This repository aims to store scripts used for information processing.
The primary purpose of this repository is to provide a centralized location for storing and managing scripts used in data and information processing. These scripts can address a variety of tasks, such as data analysis, format transformation, data cleaning, report generation, among others.
You can explore the scripts available in this repository to find those relevant to your information processing needs. If you wish to use any of the scripts, make sure to review the documentation and comments within the script to understand its functionality and requirements.
Bee species and their sp_codes are listed in the data/bee-sps.csv file. The
first objective is to create a plant checklist, which can be reviewed by a plant
taxonomy specialist. To achieve this, follow the script execution steps outlined
below.
flowchart TD
A("file: data/bee-sps.csv") --> B("download_interaction_data_from_globi.R")
B --> C("create_plant_checklist_by_bee.R")
D("Download country border from Natural Earth Data")
C --> E("add_country_to_checklist.R")
D --> |edit config.yml file with path|E
E --> F("create_plant_checklist_w_countries.R")
F --> G("output file: data/plant_checklist_w_countries.csv")
As a result of this workflow, a new file is expected in the data/ folder,
named plant_checklist_w_countries.csv. This file serves as a working document
for reviewing plant scientific names and assigning valid names if necessary.
Important
When reviewed the plant scientific names do not modify the target_taxon_name
column
It is necessary to integrate the reviewed information with the bee-plant
interaction files. To achieve this, execute the
join_bee_plant_list_with_valid_names.R script.
Finally, we should register the processed information on the SPECIES platform. The
scripts submit_network_analysis.R and submit_niche_analysis.R provide a CLI
to submit the analyses for each bee and print the link information where the
analysis could be explored. The link information should be later registered on
The Bee Tool. The scripts could be executed on a terminal as follows:
$ ./submit_network_analysis.R {sp_code}where sp_code is a species code as in data/bee-sps.csv.
Important
Submit scripts assumed that the plant reviewed file include the following
columns: Nombre Válido, Rango Taxonómico, and Nombre Válido.
If you have questions or need further information about this repository, you can contact Juan M Barrios juan.barrios@conabio.gob.mx.