Rapport 2007-2025

.Rbuildignore

@@ -1,3 +1,8 @@
+.*\.log
+.*\.tex
+.*_files
+\.Rproj\.user
+\.quarto
 ^.*\.Rproj$
 ^CITATION\.cff$
 ^LICENSE.md$
@@ -20,10 +25,10 @@
 ^inst/*\.log$
 ^inst/*css$
 ^inst/*figure$
-^inst/*rds$
 ^inst/intern_rapport$
 ^inst/output$
 ^inst/rapport$
+^inst/results.rds$
 ^inst/website$
 ^man-roxygen$
 ^organisation.yml$

.github/workflows/check_on_branch.yml

@@ -18,5 +18,3 @@ jobs:
       contents: read
     steps:
       - uses: inbo/actions/check_pkg@main
-        with:
-          aptget: libpoppler-cpp-dev

.github/workflows/check_on_different_r_os.yml

@@ -37,7 +37,7 @@ jobs:
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
-          extra-repositories: https://inbo.r-universe.dev
+          extra-repositories: https://inbo.r-universe.dev https://inla.r-inla-download.org/R/stable
 
       - uses: r-lib/actions/setup-pandoc@v2
 

.github/workflows/check_on_main.yml

@@ -17,5 +17,3 @@ jobs:
       GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: inbo/actions/check_pkg@main
-        with:
-          aptget: libpoppler-cpp-dev

.zenodo.json

@@ -1,6 +1,6 @@
 {
   "title": "abvanalysis: Analysis of the Common Breeding Bird Survey",
-  "version": "0.2.4",
+  "version": "0.2.5",
   "license": "GPL-3.0",
   "upload_type": "software",
   "description": "<p>Read in the raw data and prepare analysis datasets.<\/p>",

CITATION.cff

@@ -21,4 +21,4 @@ license: GPL-3.0
 repository-code: https://github.com/inbo/abvanalysis/
 type: software
 abstract: "Read in the raw data and prepare analysis datasets."
-version: 0.2.4
+version: 0.2.5

DESCRIPTION

@@ -1,17 +1,18 @@
 Package: abvanalysis
 Title: Analysis of the Common Breeding Bird Survey
-Version: 0.2.4
+Version: 0.2.5
 Authors@R: c(
     person("Thierry", "Onkelinx", , "thierry.onkelinx@inbo.be", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-8804-4216", affiliation = "Research Institute for Nature and Forest (INBO)")),
-    person("Research Institute for Nature and Forest (INBO)", , , "info@inbo.be", role = c("cph", "fnd"))
+    person("Research Institute for Nature and Forest (INBO)", , , "info@inbo.be", role = c("cph", "fnd"),
+           comment = c(ROR = "00j54wy13"))
   )
 Description: Read in the raw data and prepare analysis datasets.
 License: GPL-3
 URL: https://github.com/inbo/abvanalysis
 BugReports: https://github.com/inbo/abvanalysis/issues
 Depends:
-    R (>= 3.1.2)
+    R (>= 4.1.0)
 Imports:
     assertthat,
     DBI,
@@ -25,17 +26,20 @@ Imports:
     stringr,
     tibble,
     tidyr
-Suggests: 
+Suggests:
+    DT,
     effectclass,
+    gt,
     INBOmd,
     INBOtheme,
     knitr,
     pander,
     plotly,
+    quarto,
     rmarkdown,
     scales,
     tidyverse
-VignetteBuilder: 
+VignetteBuilder:
     knitr
 Additional_repositories: https://inbo.r-universe.dev
 Config/checklist/communities: inbo
@@ -44,4 +48,4 @@ Config/checklist/keywords: common breeding birds; monitoring; analysis;
 Encoding: UTF-8
 Language: en-GB
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3

