From f6286c2eac91633e869f769553e0ccc432347b95 Mon Sep 17 00:00:00 2001 From: wlangera Date: Tue, 23 Apr 2024 12:31:06 +0200 Subject: [PATCH 01/12] initial commit --- .../data_preparation/procedure_data_sovon.Rmd | 81 +++++++++++++++++++ 1 file changed, 81 insertions(+) create mode 100644 source/targets/data_preparation/procedure_data_sovon.Rmd diff --git a/source/targets/data_preparation/procedure_data_sovon.Rmd b/source/targets/data_preparation/procedure_data_sovon.Rmd new file mode 100644 index 0000000..f589460 --- /dev/null +++ b/source/targets/data_preparation/procedure_data_sovon.Rmd @@ -0,0 +1,81 @@ +--- +title: "Procedure om data te downloaden van de SOVON WFS service en verwerking via targets pipeline" +author: "Hans Van Calster & Ward Langeraert" +date: "`r Sys.Date()`" +output: html_document +--- + +```{r setup, include=FALSE} +knitr::opts_chunk$set(echo = TRUE) +``` + +# Verkrijg data via SOVON WFS service +## QGIS v3.24 +### Stappenplan + +1. een account aanmaken via + + 1. Rechten aanvragen Sovon + +2. open QGIS + + 1. zet project crs op EPSG:28992 + 1. kies `Kaartlagen` --\> `Databronnen beheren` --\> `WFS / OGC API objecten` + +3. klik `nieuw` in het dialoogvenster om een nieuwe WFS verbinding te maken + + 1. Gebruik als naam `sovon` en als url `https://portal.sovon.nl/views/wfs/453/` + 1. Klik op OK + +1. Maak een verbinding met de zopas toegevoegde WFS service + + 1. Klik op verbinden + 1. Selecteer de laag `ms:viewpoints` + - TIP: je kaan ook een query aanvragen, bv.: SELECT * FROM viewpoints WHERE jaar = 2023 + 1. vink het boxje aan 'Alleen objecten bevragen die het huidige zichtbare bereik overlappen' + 1. Klik op toevoegen + 1. Geef je gebruikersnaam en paswoord + 1. Indien QGIS vraagt voor transformatie van EPSG:28992 naar een ander CRS, kan je dit best cancellen. + +Als alles goed gaat worden nu alle data waar je toegang toe hebt gekregen gedownload (dit kan even duren). +Dit zijn de zogenaamde bezoekstippen. + +## QGIS v3.26 +### Stappenplan + +1. een account aanmaken via + + 1. Rechten aanvragen Sovon + +2. open QGIS + + 1. zet project crs op EPSG:28992 + 1. kies `Kaartlagen` --\> `Databronnen beheren` --\> `WFS / OGC API objecten` + +3. klik `nieuw` in het dialoogvenster om een nieuwe WFS verbinding te maken + + 1. Gebruik als naam `sovon` en als url `https://portal.sovon.nl/views/wfs/453/` + 1. Klik op OK + +1. Maak een verbinding met de zopas toegevoegde WFS service + + 1. Klik op Verbinden + 1. Geef je gebruikersnaam en paswoord en kik op ok + 1. Selecteer de laag `ms:viewpoints` + - TIP: je kaan ook een query aanvragen, bv.: SELECT * FROM viewpoints WHERE jaar = 2023 + 1. vink het boxje aan 'Alleen objecten bevragen die het huidige zichtbare bereik overlappen' + 1. Wijzig Coördinaten Referentiesysteem naar EPSG:28992 + 1. Klik op toevoegen + 1. Indien QGIS vraagt voor transformatie van EPSG:28992 naar een ander CRS, kan je dit best cancellen. + +Als alles goed gaat worden nu alle data waar je toegang toe hebt gekregen gedownload (dit kan even duren). +Dit zijn de zogenaamde bezoekstippen. + +# Downloaden en opslaan van de data + +Wanneer alle data gedownload zijn, kan je deze laag exporteren: + +1. Zorg dat alle data zichtbaar zijn in de view + +2. Selecteer `Kaartlagen` --\> `Opslaan als ...` en sla op als `Geojson` (of `Geopackage`) met als bestandsnaam `` en CRS `EPSG:28992`. + Klik op OK (dit kan even duren). From 4097ef71bc315f3361814ef128e180430b24a5be Mon Sep 17 00:00:00 2001 From: wlangera Date: Tue, 23 Apr 2024 15:06:33 +0200 Subject: [PATCH 02/12] rename file --- .../{procedure_data_sovon.Rmd => README.Rmd} | 38 +++++++++---------- 1 file changed, 18 insertions(+), 20 deletions(-) rename source/targets/data_preparation/{procedure_data_sovon.Rmd => README.Rmd} (63%) diff --git a/source/targets/data_preparation/procedure_data_sovon.Rmd b/source/targets/data_preparation/README.Rmd similarity index 63% rename from source/targets/data_preparation/procedure_data_sovon.Rmd rename to source/targets/data_preparation/README.Rmd index f589460..9fbd5f3 100644 --- a/source/targets/data_preparation/procedure_data_sovon.Rmd +++ b/source/targets/data_preparation/README.Rmd @@ -9,20 +9,19 @@ output: html_document knitr::opts_chunk$set(echo = TRUE) ``` -# Verkrijg data via SOVON WFS service +# Download data via SOVON WFS service ## QGIS v3.24 -### Stappenplan 1. een account aanmaken via 1. Rechten aanvragen Sovon -2. open QGIS +1. open QGIS - 1. zet project crs op EPSG:28992 - 1. kies `Kaartlagen` --\> `Databronnen beheren` --\> `WFS / OGC API objecten` + 1. Zet project crs op EPSG:28992 + 1. Kies `Kaartlagen` --\> `Databronnen beheren` --\> `WFS / OGC API objecten` -3. klik `nieuw` in het dialoogvenster om een nieuwe WFS verbinding te maken +1. klik `nieuw` in het dialoogvenster om een nieuwe WFS verbinding te maken 1. Gebruik als naam `sovon` en als url `https://portal.sovon.nl/views/wfs/453/` 1. Klik op OK @@ -31,28 +30,27 @@ knitr::opts_chunk$set(echo = TRUE) 1. Klik op verbinden 1. Selecteer de laag `ms:viewpoints` - - TIP: je kaan ook een query aanvragen, bv.: SELECT * FROM viewpoints WHERE jaar = 2023 - 1. vink het boxje aan 'Alleen objecten bevragen die het huidige zichtbare bereik overlappen' + - Vraag een query aan voor data van het nieuwe jaar, bv.: `SELECT * FROM viewpoints WHERE jaar = 2024` + 1. Vink het boxje aan 'Alleen objecten bevragen die het huidige zichtbare bereik overlappen' 1. Klik op toevoegen 1. Geef je gebruikersnaam en paswoord - 1. Indien QGIS vraagt voor transformatie van EPSG:28992 naar een ander CRS, kan je dit best cancellen. + 1. Indien QGIS vraagt voor transformatie van EPSG:28992 naar een ander CRS, kan je dit best cancellen -Als alles goed gaat worden nu alle data waar je toegang toe hebt gekregen gedownload (dit kan even duren). +Als alles goed gaat, worden nu alle data waar je toegang toe hebt gedownload (dit kan even duren). Dit zijn de zogenaamde bezoekstippen. ## QGIS v3.26 -### Stappenplan 1. een account aanmaken via 1. Rechten aanvragen Sovon -2. open QGIS +1. open QGIS - 1. zet project crs op EPSG:28992 - 1. kies `Kaartlagen` --\> `Databronnen beheren` --\> `WFS / OGC API objecten` + 1. Zet project crs op EPSG:28992 + 1. Kies `Kaartlagen` --\> `Databronnen beheren` --\> `WFS / OGC API objecten` -3. klik `nieuw` in het dialoogvenster om een nieuwe WFS verbinding te maken +1. klik `nieuw` in het dialoogvenster om een nieuwe WFS verbinding te maken 1. Gebruik als naam `sovon` en als url `https://portal.sovon.nl/views/wfs/453/` 1. Klik op OK @@ -62,16 +60,16 @@ Dit zijn de zogenaamde bezoekstippen. 1. Klik op Verbinden 1. Geef je gebruikersnaam en paswoord en kik op ok 1. Selecteer de laag `ms:viewpoints` - - TIP: je kaan ook een query aanvragen, bv.: SELECT * FROM viewpoints WHERE jaar = 2023 - 1. vink het boxje aan 'Alleen objecten bevragen die het huidige zichtbare bereik overlappen' + - Vraag een query aan voor data van het nieuwe jaar, bv.: `SELECT * FROM viewpoints WHERE jaar = 2024` + 1. Vink het boxje aan 'Alleen objecten bevragen die het huidige zichtbare bereik overlappen' 1. Wijzig Coördinaten Referentiesysteem naar EPSG:28992 1. Klik op toevoegen - 1. Indien QGIS vraagt voor transformatie van EPSG:28992 naar een ander CRS, kan je dit best cancellen. + 1. Indien QGIS vraagt voor transformatie van EPSG:28992 naar een ander CRS, kan je dit best cancellen -Als alles goed gaat worden nu alle data waar je toegang toe hebt gekregen gedownload (dit kan even duren). +Als alles goed gaat, worden nu alle data waar je toegang toe hebt gedownload (dit kan even duren). Dit zijn de zogenaamde bezoekstippen. -# Downloaden en opslaan van de data +# Exporteren en verwerking van de data Wanneer alle data gedownload zijn, kan je deze laag exporteren: From b1852010c005748f1c0f39c930e3b7b72370db1a Mon Sep 17 00:00:00 2001 From: wlangera Date: Tue, 23 Apr 2024 15:17:20 +0200 Subject: [PATCH 03/12] export and localise data --- source/targets/data_preparation/README.Rmd | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/source/targets/data_preparation/README.Rmd b/source/targets/data_preparation/README.Rmd index 9fbd5f3..64dc321 100644 --- a/source/targets/data_preparation/README.Rmd +++ b/source/targets/data_preparation/README.Rmd @@ -69,11 +69,18 @@ Dit zijn de zogenaamde bezoekstippen. Als alles goed gaat, worden nu alle data waar je toegang toe hebt gedownload (dit kan even duren). Dit zijn de zogenaamde bezoekstippen. -# Exporteren en verwerking van de data +# Exporteren en localisatie van de data Wanneer alle data gedownload zijn, kan je deze laag exporteren: 1. Zorg dat alle data zichtbaar zijn in de view -2. Selecteer `Kaartlagen` --\> `Opslaan als ...