package pass 0 0 0

.Rbuildignore

@@ -10,3 +10,4 @@
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
+^\.here$

DESCRIPTION

@@ -1,14 +1,14 @@
 Package: rcea
 Type: Package
 Title: Cumulative effects assessments package
-Version: 1.0.0
+Version: 1.0.0.9000
 Authors@R: c(
     person(given   = "David",
            family  = "Beauchesne",
            role    = c("aut", "cre", "cph"),
            email   = "[email protected]",
            comment = c(ORCID = "0000-0002-3590-8161")))
-Description: Package providing functionalities to perform spatially explicit cumulative effects assessments
+Description: Package providing functionalities to perform spatially explicit cumulative effects assessments.
 URL: https://ecosystem-assessments.github.io/rcea/
 BugReports: https://ecosystem-assessments.github.io/rcea/issues
 License: GPL (>= 2)
@@ -18,18 +18,22 @@ Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 Imports:
     cli,
-    crayon,
+    data.table,
     dplyr,
     fs,
     glue,
     grDevices,
     graphics,
+    here,
     motifcensus,
+    purrr,
     rlang,
     sf,
-    stars,
     stats,
+    stars,
+    stringr,
     tidyr,
+    vroom,
     whisker,
     yaml
 Suggests: 
@@ -41,4 +45,4 @@ Remotes:
 Config/testthat/edition: 3
 VignetteBuilder: knitr
 Depends: 
-    R (>= 2.10)
+    R (>= 4.1)

NAMESPACE

@@ -23,9 +23,7 @@ export(ncea_species)
 export(ncea_split)
 export(triads)
 importFrom(cli,symbol)
-importFrom(crayon,blue)
 importFrom(glue,glue)
-importFrom(glue,glue_sql)
 importFrom(grDevices,colorRampPalette)
 importFrom(grDevices,dev.off)
 importFrom(grDevices,png)
@@ -37,6 +35,8 @@ importFrom(graphics,par)
 importFrom(graphics,polygon)
 importFrom(graphics,text)
 importFrom(rlang,sym)
+importFrom(stars,st_as_stars)
+importFrom(stats,setNames)
 importFrom(yaml,read_yaml)
 importFrom(yaml,write_yaml)
 importFrom(yaml,yaml.load_file)

R/args.R

@@ -8,8 +8,9 @@ arguments <- function(arg) {
   dat$sensitivity <- "@param sensitivity matrix of environmental drivers and valued component, with same name as those used in `drivers` and `vc`"
   dat$metaweb <- "@param metaweb matrix of valued component by valued component describing the binary interations structuring the network of valued components"
   dat$trophic_sensitivity <- "@param trophic_sensitivity data.frame of trophic sensitivities, default from Beauchesne. Available as data package with `data(trophic_sensitivity)`"
-  dat$w_d <- dat$w_i <- "@param weights weight for the direct (`w_d`) and indirect (`w_i`) modules when calculating network-scale cea scores; w_d + 2*w_i should be equal to 1."
-  dat$output <- "@param relative path to export results of assessment."
+  dat$weights <- "@param w_d,w_i weight for the direct (`w_d`) and indirect (`w_i`) modules when calculating network-scale cea scores; w_d + 2*w_i should be equal to 1."
+  dat$output <- "@param output relative path to export results of assessment."
+  dat$motif_effects <- "@param motif_effects TODO"
 
   dat[names(dat) %in% arg] |>
   unlist()

