Expl targets

README.md

@@ -23,19 +23,31 @@ European Union's Horizon Europe Research and Innovation Programme (ID No 1010595
 <!-- community: b3 -->
 <!-- community: inbo -->
 
-### Description
-
 <!-- description: start -->
 Scripts to explore the conditions that determine the reliability of models, trends and status by comparing aggregated cubes with structured monitoring schemes.
 <!-- description: end -->
 
 This code is developed in context of **T4.5** of the [B-Cubed project](https://b-cubed.eu/).
 
+### Analyses workflow
+To download the latest version of each of the data sets run `prepare_abv_data.Rmd` and `Prepare_data_10km.Rmd`.
+Alternatively, you can download the exact same data we used by following the GBIF links in these same Rmd's.
+These data sets are saved under `data/raw`, the Rmd's further clean the data and add geometric properties.
+The cleaned data is stored in both `.csv` and `.gpkg` format under `data/interim`.
+
+To get the list of ABV birds used to filter the data in both pipelines run the `get_abv_species.R` after sourcing the functions in `taxon_mapping.R`.
+
+To run the targets pipelines, run `run_pipeline.R` in the folder of the pipeline you want to run.
+Afterwards, you can run the associated Rmd found under `reports`.
+
+
 ### Repo structure
 
 ```
-├── source                         ├ R markdown files
-│   └── R                          ├ R scripts
+├── source                         ├ 
+│   ├── pipelines                  ├ target pipelines https://books.ropensci.org/targets/
+│   ├── R                          ├ R scripts and R markdown files
+│   └── reports                    ├ reports based on output from target pipelines
 ├── data
 │   ├── raw                        ├ create this folder and store raw data, see prepare_abv_data.Rmd
 │   ├── intermediate               ├ store intermediate data

_targets.yaml

@@ -1,8 +1,8 @@
-target_workflow:
-  script: C:/R/git_repositories/comp-unstructured-data/source/pipelines/target_workflow/_targets.R
-  store: C:/R/git_repositories/comp-unstructured-data/source/pipelines/target_workflow/_targets
-  use_crew: yes
 biodiversity_indicators:
   script: C:/R/git_repositories/comp-unstructured-data/source/pipelines/biodiversity_indicators/_targets.R
   store: C:/R/git_repositories/comp-unstructured-data/source/pipelines/biodiversity_indicators/_targets
   use_crew: yes
+exploratory_analysis:
+  script: C:/R/git_repositories/comp-unstructured-data/source/pipelines/exploratory_analysis/_targets.R
+  store: C:/R/git_repositories/comp-unstructured-data/source/pipelines/exploratory_analysis/_targets
+  use_crew: yes

comp-unstructured-data.Rproj

@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: 917f1e07-7bf8-4404-b0ed-c2b02a93dc01
 
 RestoreWorkspace: Default
 SaveWorkspace: Default

data/raw/utm_grid/utm10_vlgrens_zBRU.prj

@@ -0,0 +1 @@
+PROJCS["Belge_Lambert_1972",GEOGCS["GCS_Belge_1972",DATUM["D_Belge_1972",SPHEROID["International_1924",6378388.0,297.0]],PRIMEM["Greenwich",0.0],UNIT["Degree",0.0174532925199433]],PROJECTION["Lambert_Conformal_Conic"],PARAMETER["False_Easting",150000.01256],PARAMETER["False_Northing",5400088.4378],PARAMETER["Central_Meridian",4.367486666666666],PARAMETER["Standard_Parallel_1",49.8333339],PARAMETER["Standard_Parallel_2",51.16666733333333],PARAMETER["Latitude_Of_Origin",90.0],UNIT["Meter",1.0]],VERTCS["Oostende",VDATUM["Oostende"],PARAMETER["Vertical_Shift",0.0],PARAMETER["Direction",1.0],UNIT["Meter",1.0]]

inst/en_gb.dic

@@ -1,10 +1,13 @@
 Algemene
+Anthus
 Bosonderzoek
 Broedvogelmonitoring
 Broedvogels
 Cartuyvels
 Cetti's
 Cettia
+Chloris
+Cyanistes
 Daele
 Databricks
 Dendrocopos
@@ -20,11 +23,14 @@ Laridae
 Larus
 Luscinia
 MGRS
+Motacilla
 Natuur
 OOSTENDE
 Parus
 Pielou
 Poecile
+Rmd
+Rmd's
 Saxicola
 Sui
 Teirlinckgebouw
@@ -35,23 +41,30 @@ Watervogels
 abv
 argentatus
 birdcube
+caeruleus
 cetti
+chloris
 color
+communis
 datacube
 datacubes
+domesticus
 eBird
+flava
 fuscus
 gbi
 ies
 labeled
 megarhynchos
+modularis
 montanus
 org
 rubicola
 sublicensable
 synched
 tabset
 torquatus
+trivialis
 utm
 voor
 waarnemingen