` en sla op als `Geojson` (of `Geopackage`) met als bestandsnaam `` en CRS `EPSG:28992`. +1. Selecteer `Kaartlagen` --\> `Opslaan als ...` en sla op als `.geojson` met als bestandsnaam `` en CRS `EPSG:28992`. + `YYYYMMDD` is de datum van export, `JAAR` is het jaar wanneer de data verzameld is, zie SQL query. Klik op OK (dit kan even duren). + Sla het geojson-bestand op in de folder `mbag-mas/data/mas`. + +1. De finale export die je wilt gebruiken voor data preparatie en latere analyses sla je op in een folder met als naam `JAAR` onder `C:/R/git_repositories/mbag-mas/source/targets/data_preparation/data`. + Elke folder mag slechts 1 bestand hebben met de data van dat jaar (zie verder). + +# Verwerking van de data From b48df7f4e55e50d2521353647ab8a0fbe8fa8ad6 Mon Sep 17 00:00:00 2001 From: wlangera Date: Tue, 23 Apr 2024 15:26:56 +0200 Subject: [PATCH 04/12] explain targets pipeline --- source/targets/data_preparation/README.Rmd | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/source/targets/data_preparation/README.Rmd b/source/targets/data_preparation/README.Rmd index 64dc321..8260552 100644 --- a/source/targets/data_preparation/README.Rmd +++ b/source/targets/data_preparation/README.Rmd @@ -84,3 +84,17 @@ Wanneer alle data gedownload zijn, kan je deze laag exporteren: Elke folder mag slechts 1 bestand hebben met de data van dat jaar (zie verder). # Verwerking van de data + +We verwerken de data via een pipeline met de [targets package](https://books.ropensci.org/targets/). +Dit omvat data selectie, preparatie en berekening van variabelen. + +We maken gebruik van ["dynamic branching"](https://books.ropensci.org/targets/dynamic.html) in de targets pipeline. +Dit is een manier om nieuwe targets te definiëren terwijl de pipeline actief is. +Hierbij wordt een nieuwe target gemaakt voor elk bestand. +Bij het toevoegen van een nieuwe dataset van een jaar, zal de pipeline bijgevolg enkel de berekeningen voor de data van het nieuwe jaar moeten doen en niet opnieuw de berekeningen voor de vorige jaren. +De volledige pipeline ziet er als volgt uit: + +```{r} +targets::tar_visnetwork() +``` + From b2bd19992786dd7ba0f5b77985b2a1a7fd63990c Mon Sep 17 00:00:00 2001 From: wlangera Date: Tue, 23 Apr 2024 16:59:10 +0200 Subject: [PATCH 05/12] map over files --- source/targets/data_preparation/_targets.R | 55 ++++++++++++++++------ 1 file changed, 40 insertions(+), 15 deletions(-) diff --git a/source/targets/data_preparation/_targets.R b/source/targets/data_preparation/_targets.R index c8d2c18..bdf6d34 100644 --- a/source/targets/data_preparation/_targets.R +++ b/source/targets/data_preparation/_targets.R @@ -38,24 +38,28 @@ source(file.path(mbag_dir, "source", "R", "predatoren_f.R")) # Target list list( - tarchetypes::tar_file( - name = mas_counts_sovon_file, - command = path_to_counts_sovon( - proj_path = mbag_dir, - file = "20230810_qgis_export_sovon_wfs_2023.geojson" + tarchetypes::tar_files( + name = mas_counts_sovon_files, + command = paths_to_counts_sovon( + proj_path = target_dir ) ), tar_target( name = mas_counts_sovon, command = sf::st_read( - mas_counts_sovon_file - ) + dsn = mas_counts_sovon_files, + quiet = TRUE + ), + pattern = map(mas_counts_sovon_files), + iteration = "list" ), tar_target( name = crs_pipeline, command = amersfoort_to_lambert72( mas_counts_sovon - ) + ), + pattern = map(mas_counts_sovon), + iteration = "list" ), tarchetypes::tar_file( name = sample_file, @@ -77,44 +81,65 @@ list( x = crs_pipeline, y = sample, by = dplyr::join_by(plotnaam == pointid) - ) + ), + pattern = map(crs_pipeline), + iteration = "list" ), tar_target( name = select_time_periods, command = select_within_time_periods( counts_df = select_sampled_points - ) + ), + pattern = map(select_sampled_points), + iteration = "list" ), tar_target( name = select_within_radius, command = select_within_circle_radius( counts_df = select_time_periods, radius = 300 - ) + ), + pattern = map(select_time_periods), + iteration = "list" ), tar_target( name = select_species_groups, command = dplyr::filter( select_within_radius, soortgrp %in% 1:2 - ) + ), + pattern = map(select_within_radius), + iteration = "list" ), tar_target( name = remove_double_counts, command = process_double_counted_data( counts_df = select_species_groups - ) + ), + pattern = map(select_species_groups), + iteration = "list" ), tar_target( name = remove_subspecies_names, command = adjust_subspecies_names_nl( counts_df = remove_double_counts - ) + ), + pattern = map(remove_double_counts), + iteration = "list" ), tar_target( - name = mas_data_clean, + name = add_predator_variable, command = add_predator_variables( counts_df = remove_subspecies_names + ), + pattern = map(remove_subspecies_names), + iteration = "list" + ), + tar_target( + name = mas_data_clean, + command = do.call( + what = rbind.data.frame, + args = add_predator_variable ) ) ) From 50fe97642f896cdb3c3094c34957cae30682a992 Mon Sep 17 00:00:00 2001 From: wlangera Date: Tue, 23 Apr 2024 16:59:33 +0200 Subject: [PATCH 06/12] create list with all data files --- .../targets/data_preparation/R/path_to_files.R | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/source/targets/data_preparation/R/path_to_files.R b/source/targets/data_preparation/R/path_to_files.R index 078929c..2491dd0 100644 --- a/source/targets/data_preparation/R/path_to_files.R +++ b/source/targets/data_preparation/R/path_to_files.R @@ -1,7 +1,15 @@ -# Path to raw data from SOVON -path_to_counts_sovon <- function(proj_path, file) { - file_path <- file.path(proj_path, "data", "mas", file) - return(file_path) +# Paths to raw data from SOVON +paths_to_counts_sovon <- function( + proj_path, + pattern = "qgis_export_sovon_wfs") { + # List paths to all files + file_paths <- list.files( + file.path(proj_path, "data"), + pattern = pattern, + full.names = TRUE, + recursive = TRUE) + + return(file_paths) } # Path to counting locations From c47312a24fd6308f2d14956c0edd6236d0f5d223 Mon Sep 17 00:00:00 2001 From: wlangera Date: Tue, 23 Apr 2024 16:59:45 +0200 Subject: [PATCH 07/12] update meta file --- .../data_preparation/_targets/meta/meta | 115 ++++++++++++++++-- 1 file changed, 104 insertions(+), 11 deletions(-) diff --git a/source/targets/data_preparation/_targets/meta/meta b/source/targets/data_preparation/_targets/meta/meta index ef3b3f2..aa4dd3b 100644 --- a/source/targets/data_preparation/_targets/meta/meta +++ b/source/targets/data_preparation/_targets/meta/meta @@ -1,28 +1,121 @@ name|type|data|command|depend|seed|path|time|size|bytes|format|repository|iteration|parent|children|seconds|warnings|error -.Random.seed|object|93b4d65f2506ee1c||||||||||||||| -add_predator_variable|stem|b1d6101a48661ce9|e1c93a06d9f6d4cb|d65332b68dd4f90d|-1919973047||t19836.3580925959s|448d33d82c53cd6c|1211653|qs|local|vector|||0.11|| +.Random.seed|object|9e238a4bf04635f2||||||||||||||| +add_predator_variable|pattern|c711edf6e40245ae|e1c93a06d9f6d4cb||-1919973047||||0|qs|local|list||add_predator_variable_fab8aebd|0|| +add_predator_variable_03ea80bf|branch|b1d6101a48661ce9|e1c93a06d9f6d4cb|7443180e6ceab48c|-1916797933||t19836.5939135339s|448d33d82c53cd6c|1211653|qs|local|list|add_predator_variable||0.15|| 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sample_file|stem|12ec54a1802f0ccc|9373cad8a757c886|fce4235ad2580001|1141903364|C:/R/git_repositories/mbag-mas/data/steekproefkaders/steekproef_avimap_mbag_piloot.csv|t19803.5701886462s|60ef8d6db1574934|62070|file|local|vector|||0|| -select_sampled_points|stem|f751de663336b945|b659c8f8ce392cde|ecc1e7b45b6a8d0c|-107447084||t19831.5248409952s|d8de74379de70ddb|1187211|qs|local|vector|||0.03|| -select_species_groups|stem|f9ee84b7905152e5|3f1e242af19e665d|50097636e83c673b|-1185638444||t19831.5759555089s|9d27dbe475bb2b9d|1194195|qs|local|vector|||0.04|| -select_time_periods|stem|e194aeeaa582d6a6|206ce93b3790e30c|4f8cbc5f7ebd8ca9|291324708||t19836.3456566927s|2783a0b288bff409|1201608|qs|local|vector|||0.28|| +select_sampled_points|pattern|f52e2cdbe1687d80|b659c8f8ce392cde||-107447084||||0|qs|local|list||select_sampled_points_4f539302|0|| 