.incorp, incorp.names, warn) {
     # Do they exist?
     inc.ex <- intersect(inc.names, names(dat))
 
-    # Set NAs in incorporation time to Inf so they are skipped
-    # NTS: was this really not solved before now? Just noticed problem with v3.2!
-    dat[is.na(dat[, time.incorp]), time.incorp] <- Inf
-
     # Get times and types
     if(is.numeric(time.incorp)){
       # Unique groups
@@ -29,11 +25,6 @@ prepIncorp <- function(dat, pars, time.name, time.incorp, incorp.names, warn) {
     n.incorp.vals <- rowSums(dat[, inc.ex, drop = FALSE])
     n.incorp.vals.grp <- tapply(n.incorp.vals, dat$`__group`, "[", 1)
 
-    # Sort out missing values
-    # NTS: was this really not solved before now? Just noticed problem with v3.2!
-    n.incorp.vals <- na.omit(n.incorp.vals)
-    n.incorp.vals.grp[is.na(n.incorp.vals.grp)] <- 0  
-
     # If multiple incoporation dummy variables are 1 for any row, throw error
     if (any(n.incorp.vals > 1)) {
       stop('Multiple incorporation types specified in the same row.\nYou cannot do this!')