From 9e9668d5b4b66cd67777c271db4d9f052dd5134a Mon Sep 17 00:00:00 2001 From: Damiano Oldoni Date: Wed, 22 Nov 2023 17:41:50 +0100 Subject: [PATCH] Add 12th pipeline and improve spaces --- README.md | 26 ++++++++++++++------------ 1 file changed, 14 insertions(+), 12 deletions(-) diff --git a/README.md b/README.md index 62d6ace5e..63e38f10b 100644 --- a/README.md +++ b/README.md @@ -36,10 +36,11 @@ In order to calculate an emergency index, we take into account: 1. number of occurrences per year, or simply _occurrences_ 2. area of occupancy (AOO), or simply _occupancy_ -The workflow is divided in two steps: +The workflow is divided in three steps: -1 [Assessing emerging status of alien species](https://trias-project.github.io/indicators/07_occurrence_indicators_modelling.html) +1. [Assessing emerging status of alien species](https://trias-project.github.io/indicators/07_occurrence_indicators_modelling.html) 2. [Ranking species by emerging status](https://trias-project.github.io/indicators/08_ranking_emerging_status.html) +3. [Assess the taxonomic distribution of emerging species](https://trias-project.github.io/indicators/12_taxonomic_distribution_emerging_species.html) We work with GAM (Generalized Additive Models) and decision rules to assess the emerging status of a species. @@ -77,21 +78,22 @@ The repository structure is based on [Cookiecutter Data Science](http://drivenda │ | ├── utm_1_bel : Belgian reference grid of European Environmental Agency (EEA) at 1km2 resolution │ | ├── utm_10_bel : Belgian reference grid of European Environmental Agency (EEA) at 10km2 resolution │ | ├── utm_100_bel : Belgian reference grid of European Environmental Agency (EEA) at 100km2 resolution -│ | └── utm_5_bel : Belgian reference grid at 5km2 resolution created by INBO +│ | └── utm_5_bel : Belgian reference grid at 5km2 resolution created by INBO │ └── src │ ├── gbif_download.Rmd : Script to trigger and verify a GBIF occurrence download │ ├── 01_get_data_input_checklist_indicators.Rmd : Script to manipulate taxonomic data from the Global Register of Introduced and Invasive Species - Belgium │ ├── 02_indicator_introductions_per_year.Rmd : Script to generate graphs with number of new introduced species per year -│ ├── 03_indicator_cumulative_number.Rmd: Script to generate graphs with cumulative number of introduced species per year -│ ├── 04_indicator_pathways.Rmd : Script to generate tables with pathways of introduction -│ ├── 05_occurrence_indicators_preprocessing.Rmd : Script to produce time series from the occurrence cube -│ ├── 06_occurrence_indicators_appearing_taxa.Rmd : Find appearing and reappearing taxa in the last years -│ ├── 07_occurrence_indicators_modelling.Rmd : Apply GAM and decision rules models to assess partial emerging scores -│ ├── 08_ranking_emerging_status.Rmd : Rank alien taxa based on their emerging status derived by the emerging scores -│ ├── 09_define_overlay_grid_belgium_with_protected_areas.Rmd : Visualize Belgian protected areas, superimpose the EEA reference grid and the protected areas -│ ├── 10_occurrence_species_protected_areas_level.Rmd : Assess number of observations, area of occupancy, coverage of Belgian protected areas for all species and year -│ └── 11_status_alien_species_in_protected_areas.Rmd : to find number of alien taxa and observations in protected areas and number of protected areas each alien taxon is present +│ ├── 03_indicator_cumulative_number.Rmd : Script to generate graphs with cumulative number of introduced species per year +│ ├── 04_indicator_pathways.Rmd : Script to generate tables with pathways of introduction +│ ├── 05_occurrence_indicators_preprocessing.Rmd : Script to produce time series from the occurrence cube +│ ├── 06_occurrence_indicators_appearing_taxa.Rmd : Script to find appearing and reappearing taxa in the last years +│ ├── 07_occurrence_indicators_modelling.Rmd : Script to apply GAM and decision rules models to assess partial emerging scores +│ ├── 08_ranking_emerging_status.Rmd : Script to rank alien taxa based on their emerging status derived by the emerging scores +│ ├── 09_define_overlay_grid_belgium_with_protected_areas.Rmd : Script to visualize Belgian protected areas, superimpose the EEA reference grid and the protected areas +│ ├── 10_occurrence_species_protected_areas_level.Rmd : Sript to assess number of observations, area of occupancy, coverage of Belgian protected areas for all species and year +│ ├── 11_status_alien_species_in_protected_areas.Rmd : Script to find number of alien taxa and observations in protected areas and number of protected areas each alien taxon is present +│ └── 12_taxonomic_distribution_emerging_species.Rmd : Script to produce summary tables and graphs about the taxonomic distribution of the species labelled as emerging in 07_occurrence_indicators_modelling.Rmd ``` ## Contributors