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+select_within_radius_39e75cec|branch|597c823448e8ec03|b43ee3d813fbfa23|c13d159d3354fcc8|-1811556608||t19836.6221418979s|80c0be946e02aafd|1796|qs|local|list|select_within_radius||0.21|| +select_within_radius_538419f2|branch|f9ee84b7905152e5|b43ee3d813fbfa23|509018c7122b1cee|611654093||t19836.5938778636s|9d27dbe475bb2b9d|1194195|qs|local|list|select_within_radius||0.28|| +select_within_radius_6635b64e|branch|597c823448e8ec03|b43ee3d813fbfa23|a78a212b997c9035|-1937567145||t19836.6103693475s|80c0be946e02aafd|1796|qs|local|list|select_within_radius||0.19|| +select_within_radius_6a384fb1|branch|f9ee84b7905152e5|b43ee3d813fbfa23|30cd8dca9685b851|-273477156||t19836.6212770526s|9d27dbe475bb2b9d|1194195|qs|local|list|select_within_radius||0.3|| +select_within_radius_730aa92e|branch|f9ee84b7905152e5|b43ee3d813fbfa23|d58b5b6016a3cc70|1596416445||t19836.6212829376s|9d27dbe475bb2b9d|1194195|qs|local|list|select_within_radius||0.29|| +select_within_radius_75edd584|branch|f9ee84b7905152e5|b43ee3d813fbfa23|0bd870f6cbcd77c1|336962899||t19836.5780894524s|9d27dbe475bb2b9d|1194195|qs|local|list|select_within_radius||0.32|| select_within_time_periods|function|2798499bd63b690b||||||||||||||| target_dir|object|5289a857edb685f1||||||||||||||| From 7fe5ba9a8bc1579eaafa55ea24c3c9e918e9add4 Mon Sep 17 00:00:00 2001 From: wlangera Date: Tue, 23 Apr 2024 17:12:43 +0200 Subject: [PATCH 08/12] update meta file --- .../data_preparation/_targets/meta/meta | 156 +++++------------- 1 file changed, 37 insertions(+), 119 deletions(-) diff --git a/source/targets/data_preparation/_targets/meta/meta b/source/targets/data_preparation/_targets/meta/meta index aa4dd3b..548b4ee 100644 --- a/source/targets/data_preparation/_targets/meta/meta +++ b/source/targets/data_preparation/_targets/meta/meta @@ -1,121 +1,39 @@ name|type|data|command|depend|seed|path|time|size|bytes|format|repository|iteration|parent|children|seconds|warnings|error 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an object of class list -crs_pipeline_23d6c59a|branch|24316d2285354371|fc01a4ccb0c4ce92|0e4d678360b8eaad|-1915834548||t19836.5766195312s|cd33a8123b9ea861|1405399|qs|local|list|crs_pipeline||0.74|| -crs_pipeline_89300e17|branch|24316d2285354371|fc01a4ccb0c4ce92|513b3e2cfc02bd9a|-1241093430||t19836.5938371305s|cd33a8123b9ea861|1405399|qs|local|list|crs_pipeline||0.88|| -crs_pipeline_916fc15e|branch|24316d2285354371|fc01a4ccb0c4ce92|a8efcc518d143ecd|1475784767||t19836.6212489149s|cd33a8123b9ea861|1405399|qs|local|list|crs_pipeline||0.77|| -crs_pipeline_a6fccf30|branch|24316d2285354371|fc01a4ccb0c4ce92|2161b38eb50ed963|1565461203||t19836.6212374914s|cd33a8123b9ea861|1405399|qs|local|list|crs_pipeline||0.89|| -crs_pipeline_bab56df4|branch|dc40426eaed26833|fc01a4ccb0c4ce92|ba7a51299fd664c8|-954770632||t19836.6221335285s|81cd54fe76eb3bab|1571|qs|local|list|crs_pipeline||0.3|| 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mas_counts_sovon_files_4776d7dc|branch|8b786fe9ff0cbd2e|c52338d7124b0a05|ef46db3751d8e999|-1411769136|C:/R/git_repositories/mbag-mas/source/targets/data_preparation/data/2023/20230810_qgis_export_sovon_wfs_2023.geojson|t19579.6291970393s|ce6386d2aec493f8|24420334|file|local|vector|mas_counts_sovon_files||0|| -mas_counts_sovon_files_6275cd19|branch|8b786fe9ff0cbd2e|c52338d7124b0a05|ef46db3751d8e999|-962776456|C:/R/git_repositories/mbag-mas/source/targets/data_preparation/data/2018_2022/20240810_qgis_export_sovon_wfs_2023.geojson|t19579.6291970393s|ce6386d2aec493f8|24420334|file|local|vector|mas_counts_sovon_files||0|| -mas_counts_sovon_files_94b65fdb|branch|23b1a13da18e6c94|c52338d7124b0a05|ef46db3751d8e999|1082442049|C:/R/git_repositories/mbag-mas/source/targets/data_preparation/data/2024/20241111_qgis_export_sovon_wfs_2023.geojson|t19836.6219818729s|b213247e12909598|3811|file|local|vector|mas_counts_sovon_files||0|| 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-remove_subspecies_names_c3999d19|branch|707aba61d2e09b17|6192e8e36bfb46d7|612432e541eb00d6|1124951305||t19836.6103752379s|1416663ce6eb40fb|1821|qs|local|list|remove_subspecies_names||0.06|| -remove_subspecies_names_d6ede689|branch|35f7dbbf56f35d05|6192e8e36bfb46d7|f09aa74eae05883b|-1890658710||t19836.5939049165s|ca0af1b203c1cf95|1195963|qs|local|list|remove_subspecies_names||0.14|| -remove_subspecies_names_e0b28f63|branch|707aba61d2e09b17|6192e8e36bfb46d7|61a997f9a4ba629e|1960184550||t19836.6221475878s|1416663ce6eb40fb|1821|qs|local|list|remove_subspecies_names||0.05|| -remove_subspecies_names_e201d235|branch|35f7dbbf56f35d05|6192e8e36bfb46d7|f7b87065df7ae89b|-143919116||t19836.5939091217s|ca0af1b203c1cf95|1195963|qs|local|list|remove_subspecies_names||0.15|| -remove_subspecies_names_f8bc5a35|branch|35f7dbbf56f35d05|6192e8e36bfb46d7|0af212d1e6f08a58|2106684947||t19836.621303701s|ca0af1b203c1cf95|1195963|qs|local|list|remove_subspecies_names||0.14|| 