Merge pull request #4 from geco-bern/streamline-parallel-code

Update grsofun_tidy() for map2tidy v2.0

DESCRIPTION

@@ -1,34 +1,43 @@
 Package: grsofun
 Title: Global rsofun
-Version: 0.1
-Authors@R: 
+Version: 0.2
+Authors@R:c(
     person(
       given = "Benjamin",
       family = "Stocker",
       email = "[email protected]",
       role = c("aut", "cre"),
-      comment = c(ORCID = "0000-0003-2697-9096")
+      comment = c(ORCID = "0000-0003-2697-9096")),
+    person(
+      given = "Fabian",
+      family = "Bernhard",
+      email = "[email protected]",
+      role = c("aut"),
+      comment = c(ORCID = "0000-0003-0338-0961"))
     )
-Description: A wrapper for global rsofun runs
+Description: A wrapper for global rsofun runs.
 License: AGPL-3
 Encoding: UTF-8
 Imports: 
     zoo,
     dplyr,
+    readr,
     tidyr,
-    magrittr,
+    lubridate,
     purrr,
     multidplyr,
     parallel,
-    map2tidy,
+    map2tidy (>= 2.1.0),
     rsofun,
+    rgeco
 Suggests:
     here,
     cowplot,
     rnaturalearth,
     ggplot2,
 Remotes:
     geco-bern/map2tidy,
+    geco-bern/rgeco,
     geco-bern/rsofun,
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1

NAMESPACE

@@ -4,8 +4,6 @@ export(grsofun)
 export(grsofun_collect)
 export(grsofun_collect_byilon)
 export(grsofun_run)
-export(grsofun_run_bychunk)
 export(grsofun_run_byilon)
 export(grsofun_tidy)
-export(grsofun_tidy_byvar)
 export(read_forcing_byvar_byilon)

R/grsofun.R

@@ -3,7 +3,7 @@ grsofun <- function(par, settings){
 
   # Convert forcing files to a tidy format
   # Checks by file. If tidy already, skips automatically
-  settings <- grsofun_tidy(settings)
+  tidy_out <- grsofun_tidy(settings)
 
   # Run rsofun
   # Parallelizes runs to chunks of longitudinal bands

R/grsofun_collect.R

@@ -10,7 +10,8 @@ grsofun_collect <- function(
   if (settings$ncores_max == 1){
 
     # un-parallel alternative
-    df <- tibble(ilon = seq(settings$grid$len_ilon)) |>
+    len_ilon <- settings$grid$len_ilon
+    df <- dplyr::tibble(ilon = seq(len_ilon)) |>
       dplyr::mutate(out = purrr::map(
         ilon,
         ~grsofun_collect_byilon(
@@ -47,16 +48,16 @@ grsofun_collect <- function(
                                     "purrr",
                                     "tidyr",
                                     "readr",
-                                    "here",
-                                    "magrittr"
+                                    "here"
       )) |>
       multidplyr::cluster_assign(
         grsofun_collect_byilon = grsofun_collect_byilon   # make the function known for each core
       )
 
     # distribute computation across the cores, calculating for all longitudinal
     # indices of this chunk
-    df <- tibble(ilon = seq(settings$grid$len_ilon)) |>
+    len_ilon <- settings$grid$len_ilon
+    df <- dplyr::tibble(ilon = seq(len_ilon)) |>
       multidplyr::partition(cl) |>
       dplyr::mutate(out = purrr::map(
         ilon,
@@ -69,7 +70,7 @@ grsofun_collect <- function(
 
     if (return_data){
       df <- df |>
-        collect() |>
+        dplyr::collect() |>
         dplyr::mutate(len = purrr::map_int(out, ~nrow(.))) |>
         dplyr::filter(len > 0) |>
         dplyr::select(-len) |>
@@ -114,10 +115,10 @@ grsofun_collect_byilon <- function(
         month = lubridate::month(date)
       ) |>
       dplyr::group_by(sitename, year, month) |>
-      summarise(across(all_of(vars), \(x) mean(x, na.rm = TRUE)), .groups = "drop") |>
+      dplyr::summarise(dplyr::across(dplyr::all_of(vars), \(x) mean(x, na.rm = TRUE)), .groups = "drop") |>
 
       # add lon and lat to data frame
-      left_join(
+      dplyr::left_join(
         ddf |>
           dplyr::select(sitename, site_info) |>
           tidyr::unnest(site_info) |>
@@ -126,7 +127,7 @@ grsofun_collect_byilon <- function(
       )
 
   } else {
-    mdf <- tibble()
+    mdf <- dplyr::tibble()
   }
 
   if (return_data){