enable setting se arg to dht() to turn off calculation of uncertainty

(for bootdht) addresses #44

R/ds.R

@@ -95,6 +95,7 @@
 #' @param max.adjustments maximum number of adjustments to try (default 5) only
 #' used when `order=NULL`.
 #' @param er.method encounter rate variance calculation: default = 2 gives the method of Innes et al, using expected counts in the encounter rate. Setting to 1 gives observed counts (which matches Distance for Windows) and 0 uses binomial variance (only useful in the rare situation where study area = surveyed area). See [`dht.se`][mrds::dht.se] for more details.
+#' @param dht.se should uncertainty be calculated when using `dht`? Safe to leave as `TRUE`, used in `bootdht`.
 #' @return a list with elements:
 #'   * `ddf` a detection function model object.
 #'   * `dht` abundance/density information (if survey region data was supplied,
@@ -293,7 +294,7 @@ ds <- function(data, truncation=ifelse(is.null(cutpoints),
              region.table=NULL, sample.table=NULL, obs.table=NULL,
              convert.units=1, er.var=ifelse(transect=="line", "R2", "P3"),
              method="nlminb", quiet=FALSE, debug.level=0,
-             initial.values=NULL, max.adjustments=5, er.method=2){
+             initial.values=NULL, max.adjustments=5, er.method=2, dht.se=TRUE){
 
   # capture the call
   this_call <- match.call(expand.dots = FALSE)
@@ -707,7 +708,7 @@ ds <- function(data, truncation=ifelse(is.null(cutpoints),
           dht.res <- NULL
         }else{
           dht.res <- dht(model, region.table, sample.table,
-                         options=dht_options, se=TRUE)
+                         options=dht_options, se=dht.se)
         }
       }else{
         message("No obs.table supplied nor does data have Region.Label and Sample.Label columns, only estimating detection function.\n")
@@ -726,7 +727,7 @@ ds <- function(data, truncation=ifelse(is.null(cutpoints),
         dht.res <- NULL
       }else{
         dht.res <- dht(model, region.table, sample.table, obs.table,
-                       options=dht_options, se=TRUE)
+                       options=dht_options, se=dht.se)
       }
     }
   }else{