Updated site and documentation

Author: jaseeverett

.Rbuildignore

@@ -7,3 +7,5 @@
 ^docs$
 ^pkgdown$
 ^\.github$
+^doc$
+^Meta$

.gitignore

@@ -8,3 +8,5 @@ Ancillary/*
 
 inst/doc
 docs
+/doc/
+/Meta/

NAMESPACE

@@ -17,13 +17,8 @@ export(plotTimeSeries)
 export(reduceAll)
 export(reduceSize)
 export(reduceSpecies)
-export(untibble)
 export(validateGroups)
 export(zoomss_model)
-export(zoomss_mvf)
-export(zoomss_params)
-export(zoomss_run)
-export(zoomss_setup)
 importFrom(magrittr,"%>%")
 importFrom(rlang,":=")
 importFrom(rlang,.data)

R/utils.R

@@ -317,7 +317,6 @@ averageTimeSeries = function(mdl, var, n_years = 10){
 #' @param tibble A tibble or data frame object to convert
 #'
 #' @return Plain data frame without tibble attributes
-#' @export
 #'
 untibble <- function (tibble) {
   data.frame(unclass(tibble), check.names = FALSE, stringsAsFactors = FALSE)

R/zoomss_mvf.R

@@ -31,7 +31,6 @@
 #' @param S Matrix of source terms
 #'
 #' @return Updated abundance matrix (Nb) with new size-class distributions
-#' @export
 #'
 #' @examples
 #' \dontrun{

R/zoomss_params.R

@@ -39,7 +39,6 @@
 #'     \item temp_eff_zoo_ts, temp_eff_fish_ts: Time series of temperature effects
 #'     \item Additional biological and physical parameters
 #'   }
-#' @export
 #'
 #' @examples
 #' \dontrun{

R/zoomss_run.R

@@ -40,7 +40,6 @@
 #'     \item w: Size class weights (g)
 #'     \item Additional time series data and model results
 #'   }
-#' @export
 #'
 #' @examples
 #' \dontrun{

R/zoomss_setup.R

@@ -44,7 +44,6 @@
 #'     \item time: Time array for storing time values (initialized as NA)
 #'     \item Additional model structure components
 #'   }
-#' @export
 #'
 #' @examples
 #' \dontrun{

_pkgdown.yml

@@ -1,6 +1,7 @@
 url: https://MathMarEcol.github.io/zoomss
 development:
-  destination:
+  mode: devel
+  destination: docs
   version_label: info
   version_tooltip: The package is in the early stages of development. Use with caution.
 reference:
@@ -34,5 +35,10 @@ reference:
   - untibble
 navbar:
   structure:
-    right: [github]
-
+    right: [github, search]
+template:
+  bootstrap: 5
+  bootswatch: lumen #cerulean materia sandstone zephyr yeti
+  bslib:
+    toc: true
+    toc-expand: 3