Expl targets#7

Merged

EmmaCartuyvels1 merged 82 commits intomainfrom

Aug 26, 2025

Commits on Mar 4, 2025

Update names of pipelines
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Small aesthetic changes to layout markdowns
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Create functions to add observation cyclus and correct species names
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Add markdwon report for expl_ana_targets
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Update meta
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Commits on Mar 6, 2025

Change order of arguments
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Create list of analysed species in ABV, with scientific names
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Update species names so that they match in both data sets
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Extend pipeline
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Add plot
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Commits on Mar 9, 2025

Add function to add rareness category
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Add documentation
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Commits on Mar 10, 2025

Add additional comparisons
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Add code for debugging
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Add function to compare trends and functionality to keep category info in output
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Add "filter" to weigh data based on total observations in time periods
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Update meta
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Commits on Mar 11, 2025

Add trend comparison over cyclus
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Clean data reading
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Move file
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Functions imported from mbag-mas to find scientific name
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Update data name
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Update meta
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Apply filter 3 to both ABV and cube data
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Commits on Mar 17, 2025

projectId
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Test for species names
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Add titles to all plots indicating structured or unstructered data was used
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Add histogram for coordinata uncertainty
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Commits on Mar 24, 2025

Add 10km utm grid
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Load data aggregated at 10km² for comparison
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Fix text
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Commits on Mar 27, 2025

Fix error in settings of coordinate uncertainty, regenerate cubes
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Regenerate cube now that random grid desgination is fixed
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Commits on Apr 1, 2025

Add branching to pipeline for year/cycle and 1km/10km
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Simplify visnetwork
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Add ways to identify different branches data
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update meta
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Add filter for the correct data from the right branch of the pipeline
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Commits on Apr 7, 2025

Exclude fossil specimens and specimens living in collections
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Rerun pipeline
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Commits on Apr 11, 2025

Add identifiers for branching over dateset, time period and spatial resolution
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Change names for easier use in targets pipeline and turn randomisation off for ABV data
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Rewrite functions to work in the branched target pipeline
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Simplify pipeline with branching
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Update meta
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Small aesthetic changes
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Simplify pipeline for trend comparison
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.
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Rewrite tren comparison function to work in braching pipeline
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Update meta
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Add category to range_comp data
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Update meta
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First adaptations to new outputs from timeline, categories aren't correct yet
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Commits on Apr 14, 2025

Update meta
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Some more adjustments to deal with the branching
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Extract correct data from pipeline
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Commits on Apr 15, 2025

Get data from GBIF now that randomization is fixed, set uncertainty to 10km for coordinate uncertainty = NA as explained in the milestone report
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Get data from GBIF now that randomization is fixed
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Drop rows with NA's
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Make sure data is grouped (important when looking per cyclus)
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Update meta
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Adjust visualisation
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Update pipeline to include branching
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Update data reading functions
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Update meta
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Commits on Apr 16, 2025

coding style
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Commits on Apr 17, 2025

Add filter 4
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Update meta
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Add different visualisations, to do: limit shared data to best and worst correlations
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Commits on Apr 18, 2025

Script to generate figure for visualising the principles of the trend analysis
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Add plot layouts to use in report
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Commits on Aug 4, 2025

pull origin
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some coding style
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Merge pull request #6 from b-cubed-eu/review-ward
wlangera
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Fix checklist stuff
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Commits on Aug 5, 2025

Update data names and following dependencies
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Commits on Aug 12, 2025

Update README
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Remove old versions of code and move certain scripts
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Add documentation to README
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Checklist
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Add title
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Commits on Aug 26, 2025

Update README.md

EmmaCartuyvels1
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wlangera
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