Protcon pipeline

[jmlord]

• Add files via upload

• Add files via upload

• Add files via upload

• Delete pipeline protectedareas decade.json

• Delete pipeline HumanFootprint Colombia.json

• Update load_collection.R

• Add files via upload

• Add files via upload

• Find&replace with new io nomenclature

• Delete protcon_function.R

• Delete protcon_function.yml

• Add files via upload

• Add files via upload

• Add files via upload

• fix output

• fix output

jj

• Update protcon pipeline

• dpC por dpC_out

Cambio de nombre

• Update stutdyarea_to_wkt

Update of studyarea_to_wkt to be used in the workshop of July 31, 2023

• Draft yml dpc

Borrador en español de los textos yml del dpc

• prueba yml

esto es una pry¿ueba

• changes in yml dPC

Changes are made in the description of the .yml arguments for the dPC indicator, some sections are translated and some disclaimers are included.

• complete dPC index

A part of the routine that was missing for the dPC indicator, is inserted

• reclassify footprint

• studyarea_togrid Bloque2

• auk filter - auk zf update2

We have updated the auk_filter step script from the filter request (e.g. bbox- sp ) to the eBird zf table. The inputs and outputs were adjusted and tested in ByB with the documentation revised by Lina and Helena. The next step is to integrate the pipeline with the covars script step. However The inputs, ebd_file=ebd_CO_relDec-2022 and ebd_sampling_file=ebd_samp_Col_relDec-2022-002, should be manually loaded into the repository/00_auk_filter/input directory, as their size is too large to be accommodated in GIT. We could consider downsizing the dataset to a specific region in order to provide a functional pilot without going through that step.

• change in dPC routine

change the way of presenting the final results

• change in dPC

cambiar manera de presentar los resultados finales

• change in dPC

change the way of presenting the final results

• adjust reclassify

• Update pp.R

• auk_filter ajustado

Se ajusto auk_filter para salida en archivo zf. El input de entrada se configuro con la sp Setophaga fusca por temas de espacio. El scriot solo funciona con esa especie, debemos ajustar los big data para llamar la base de datos completa desde azure mediante un http request.

• dpc work

• 1ra version eBird Format

Rutina para preparar datos en el formato unmarked para que ingresen al modulo del modelo de ocupación

• ebird format run ByB

Codigo ebird format funcional

• drafts 25 08

• .yml protcon

Fixed some .yaml file attributes for the protcon prompt.

• update protcon test

pruebas protcon con diferentes unidades administrativas

• copy complete

• corrects

• ajustes protcon

• Protcon pipeline

• Update studyarea_to_WKT.yml

eliminate tab

• Syntax Error Correction

• Update spatial_to_DistanceMatrix.yml

• Update Protcon pipeline.json

• error validation correction

• syntax correction

• Update spatial_to_DistanceMatrix.R

• test

• add images documentation/delete README.html

add the images of the documentation in Rmd for the protcon pipeline

• partial commit of JM's comments

-included author, name and external link in script of protcon pipe -deleted .DS_Store -deleted scripts/.DS_Store -deleted README.html -deleted protcon_test -correct errors in .gpkg for studyarea_to_WKT and spatial_to_DistanceMatrix

• Update Colombian_protected_areas.gpkg

correct corrupt Colombian_protected_areas.gpkg file

• Update Colombian_protected_areas.gpkg

• modified readme

• Update README.md

• Update README.md

• Update README.md

• delete files

delete redundant files for the Protcon calculation

• correction of labels and adding fields in YMAL

All corrections and comment made by JM

• mimic commit from upstream/main

• Update Colombian_protected_areas.gpkg

reupload .gpkg corrupt file

• Allowing null values

• Minor modifications

• re-saved pipeline to get latest changes in yml

• replace corrupt images/change ounput .Rmd

• corrupts .gpkg

• last comments ProtCon

• protcon analysis typo

• external link

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[jmlord]

Straging version of this PR: https://github.com/GEO-BON/bon-in-a-box-pipelines/pull/81

[glaroc]

I made an API endpoint that returns a GEOJSON with all the WDPA protected for a given country:

https://geoio.biodiversite-quebec.ca/wdpa_country_geojson/?country_name=Nicaragua

Or for a state/province/region

https://geoio.biodiversite-quebec.ca/wdpa_state_geojson/?country_name=Colombia&state_name=Putumayo

So now we can make this pipeline general without the need for local files.

[glaroc]

Hi, I pushed a branch (https://github.com/GEO-BON/bon-in-a-box-pipelines/tree/protcon_wdpa) that is based on the WDPA data. So the idea is that this does not require local data, it fetches data from the API that returns both the protected areas within the state/province and the state/province polygon.

I wasn't sure what was the logic behind creating the spatial unit groups, so I left it as is. However, with the data I tested, it can create empty geometries that I am removing. Could someone at Humboldt who worked on this pipeline please try out the code from this branch and see if the results make sense ? @vicjulrin ?

[jmlord]

@jupinator see Guillaume's comment above