The CAPFITOGEN3 tools have been updated

This week, an update of the scripts (or code lines) for the CAPFITOGEN3 tools has been made available to users, featuring several new developments.

This update was partly necessary because the R packages known as rgdal, rgeos, and maptools, which are very important for the functioning of many tools, were retired from R. Their functions had to be replaced by similar ones provided by other R packages. Previously, users had to add the old or deprecated R packages to their local R installation, which created considerable complexity and errors in the installation and functioning of both R and the CAPFITOGEN3 tools. For this reason, it was also necessary to work with older versions of R, not the most current one, which also caused problems.

Thus, several advantages of the newly updated version of CAPFITOGEN3 can be listed. Among them:

• Now, the scripts can work with the latest version of R available or any relatively recent version that the user has installed on their computer.
• To use the CAPFITOGEN3 scripts, it is only necessary to install R and run the scripts. An initial part of each script will check if the required packages are already installed, and if they are not found, it will download and install the necessary packages for the correct functioning of each tool.
• The scripts have been adjusted to perform the same well-known processes of each tool, without issues caused by the deprecation of the rgdal, rgeos, and maptools packages.

Additionally, the GEOQUAL tool has been adjusted in two ways: updating the previous GEOQUAL tool and introducing a new one tool to perform the same georeferencing quality analysis, but with significant advantages over the original. Description about these new features of GEOQUALv2 (as the new GEOQUAL tool is called) will be published soon on the CAPFITOGEN3 website. It is important to note that the inclusion of the new GEOQUALv2 has increased the size of the .zip file that interested users need to download, from 2.9 GB to almost 6.1 GB.

Finally, since there has been no evidence of use of modela, mcompare, and selecVIF tools by users over the last 8 years since their launch, these have been removed from the toolbox, to make the installer slightly lighter in view of the increase in GB due to the new GEOQUALv2.

We hope that all CAPFITOGEN3 users benefit from this major update of the toolbox. This effort to update the CAPFITOGEN3 tools and make them available to support agrobiodiversity conservation activities has been partially made possible thanks to the BioDT (Biodiversity Digital Twins) project (https://biodt.eu/).