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inbo / esas

R package to access and process ESAS data
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6 functions #1

Open peterdesmet opened 2 months ago

peterdesmet commented 2 months ago

@nicolasvanermen has added 6 functions to the repository. These need to be assessed and reworked:

  1. Read_ESAS_Tables: read 4 ESAS tables and return as a list

  2. Transform_ESAS_Tables_4_Upload: convert the list of 4 tables (output of Read_ESAS_Tables) to a matrix format, so these can be uploaded to ICES

  3. Export_ESAS_Upload_Matrix: write output of Transform_ESAS_Tables_4_Upload

  4. Create_ESAS_Table: convert output from Read_ESAS_Tables to a single "mega" table

  5. Calculate_Detection_P_Ship_Based_Surveys: perform a distance analyses on the single "mega" table (output of Create_ESAS_Table) and a vector of species. This function only takes into account ship-based surveys that used the standard ESAS method and does not take in account any covariates regarding observation conditions. The output is a dataframe with species-specific detection probabilities

  6. Create_Seabird_Density_Cross_Table: create a crosstable with distance-corrected seabird densities per position for a vector of species based on the output of Create_ESAS_Table and Calculate_Detection_P_Ship_Based_Surveys

nicolasvanermen commented 1 month ago

A download of the ESAS data (executed 30/04/2024) is available at https://drive.google.com/drive/folders/1-aA_zshtZhsk1Tp2Cyd20o0VvLojxoXd

nicolasvanermen commented 1 month ago

A chunk of Belgian SAS data (that needed to be converted to a matrix format prior to upload to ICES DC): https://drive.google.com/drive/folders/1nwFBctE15CRrKd7d-y2xD_JOw042zHE-

nicolasvanermen commented 1 month ago

A dataframe with detection probabilities of 23 seabird species, calculated across the full ESAS database is available at https://drive.google.com/file/d/1JMPnYkujI4lqhB1omqey6iNv58zp0eh4/view?usp=drive_link