Fixes #113

DESCRIPTION

@@ -18,7 +18,7 @@ Description: Animal abundance estimation via conventional, multiple covariate
     fitting is performed via maximum likelihood. Also included are diagnostics
     and plotting for fitted detection functions. Abundance estimation is via a
     Horvitz-Thompson-like estimator.
-Version: 3.0.0.9001
+Version: 3.0.0.9004
 URL: https://github.com/DistanceDevelopment/mrds/
 BugReports: https://github.com/DistanceDevelopment/mrds/issues
 Depends:

NEWS.md

@@ -3,6 +3,8 @@
 Bug Fixes
 
 * Fixed formatting issue in flnl.grad help
+* Now displays a warning if the user tries to fit a detection function with covariates using MCDS.exe which is not either a half-normal or a hazard rate model. (Issue #113)
+* Fixed so that the MCDS.exe does not try to fit a negative exponential in place of a gamme key function. (Issue #113)
 
 # mrds 3.0.0
 

R/ddf.ds.R

@@ -224,6 +224,21 @@ ddf.ds <-function(dsmodel, mrmodel = NULL,
   if(control$optimizer == "MCDS" && system.file("MCDS.exe", package="mrds") == ""){
     stop("You have chosen to use the MCDS.exe optimizer but it cannot be found!", call. = FALSE)
   }
+
+  # Validate options are suitable for MCDS
+  if(control$optimizer %in% c("MCDS","both") && system.file("MCDS.exe", package="mrds") != ""){
+    MCDS.options.valid <- validate.MCDS.options(model)
+    # If NULL there are no issues
+    if(!is.null(MCDS.options.valid)){
+      R.opt.message <- ifelse(control$optimizer == "MCDS",
+                              "The R optimizer will be used instead.",
+                              "Only the R optimizer will be used.")
+      # Otherwise there are issues so use the R optimizer
+      warning(paste(MCDS.options.valid, R.opt.message, sep = " "),
+              immediate. = TRUE, call. = FALSE)
+      control$optimizer <- "R"
+    }
+  }
 
   # run MCDS.exe if it's there
   if(control$optimizer %in% c("MCDS","both") && system.file("MCDS.exe", package="mrds")!=""){

R/mcds_tools.R

@@ -254,7 +254,7 @@ create.command.file <- function(dsmodel=call(), data,
   }else if(mod.vals$key == "unif"){
     cat("UNIFORM", file=command.file.name, append=TRUE)
   }else{
-    cat("NEXPON", file=command.file.name, append=TRUE)
+    stop("Unrecognised key function for the detection function in MCDS.exe", call. = FALSE)
   }
 
   adj.pres <- FALSE
@@ -639,3 +639,29 @@ create.data.file <- function(data, dsmodel, data.file){
                  cluster = cluster)
   return(output)
 }
+
+
+validate.MCDS.options <- function(model){
+  # Validates the options are suitable for MCDS
+
+  # Extract values from the formula
+  mod_paste <- paste(model)
+  mod.vals <- try(eval(parse(text=mod_paste[2:length(mod_paste)])))
+
+  # Check if the user is trying to fit a gamma model
+  if(mod.vals$key == "gamma"){
+    return("MCDS.exe cannot fit a gamma detection function model.")
+  }
+
+  # Check if there are covariates
+  if(mod.vals$formula != ~1){
+    # if so only HN and HR permitted
+    if(!mod.vals$key %in% c("hn", "hr")){
+      return("MCDS.exe can only fit covariates with the half-normal and hazard rate key functions.")
+    }
+  }
+
+  # If no issue return NULL
+  return(NULL)
+}
+