LICENSE.md

@@ -1,4 +1,4 @@
-### GNU GENERAL PUBLIC LICENSE
+# GNU GENERAL PUBLIC LICENSE
 
 Version 3, 29 June 2007
 

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(copy_manifest_objects)
 export(get_field_id)
 export(get_linear_lincomb)
 export(get_nonlinear_lincomb)
@@ -27,14 +28,14 @@ importFrom(assertthat,is.number)
 importFrom(assertthat,is.string)
 importFrom(assertthat,noNA)
 importFrom(digest,sha1)
-importFrom(dplyr,"%>%")
 importFrom(dplyr,across)
 importFrom(dplyr,anti_join)
 importFrom(dplyr,arrange)
 importFrom(dplyr,bind_cols)
 importFrom(dplyr,bind_rows)
 importFrom(dplyr,count)
 importFrom(dplyr,distinct)
+importFrom(dplyr,everything)
 importFrom(dplyr,filter)
 importFrom(dplyr,full_join)
 importFrom(dplyr,group_by)
@@ -58,19 +59,24 @@ importFrom(git2rdata,push)
 importFrom(git2rdata,read_vc)
 importFrom(git2rdata,recent_commit)
 importFrom(git2rdata,rm_data)
+importFrom(git2rdata,update_metadata)
 importFrom(git2rdata,verify_vc)
 importFrom(git2rdata,write_vc)
 importFrom(methods,slot)
+importFrom(n2kanalysis,connect_inbo_s3)
 importFrom(n2kanalysis,display)
 importFrom(n2kanalysis,get_data)
 importFrom(n2kanalysis,get_file_fingerprint)
 importFrom(n2kanalysis,get_result)
 importFrom(n2kanalysis,get_status_fingerprint)
+importFrom(n2kanalysis,manifest_yaml_to_bash)
 importFrom(n2kanalysis,n2k_composite)
 importFrom(n2kanalysis,n2k_inla)
 importFrom(n2kanalysis,n2k_manifest)
+importFrom(n2kanalysis,read_manifest)
 importFrom(n2kanalysis,read_model)
 importFrom(n2kanalysis,status)
+importFrom(n2kanalysis,store_manifest)
 importFrom(n2kanalysis,store_manifest_yaml)
 importFrom(n2kanalysis,store_model)
 importFrom(purrr,map)

NEWS.md

@@ -1,3 +1,8 @@
+# abvanalysis 0.2.5
+
+* Import only the observations from the target species.
+* Provided more metadata about the imported data.
+
 # abvanalysis 0.2.4
 
 * Update checklist machinery

R/copy_manifest_objects.R

@@ -0,0 +1,44 @@
+#' Copy all object of the most recent manifest
+#' @inheritParams n2kanalysis::store_model
+#' @param target_folder Where to store the objects
+#' @export
+#' @importFrom dplyr filter
+#' @importFrom n2kanalysis connect_inbo_s3 read_manifest read_model
+#'   store_manifest store_model
+#' @importFrom rlang .data
+copy_manifest_objects <- function(
+  base,
+  project,
+  target_folder = ".",
+  overwrite = FALSE
+) {
+  manifest <- read_manifest(base = base, project = project)
+  store_manifest(manifest, base = target_folder, project = project)
+  manifest |>
+    slot("Manifest") |>
+    filter(is.na(.data$parent)) -> todo
+  file.path(target_folder, project) |>
+    list.files(recursive = TRUE) -> local_objects
+  if (overwrite) {
+    grepv("(converged|insufficient_data)", local_objects) -> local_objects
+  }
+  basename(local_objects) |>
+    gsub(pattern = "\\.rds$", replacement = "") -> done
+  for (hash in todo$fingerprint[!todo$fingerprint %in% done]) {
+    message(hash)
+    x <- try(read_model(hash, base = base, project = project))
+    while (inherits(x, "try-error")) {
+      browser()
+      connect_inbo_s3()
+      x <- try(read_model(hash, base = base, project = project))
+    }
+    store_model(
+      x,
+      base = target_folder,
+      project = project,
+      overwrite = overwrite
+    )
+    rm(x)
+    gc()
+  }
+}