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-select_time_periods_bec6cd1a|branch|b51ba8c0de00e056|206ce93b3790e30c|5f35b22b23ee4453|-1877410562||t19836.6103658885s|5cc80c0464196ae6|1789|qs|local|list|select_time_periods||0.19|| -select_time_periods_cc4899c8|branch|e194aeeaa582d6a6|206ce93b3790e30c|a7bc43ba2d359d88|490357046||t19836.5780760268s|2783a0b288bff409|1201608|qs|local|list|select_time_periods||0.42|| -select_time_periods_eb27e515|branch|b51ba8c0de00e056|206ce93b3790e30c|734b23e167efb3b6|1116365135||t19836.6221384014s|5cc80c0464196ae6|1789|qs|local|list|select_time_periods||0.18|| -select_within_circle_radius|function|880681aea06f4662||||||||||||||| -select_within_radius|pattern|1bbeb1522cf7f38f|b43ee3d813fbfa23||-523127267||||0|qs|local|list||select_within_radius_730aa92e|0|| -select_within_radius_1b92f1d5|branch|597c823448e8ec03|b43ee3d813fbfa23|7435537d80f25fda|1497692718||t19836.6097774601s|80c0be946e02aafd|1796|qs|local|list|select_within_radius||0.19|| -select_within_radius_32d9e048|branch|f9ee84b7905152e5|b43ee3d813fbfa23|30af0d905ff55610|1830010867||t19836.5780953834s|9d27dbe475bb2b9d|1194195|qs|local|list|select_within_radius||0.28|| -select_within_radius_37bac648|branch|f9ee84b7905152e5|b43ee3d813fbfa23|8c9866c98b7d59aa|-1003651249||t19836.5938836525s|9d27dbe475bb2b9d|1194195|qs|local|list|select_within_radius||0.29|| -select_within_radius_39e75cec|branch|597c823448e8ec03|b43ee3d813fbfa23|c13d159d3354fcc8|-1811556608||t19836.6221418979s|80c0be946e02aafd|1796|qs|local|list|select_within_radius||0.21|| -select_within_radius_538419f2|branch|f9ee84b7905152e5|b43ee3d813fbfa23|509018c7122b1cee|611654093||t19836.5938778636s|9d27dbe475bb2b9d|1194195|qs|local|list|select_within_radius||0.28|| -select_within_radius_6635b64e|branch|597c823448e8ec03|b43ee3d813fbfa23|a78a212b997c9035|-1937567145||t19836.6103693475s|80c0be946e02aafd|1796|qs|local|list|select_within_radius||0.19|| -select_within_radius_6a384fb1|branch|f9ee84b7905152e5|b43ee3d813fbfa23|30cd8dca9685b851|-273477156||t19836.6212770526s|9d27dbe475bb2b9d|1194195|qs|local|list|select_within_radius||0.3|| -select_within_radius_730aa92e|branch|f9ee84b7905152e5|b43ee3d813fbfa23|d58b5b6016a3cc70|1596416445||t19836.6212829376s|9d27dbe475bb2b9d|1194195|qs|local|list|select_within_radius||0.29|| -select_within_radius_75edd584|branch|f9ee84b7905152e5|b43ee3d813fbfa23|0bd870f6cbcd77c1|336962899||t19836.5780894524s|9d27dbe475bb2b9d|1194195|qs|local|list|select_within_radius||0.32|| -select_within_time_periods|function|2798499bd63b690b||||||||||||||| -target_dir|object|5289a857edb685f1||||||||||||||| +mas_counts_sovon_files|pattern|d05dd6ed5800bb4f|c52338d7124b0a05||1920956259||||24420334|file|local|vector||mas_counts_sovon_files_4776d7dc|0|| 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+remove_double_counts_2183673c|branch|33d4032f50d2b5ed|56d403ffe2f51374|120e9624994e724f|-1583060927||t19836.6334707344s|d83934c08084e74c|1195980|qs|local|list|remove_double_counts||0.25|| +remove_double_counts|pattern|ce670e4fc993ec75|56d403ffe2f51374||-48525810||||1195980|qs|local|list||remove_double_counts_2183673c|0.25|| +remove_subspecies_names_8033c49b|branch|35f7dbbf56f35d05|6192e8e36bfb46d7|d6984430fdb56526|425039760||t19836.6334751919s|ca0af1b203c1cf95|1195963|qs|local|list|remove_subspecies_names||0.14|| +remove_subspecies_names|pattern|fd8ec86a8f1eafb1|6192e8e36bfb46d7||1657860091||||1195963|qs|local|list||remove_subspecies_names_8033c49b|0.14|| +add_predator_variable_fab8aebd|branch|b1d6101a48661ce9|e1c93a06d9f6d4cb|6d94daf6feaabdba|-1267021414||t19836.6334798554s|448d33d82c53cd6c|1211653|qs|local|list|add_predator_variable||0.16|| +add_predator_variable|pattern|c711edf6e40245ae|e1c93a06d9f6d4cb||-1919973047||||1211653|qs|local|list||add_predator_variable_fab8aebd|0.16|| +mas_data_clean|stem|096fa44bcce83c2b|c1c9cd3b3ad87047|43644c6618e3ad51|-1942276229||t19836.6334834708s|7f547d7553c65753|1235598|qs|local|vector|||0.06|| From 00e2457da62807d390da011248bf79ee4eb31868 Mon Sep 17 00:00:00 2001 From: wlangera Date: Tue, 23 Apr 2024 17:15:40 +0200 Subject: [PATCH 09/12] use glimpse instead of visnetwork --- source/targets/data_preparation/README.