diff --git a/README.md b/README.md index 35f71745bc6b5e4b05cdc2639c6b38e7d01dee01..e3aa5ea57899c5cef869d495fd302c3e1ed32ea7 100644 --- a/README.md +++ b/README.md @@ -17,7 +17,7 @@ This repository implements a species distribution modeling comparison study for The workflow is divided into several stages, each represented by scripts in the `R/` directory. Below is a summary of the key steps: ### 1. Data Preparation -Pre-processing of species-specific and environmental information for model fitting and results analysis. +Pre-process species-specific and environmental information for model fitting and results analysis. - **`01_01_range_preparation.R`**: Process species range maps and calculate range dissimilarity. - **`01_02_traits_preparation.R`**: Prepare species trait data and calculate functional distances. @@ -25,7 +25,7 @@ Pre-processing of species-specific and environmental information for model fitti - **`01_04_raster_preparation.R`**: Prepare environmental raster layers for modeling for data extraction. ### 2. Presence/Absence Data Processing -Querying of presence data from Symobio DB, sampling of absence data and initial exploration of the dataset. +Query presence data from Symobio DB, sample absence data, initial exploration of the dataset. - **`02_01_presence_data_preparation.R`**: Query species occurrence data from Symobio DB, extract environmental variables from raster files. - **`02_02_absence_data_preparation.R`**: Sample pseudo-absence points, extract environmental variables from raster files. @@ -41,6 +41,7 @@ Scripts for model fitting - **`03_04_modelling_msdm_rf.R`**: Fit multi-species distribution model (MSDM) based on Random Forest with species identity as factor. ### 4. Analysis and Reporting +Analyse modeling results - **`04_01_performance_report.qmd`**: Generate an interactive performance evaluation of implemented SDM algorithms. - **`04_02_publication_analysis.R`**: Explore results in depth, analyse @@ -59,5 +60,4 @@ Scripts for model fitting ## Additional Notes - Ensure that all required input data (e.g., range maps, raster files) is available in the expected directories. -- Outputs from each script are typically saved to disk and used as inputs for subsequent scripts. -- Refer to the README.md file for any additional project-specific instructions. \ No newline at end of file +- Outputs from each script are typically saved to disk and used as inputs for subsequent scripts. \ No newline at end of file diff --git a/renv.lock b/renv.lock index f26410cb14212625520b03936671b2e3ef081034..a2c88a34dae929bbef73bddfcfdc68ef45e01d85 100644 --- a/renv.lock +++ b/renv.lock @@ -1069,21 +1069,6 @@ ], "Hash": "33698c4b3127fc9f506654607fb73676" }, - "dismo": { - "Package": "dismo", - "Version": "1.3-16", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "Rcpp", - "methods", - "raster", - "sp", - "terra" - ], - "Hash": "5c8646b40ba69146afc070aaea9f893c" - }, "doBy": { "Package": "doBy", "Version": "4.6.24", @@ -1432,6 +1417,20 @@ ], "Hash": "afe1507511629f44572e6c53b9baeb7c" }, + "gam": { + "Package": "gam", + "Version": "1.22-5", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "foreach", + "methods", + "splines", + "stats" + ], + "Hash": "453698a6f7535fbb77841e8015b5ee57" + }, "gargle": { "Package": "gargle", "Version": "1.5.2", @@ -1454,6 +1453,19 @@ ], "Hash": "fc0b272e5847c58cd5da9b20eedbd026" }, + "gbm": { + "Package": "gbm", + "Version": "2.2.2", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "lattice", + "parallel", + "survival" + ], + "Hash": "17e2c9092ea23e84803fa07b62c5348a" + }, "generics": { "Package": "generics", "Version": "0.1.3", @@ -2659,6 +2671,19 @@ ], "Hash": "0595fe5e47357111f29ad19101c7d271" }, + "ranger": { + "Package": "ranger", + "Version": "0.17.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "Matrix", + "R", + "Rcpp", + "RcppEigen" + ], + "Hash": "9fe0f505fe36cac3207e0790d21b3676" + }, "rappdirs": { "Package": "rappdirs", "Version": "0.3.3", @@ -3098,18 +3123,6 @@ ], "Hash": "75940133cca2e339afce15a586f85b11" }, - "spatialEco": { - "Package": "spatialEco", - "Version": "2.0-2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "sf", - "terra" - ], - "Hash": "d0352030add66f0c73ff5d7473b7aef1" - }, "stringdist": { "Package": "stringdist", "Version": "0.9.12",