R/get_field_id.R

@@ -4,7 +4,7 @@
 #' @param field_name The name of the field.
 #' @export
 #' @importFrom assertthat assert_that
-#' @importFrom git2rdata read_vc write_vc
+#' @importFrom git2rdata read_vc update_metadata write_vc
 get_field_id <- function(repo, table_name, field_name) {
   assert_that(
     inherits(repo, "git_repository"), is.string(table_name),
@@ -19,6 +19,16 @@ get_field_id <- function(repo, table_name, field_name) {
       file = "database_id", root = repo, sorting = c("table", "field"),
       stage = TRUE
     )
+    update_metadata(
+      file = "database_id", root = repo, stage = TRUE, name = "database_id",
+      title = "Database id for tables and fields",
+      description =
+        "This table describes to which table and field an id refers.",
+      field_description = c(
+        id = "Unique identifier", table = "Name of the table",
+        field = "Name of the field"
+      )
+    )
     return(1L)
   }
 
@@ -40,5 +50,15 @@ get_field_id <- function(repo, table_name, field_name) {
       )
     )
   )
+  update_metadata(
+    file = "database_id", root = repo, stage = TRUE, name = "database_id",
+    title = "Database id for tables and fields",
+    description =
+      "This table describes to which table and field an id refers.",
+    field_description = c(
+      id = "Unique identifier", table = "Name of the table",
+      field = "Name of the field"
+    )
+  )
   return(current_max + 1L)
 }

R/get_linear_lincomb.R

@@ -3,8 +3,8 @@
 #' @param formula the formula for the trend component
 #' @export
 #' @importFrom assertthat assert_that has_name is.string
-#' @importFrom dplyr %>% across bind_cols bind_rows distinct group_by inner_join
-#' mutate rename select summarise
+#' @importFrom dplyr across bind_cols bind_rows distinct everything group_by
+#' inner_join mutate rename select summarise
 #' @importFrom rlang :=
 #' @importFrom stats model.matrix
 get_linear_lincomb <- function(
@@ -20,30 +20,30 @@ get_linear_lincomb <- function(
     has_name(stratum_weights, "weight"), has_name(stratum_weights, stratum_var)
   )
 
-  dataset %>%
-    select(c(stratum_var, time_var)) %>%
-    distinct() %>%
+  dataset |>
+    select(c(stratum_var, time_var)) |>
+    distinct() |>
     inner_join(stratum_weights, by = stratum_var) -> all_weight
   model.matrix(object = formula, all_weight) -> mm
-  (as.data.frame(mm) * all_weight$weight) %>%
-    mutate(ID = sprintf("linear_estimate_%02i", all_weight[[time_var]])) %>%
-    group_by(.data$ID) %>%
-    summarise(across(.fns = sum)) -> mm
-  stratum_weights %>%
+  (as.data.frame(mm) * all_weight$weight) |>
+    mutate(ID = sprintf("linear_estimate_%02i", all_weight[[time_var]])) |>
+    group_by(.data$ID) |>
+    summarise(across(.cols = everything(), .fns = sum)) -> mm
+  stratum_weights |>
     mutate("{time_var}" := 1) -> trend_weight # nolint: object_name_linter.
   mm_trend <- model.matrix(object = formula, trend_weight)
   mm_trend <- as.data.frame(mm_trend) * trend_weight$weight
   mm_trend[, -grep(":", colnames(mm_trend))] <- 0
   if (has_name(mm_trend, "(Intercept)")) {
     mm_trend$`(Intercept)` <- 0
   }
-  mm_trend %>%
-    summarise(across(.fns = sum)) %>%
-    mutate(ID = "linear_trend") %>%
+  mm_trend |>
+    summarise(across(.cols = everything(), .fns = sum)) |>
+    mutate(ID = "linear_trend") |>
     bind_rows(mm) -> weights
   w_names <- weights$ID
-  weights %>%
-    select(-"ID") %>%
+  weights |>
+    select(-"ID") |>
     as.list() -> weights
   names(weights[[1]]) <- w_names
   weights