exported plotting functionality

pkg/DESCRIPTION

@@ -13,5 +13,8 @@ URL: https://github.com/markvanderloo/rtrim
 BugReports: https://github.com/markvanderloo/rtrim/issues
 Date: 2015-06-12
 Suggests:
-    testthat
+    testthat,
+    knitr,
+    rmarkdown
 RoxygenNote: 5.0.1
+VignetteBuilder: knitr

pkg/NAMESPACE

@@ -2,6 +2,7 @@
 
 S3method(coef,trim)
 S3method(gof,trim)
+S3method(plot,trim.overall)
 S3method(print,trim.coef)
 S3method(print,trim.gof)
 S3method(print,trim.index)

pkg/R/trim_post.R

@@ -504,7 +504,7 @@ print.trim.wald <- function(x,...) {
 #' Extract information of TRIM overall slope
 #'
 #' @param x TRIM output object
-#' @param which Selector to choose between "imputed" or "model" counts
+#' @param which Choose between "imputed" or "model" counts
 #'
 #' @return a list containing information overall slope coefficients (\code{coef}),
 #'   the p-value of the overall slope (\code{p}),
@@ -558,7 +558,15 @@ print.trim.overall <- function(x,...) {
 #-------------------------------------------------------------------------------
 #                                                                           Plot
 
-plot.trim.overall <- function(X, imputed=TRUE, ...) {
+#' Plot overall slope
+#'
+#' @param x An object of class \code{trim.overall} (returned by \code{\link{overall}})
+#' @param imputed Toggle to show imputed counts 
+#' @param ... Further options passed to \code{\link[graphics]{plot}}
+#'
+#' @export
+plot.trim.overall <- function(x, imputed=TRUE, ...) {
+  X <- x
   title <- attr(X, "title")
 
   J <- X$J

pkg/R/trim_workhorse.R

@@ -69,7 +69,12 @@ trim_estimate <- local({
   stopifnot(class(site.id) %in% c("integer","character","factor"))
   stopifnot(length(site.id)==n)
 
+  if (length(covars)>0){
+    message("Covariates are not implemented net and wil currently be ignored")
+  }
+
   # \verb!model! should be in the range 1 to 3
+  model <- model[1]
   stopifnot(model %in% 1:3)
 
   # Convert time and site to factors, if they're not yet