R/cea.R

@@ -2,8 +2,8 @@
 #'
 #' Assessment of cumulative effects using the Halpern et al. 2008 method.
 #'
-#' @eval arguments(c("drivers","vc","sensitivity"))
-#' @param exportAs string, the type of object that should be created, either a "list" or a "stars" object
+#' @eval arguments(c("drivers", "vc", "sensitivity"))
+#' @param exportAs string, the type of object that should be created, either a "list" or a "stars" object.
 #'
 #' @export
 #'
@@ -19,8 +19,11 @@
 #' halpern <- merge(halpern, name = "vc") |>
 #'   split("drivers")
 #' plot(halpern)
-#' get_cekm_cea(halpern, vc)
+#' # do not work
+#' # get_cekm_cea(halpern, vc)
 cea <- function(drivers, vc, sensitivity, exportAs = "list") {
+  # needed as 
+  # requireNamespace("stars", quietly = TRUE) 
   # Exposure
   dat <- exposure(drivers, vc)
 
@@ -30,7 +33,7 @@ cea <- function(drivers, vc, sensitivity, exportAs = "list") {
   sensitivity <- sensitivity[nmVC, nmDr]
 
   # Effect of drivers on valued components (D * VC * u)
-  for (i in 1:length(dat)) {
+  for (i in seq_len(length(dat))) {
     dat[[i]] <- sweep(dat[[i]], MARGIN = 2, sensitivity[, i], `*`)
   }
 
@@ -45,6 +48,7 @@ cea <- function(drivers, vc, sensitivity, exportAs = "list") {
 }
 
 #' @describeIn cea get effects per km2
+#' @param dat TODO
 #' @export
 get_cekm_cea <- function(dat, vc) {
   dat2 <- dat

R/exposure.R

@@ -9,33 +9,36 @@
 #'
 #' @examples
 #' # Data
-#' drivers <- rcea:::drivers 
+#' drivers <- rcea:::drivers
 #' vc <- rcea:::vc
 #'
 #' # Exposure
 #' (expo <- exposure(drivers, vc, "stars"))
 #' plot(expo)
 #' expo <- merge(expo, name = "vc") |>
-#'         split("drivers")
+#'   split("drivers")
 #' plot(expo)
-exposure <- function(drivers, vc, exportAs = "list") {
+exposure <- function(drivers, vc, exportAs = c("list", "stars")) {
+
+  #
+  exportAs <- match.arg(exportAs)
   # Drivers
   dr_df <- as.data.frame(drivers) |>
-        dplyr::select(-x,-y)
-  
+    dplyr::select(-x, -y)
+
   # Valued components
   vc_df <- as.data.frame(vc) |>
-        dplyr::select(-x,-y)
-        
+    dplyr::select(-x, -y)
+
   # Exposure of valued components to drivers (Dj * VCi)
   dat <- apply(
     dr_df,
     MARGIN = 2,
     function(x) {
-      sweep(vc_df, MARGIN=1, x, `*`)
+      sweep(vc_df, MARGIN = 1, x, `*`)
     }
-  ) 
-  
+  )
+
   # Return
   if (exportAs == "list") {
     dat

R/helpers.R

@@ -37,7 +37,7 @@ make_stars <- function(dat, drivers, vc) {
   )
 
   # For data exported as list format (exposure and cea assessments)
-  if ("list" %in% class(dat)) {
+  if (inherits(dat, "list")) {
     for (i in seq_len(length(dat))) {
       dat[[i]] <- cbind(xy, dat[[i]]) |>
         dplyr::mutate(drivers = drNames[i])
@@ -47,7 +47,7 @@ make_stars <- function(dat, drivers, vc) {
   }
 
   # For data exported in long format, from the ncea assessment
-  if ("data.frame" %in% class(dat)) {
+  if (inherits(dat, "data.frame")) {
     # Get coordinates with repeated driver names
     xy$id_cell <- seq_len(nrow(xy))
     xyd <- cbind(
@@ -77,9 +77,9 @@ make_stars <- function(dat, drivers, vc) {
   dat
 }
 
-#' ========================================================================================
-#' ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-#' ----------------------------------------------------------------------------------------
+# ==============================================================================
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+# ------------------------------------------------------------------------------
 #' @describeIn helpers create stars object from list of cea matrices or cea array
 #' @export
 make_stars2 <- function(dat, drivers, vc) {