CAPFITOGEN3 local mode

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:

R (4.2.2. is the last version published for 09/03/2023): https://cran.r-project.org/bin/windows/base/

RStudio desktop (please choose the free version): https://rstudio.com/products/rstudio/download/#download

Be aware that some R packages requireb by CAPFITOGEN3 tools will attempt to install (if not already installed) at the time of using each tool (it may delay the first run of each tool) and the latest version of R may not support older versions of the packages.

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 07/03/2023)

to install it locally on their PC. The user will obtain a file called ‘CAPFITOGEN3.zip’ (1.9 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.

Finally, the user needs to download the file ‘scripts.zip’ (249 KB) from here. (Last update 07/03/2023)

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.

When using CAPFITOGEN3 (whatever tool or parameters) scripts in RStudio, note these scripts are encoded in UTF-8 and RStudio by default will try to open them as if they were encoded in ISO-8859-1. However you should not have problems to display them following these directions: open any CAPFITOGEN3 script in RStudio (since RStudio is configured to open scripts in ISO-8859-1 code by default, not a single line will be displayed in the text editor tab). Then go to the option “File – Reopen with Encoding…” and in the popup menu for encoders select “UTF-8″, and please do not forget to click on the option “Set as default encoding for source files” and finally click on the “OK” button. Immediately the script should appear in the text editor tab showing its lines.

 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.

Working with R 3.6.3 version

If you wish it, you can work CAPFITOGEN3 tools under the R version most of tools were designed. If so, you have to download the  3.6.3 version from here:

R 3.6.3: https://cran.r-project.org/bin/windows/base/old/3.6.3/

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.