fixes after changes to detect jags

BiologicalRecordsCentre · Jun 17, 2024 · b37e9f1 · b37e9f1
1 parent 48c6c5b
commit b37e9f1
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Showing 10 changed files with 4,121 additions and 19 deletions.
diff --git a/.gitignore b/.gitignore
@@ -11,4 +11,5 @@ error_reproduction_scripts
 
 # To reduce repo size
 vignettes/vignette_files
-vignettes/vignette_cache
+vignettes/vignette_cache
+inst/doc/BRCindicators_files
diff --git a/R/bayesian_meta_analysis.R b/R/bayesian_meta_analysis.R
@@ -43,11 +43,9 @@
 #'             A generic method for estimating and smoothing multispecies biodiversity indices, robust to intermittent data. 
 #'             \emph{Journal of Agricultural Biological and Environmental Statistics}, in revision.
 #' @export
-#' @examples 
-#' 
-#' # Only run if there is a JAGS installation
-#' if(suppressWarnings(runjags::testjags(silent = TRUE)$JAGS.found)){
 #' 
+#' @examples 
+#' \dontrun{
 #' # Create some example data in the format required
 #' data <- data.frame(species = rep(letters, each = 50),
 #'                    year = rep(1:50, length(letters)),
@@ -60,8 +58,7 @@
 #' # Plot the resulting indicator
 #' plot_indicator(indicator = bma_indicator[,'Index.Mprime'],
 #'                CIs = bma_indicator[,c(3,4)])
-#'    
-#'    }
+#' }
 
 bma <- function (data,
               plot = TRUE,

diff --git a/benchmarking/package_notes_and_benchmarking.Rmd b/benchmarking/package_notes_and_benchmarking.Rmd
diff --git a/inst/doc/BRCindicators.html b/inst/doc/BRCindicators.html
diff --git a/inst/doc/BRCindicators.html.orig b/inst/doc/BRCindicators.html.orig
diff --git a/man/bma.Rd b/man/bma.Rd
diff --git a/vignettes/BRCindicators.Rmd b/vignettes/BRCindicators.Rmd
diff --git a/vignettes/BRCindicators.html b/vignettes/BRCindicators.html