Welcome to CAPFITOGEN3 local mode
Local mode is the most recent version of the tools. In this version, the user must download and install on their PC software associated with R and a set of folders and files to analyze information locally. Users only need to have an internet connection to download the software installers and data sets prepared for this version. Local mode has only been tested on Windows operating system, but it may work on other systems if the appropriate software installers are downloaded. Unlike version 2.0, CAPFITOGEN3 local mode does not use a web form interface, since the installation and operation of the virtual server connecting the interface with R caused problems to some users. For the new version, the user is presented with the scripts (programming lines) to configure and run the tools; however, it is not necessary to have any prior knowledge of R or its language to apply the scripts. The user configures each parameter through a script (as in the web form of version 2.0) to produce all the elements that the script of the corresponding tool requires to execute the functions and obtain the desired results. For more detailed information on how to use CAPFITOGEN3 local mode, please download the explanation here.
Steps to install CAPFITOGEN3 local mode
In summary, the user must download a set of folders and files necessary to run the tools, the scripts which are the core of CAPFITOGEN3, and the R and Rstudio installers. For local mode, this version also requires the user to download and install R and RStudio from the following links:
RStudio desktop (free version): https://rstudio.com/products/rstudio/download/#download
Once these programs are installed, the user must download the set of folders and files from
https://drive.google.com/file/d/19TE3H-_b2JD9Zl2aQy7pTThX_coDFo-m/view?usp=sharing (Last update 16/05/2022)
to install it locally on their PC. The user will obtain a file called ‘CAPFITOGEN3.zip’ (2 GB). When unzipping this file in a path on the hard drive (it is recommended that this is done directly to the root of the disk), a folder called ‘CAPFITOGEN3’ will appear. Within this folder, the user will find the complete set of folders and files necessary to run the tools.
Then, it is necessary to download the set of R packages required by the tool scripts. To do this, the user needs to download the file ‘library_forR3.6.3.zip’ (162 MB) from here. (Last update 17/01/2022)
After unzipping it, a folder called ‘library’ will appear, which should replace the folder with the same name located in the path where R was installed (in Windows OS it is usually the path C:\Program Files\R\R-3.6.3). To replace this folder, it is necessary to first remove the ‘library’ folder from the original R installation, and then copy and paste the ‘library’ folder that was downloaded. Then, the path to ‘library’ folder will be: …\Program Files\R\R-3.6.3\library, and to find, for example, the folder containing the files required for the package ‘ade4′ will be: …\Program Files\R\R-3.6.3\library\ade4. Please check that the location of the replaced folder ‘library’ meets these requirements.
Finally, the user needs to download the file ‘scripts.zip’ (249 KB) from here. (Last update 16/05/2022)
After unzipping this file, the folders with the parameter scripts (in Spanish and English) and the tool scripts will appear. The folders of scripts can be saved anywhere in the local drive. Just by double-clicking on any of the scripts in those folders (identified with the name of each tool), the user can start configuring the parameters and running the tool. For more details on how to use CAPFITOGEN3 local mode in RStudio, please download this file.
How to use Modela tool
The process of updating and improving the CAPFITOGEN tool scripts was carried out for all the tools except for Modela since this tool requires R version 3.1.2 (which can be downloaded from here), and the same set of R packages that CAPFITOGEN version 2.0 used (which can be downloaded here). Once you have opened R version 3.1.2 in RStudio and have replaced the ‘library’ folder of the original R 3.1.2 installation with the ‘library’ folder contained in the library_forR3.1.2.zip file, you will be able to perform processes using Modela. Trying to run this tool using a more recent version of R (such as R 3.6.3) will generate errors because of the biomod2 package.