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/source/targets/data_preparation/README.Rmd b/source/targets/data_preparation/README.Rmd index 8260552..898df82 100644 --- a/source/targets/data_preparation/README.Rmd +++ b/source/targets/data_preparation/README.Rmd @@ -95,6 +95,6 @@ Bij het toevoegen van een nieuwe dataset van een jaar, zal de pipeline bijgevolg De volledige pipeline ziet er als volgt uit: ```{r} -targets::tar_visnetwork() +targets::tar_glimpse() ``` From 7e046cc713515e787cb0d9f3993d10fd88733c98 Mon Sep 17 00:00:00 2001 From: wlangera Date: Wed, 24 Apr 2024 10:29:05 +0200 Subject: [PATCH 10/12] qgis version --- source/targets/data_preparation/README.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/source/targets/data_preparation/README.Rmd b/source/targets/data_preparation/README.Rmd index 898df82..9435844 100644 --- a/source/targets/data_preparation/README.Rmd +++ b/source/targets/data_preparation/README.Rmd @@ -39,7 +39,7 @@ knitr::opts_chunk$set(echo = TRUE) Als alles goed gaat, worden nu alle data waar je toegang toe hebt gedownload (dit kan even duren). Dit zijn de zogenaamde bezoekstippen. -## QGIS v3.26 +## QGIS v3.26-3.28 1. een account aanmaken via From a0e082ce586ad9d6848619be7f9c415ee295542b Mon Sep 17 00:00:00 2001 From: wlangera Date: Wed, 24 Apr 2024 11:00:18 +0200 Subject: [PATCH 11/12] clarify sql query --- source/targets/data_preparation/README.Rmd | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/source/targets/data_preparation/README.Rmd b/source/targets/data_preparation/README.Rmd index 9435844..5d97572 100644 --- a/source/targets/data_preparation/README.Rmd +++ b/source/targets/data_preparation/README.Rmd @@ -30,7 +30,7 @@ knitr::opts_chunk$set(echo = TRUE) 1. Klik op verbinden 1. Selecteer de laag `ms:viewpoints` - - Vraag een query aan voor data van het nieuwe jaar, bv.: `SELECT * FROM viewpoints WHERE jaar = 2024` + - Vraag een query aan ('Query maken') voor data van het nieuwe jaar, bv.: `SELECT * FROM viewpoints WHERE jaar = 2024` 1. Vink het boxje aan 'Alleen objecten bevragen die het huidige zichtbare bereik overlappen' 1. Klik op toevoegen 1. Geef je gebruikersnaam en paswoord @@ -60,7 +60,7 @@ Dit zijn de zogenaamde bezoekstippen. 1. Klik op Verbinden 1. Geef je gebruikersnaam en paswoord en kik op ok 1. Selecteer de laag `ms:viewpoints` - - Vraag een query aan voor data van het nieuwe jaar, bv.: `SELECT * FROM viewpoints WHERE jaar = 2024` + - Vraag een query aan ('Query maken') voor data van het nieuwe jaar, bv.: `SELECT * FROM viewpoints WHERE jaar = 2024` 1. Vink het boxje aan 'Alleen objecten bevragen die het huidige zichtbare bereik overlappen' 1. Wijzig Coördinaten Referentiesysteem naar EPSG:28992 1. Klik op toevoegen @@ -80,7 +80,7 @@ Wanneer alle data gedownload zijn, kan je deze laag exporteren: Klik op OK (dit kan even duren). Sla het geojson-bestand op in de folder `mbag-mas/data/mas`. -1. De finale export die je wilt gebruiken voor data preparatie en latere analyses sla je op in een folder met als naam `JAAR` onder `C:/R/git_repositories/mbag-mas/source/targets/data_preparation/data`. +1. De finale export die je wilt gebruiken voor data preparatie en latere analyses sla je op in een folder met als naam `JAAR` onder `mbag-mas/source/targets/data_preparation/data`. Elke folder mag slechts 1 bestand hebben met de data van dat jaar (zie verder). # Verwerking van de data @@ -97,4 +97,3 @@ De volledige pipeline ziet er als volgt uit: ```{r} targets::tar_glimpse() ``` - From db3ed07d4c2f562db5f4872d60ea65eec071f9ec Mon Sep 17 00:00:00 2001 From: wlangera Date: Wed, 24 Apr 2024 11:08:40 +0200 Subject: [PATCH 12/12] do not create row names when rbinding --- source/targets/data_preparation/_targets.R | 2 +- .../data_preparation/_targets/meta/meta | 88 ++++++++++++------- 2 files changed, 55 insertions(+), 35 deletions(-) diff --git a/source/targets/data_preparation/_targets.R b/source/targets/data_preparation/_targets.R index bdf6d34..d7b8146 100644 --- a/source/targets/data_preparation/_targets.R +++ b/source/targets/data_preparation/_targets.R @@ -139,7 +139,7 @@ list( name = mas_data_clean, command = do.call( what = rbind.data.frame, - args = add_predator_variable + args = c(add_predator_variable, make.row.names = FALSE) ) ) ) diff --git a/source/targets/data_preparation/_targets/meta/meta b/source/targets/data_preparation/_targets/meta/meta index 548b4ee..329a8e4 100644 --- a/source/targets/data_preparation/_targets/meta/meta +++ b/source/targets/data_preparation/_targets/meta/meta @@ -1,39 +1,59 @@ name|type|data|command|depend|seed|path|time|size|bytes|format|repository|iteration|parent|children|seconds|warnings|error -target_dir|object|5289a857edb685f1 -select_within_circle_radius|function|880681aea06f4662 -select_within_time_periods|function|2798499bd63b690b -kraaiachtigen_f|function|32a6f93504fb3f7a -roofvogels_f|function|ff0ef1f62c67a283 -amersfoort_to_lambert72|function|7a05a501641027b3 -.Random.seed|object|c7a7455c02ed5227 -process_double_counted_data|function|705fe098ec314f30 -paths_to_counts_sovon|function|3dfadc517ce46981 -mbag_dir|object|73add2da6d24990f -adjust_subspecies_names_nl|function|50a4c7e8d7a82397 -path_to_samples|function|5ecc4024b743a014 -predatoren_f|function|febc8f3bf40ecb7d 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+select_species_groups_f7e0a6a0|branch|f9ee84b7905152e5|3f1e242af19e665d|18248565ac075282|824669762||t19837.3755272638s|9d27dbe475bb2b9d|1194195|qs|local|list|select_species_groups||0.02|| +select_time_periods|pattern|7826a632a7f2449b|206ce93b3790e30c||291324708||||2247642|qs|local|list||select_time_periods_106885d3*select_time_periods_29eeb0e5|0.59|| select_time_periods_00ee06b7|branch|e194aeeaa582d6a6|206ce93b3790e30c|2e587d1043c214a5|1334375700||t19836.6334562646s|2783a0b288bff409|1201608|qs|local|list|select_time_periods||0.52|| -select_time_periods|pattern|35f1b085c884b08e|206ce93b3790e30c||291324708||||1201608|qs|local|list||select_time_periods_00ee06b7|0.52|| +select_time_periods_106885d3|branch|06c7e3bf807396d0|206ce93b3790e30c|20ba66030adc44e5|195757004||t19837.3755096047s|4920a3c8cbb29c0c|1046034|qs|local|list|select_time_periods||0.33|| +select_time_periods_29eeb0e5|branch|e194aeeaa582d6a6|206ce93b3790e30c|83e2769cddc8e49b|-1029364792||t19837.3755147218s|2783a0b288bff409|1201608|qs|local|list|select_time_periods||0.26|| +select_within_circle_radius|function|880681aea06f4662||||||||||||||| +select_within_radius|pattern|87eb19e22f8fb771|b43ee3d813fbfa23||-523127267||||2221551|qs|local|list||select_within_radius_dcff1891*select_within_radius_2565ae04|0.38|| +select_within_radius_2565ae04|branch|f9ee84b7905152e5|b43ee3d813fbfa23|010a05c2966bd8d0|-237587632||t19837.3755230418s|9d27dbe475bb2b9d|1194195|qs|local|list|select_within_radius||0.19|| select_within_radius_730aa92e|branch|f9ee84b7905152e5|b43ee3d813fbfa23|d58b5b6016a3cc70|1596416445||t19836.6334621581s|9d27dbe475bb2b9d|1194195|qs|local|list|select_within_radius||0.29|| -select_within_radius|pattern|1bbeb1522cf7f38f|b43ee3d813fbfa23||-523127267||||1194195|qs|local|list||select_within_radius_730aa92e|0.29|| -select_species_groups_9005462e|branch|f9ee84b7905152e5|3f1e242af19e665d|653a67f1416430f0|1024928494||t19836.6334651819s|9d27dbe475bb2b9d|1194195|qs|local|list|select_species_groups||0.03|| -select_species_groups|pattern|ffbbc3442f1203be|3f1e242af19e665d||-1185638444||||1194195|qs|local|list||select_species_groups_9005462e|0.03|| -remove_double_counts_2183673c|branch|33d4032f50d2b5ed|56d403ffe2f51374|120e9624994e724f|-1583060927||t19836.6334707344s|d83934c08084e74c|1195980|qs|local|list|remove_double_counts||0.25|| -remove_double_counts|pattern|ce670e4fc993ec75|56d403ffe2f51374||-48525810||||1195980|qs|local|list||remove_double_counts_2183673c|0.25|| -remove_subspecies_names_8033c49b|branch|35f7dbbf56f35d05|6192e8e36bfb46d7|d6984430fdb56526|425039760||t19836.6334751919s|ca0af1b203c1cf95|1195963|qs|local|list|remove_subspecies_names||0.14|| -remove_subspecies_names|pattern|fd8ec86a8f1eafb1|6192e8e36bfb46d7||1657860091||||1195963|qs|local|list||remove_subspecies_names_8033c49b|0.14|| -add_predator_variable_fab8aebd|branch|b1d6101a48661ce9|e1c93a06d9f6d4cb|6d94daf6feaabdba|-1267021414||t19836.6334798554s|448d33d82c53cd6c|1211653|qs|local|list|add_predator_variable||0.16|| -add_predator_variable|pattern|c711edf6e40245ae|e1c93a06d9f6d4cb||-1919973047||||1211653|qs|local|list||add_predator_variable_fab8aebd|0.16|| -mas_data_clean|stem|096fa44bcce83c2b|c1c9cd3b3ad87047|43644c6618e3ad51|-1942276229||t19836.6334834708s|7f547d7553c65753|1235598|qs|local|vector|||0.06|| +select_within_radius_dcff1891|branch|482c066fc0b0f032|b43ee3d813fbfa23|0d8a75fc941e0264|1251980147||t19837.3755189017s|d12ae4d089c90245|1027356|qs|local|list|select_within_radius||0.19|| +select_within_time_periods|function|2798499bd63b690b||||||||||||||| +target_dir|object|5289a857edb685f1|||||||||||||||