Download from internet

CAPFITOGEN tools (latest update) available through an internet download

For any interested in use the CAPFITOGEN tools (completely in english), the latest version can be downloaded from Google Drive service.

There are two available versions (1.2 and 2.0) with the following improvements in addition to features included in version 1.0 (released in March 2013):

  •  Easier system installation
  • Version 1.2 includes the following eight tools:
  1. TesTable: Detection and correction of errors and problems in the input tables.
  2. GEOQUAL:Performs quality assessment of geo-referenced passport data (collecting sites).
  3. ELC mapas: Provides maps of eco-geographical terrain characterization (ELC as acronym in English) which, for a given species, show adaptive scenarios for a country or region.
  4. Representa: Allows the user to analyze an eco-geographical representativeness of a given species within a germplasm collection.
  5. ECOGEO: An eco-geographical characterization of the germplasm collecting sites. The user can work with more than one hundred available variables.
  6. DIV mapas: Allows the user to obtain maps of eco-geographic, phenotypic and/or genotypic diversity, obtained by determining averaged ecogeographical, phenotypic or genotypic distances by neighborhood or influence zones, respectively.
  7. ColNucleo: Allows the user to obtain eco-geographical core collections from ELC maps (from “ELC mapas” tool).
  8. FIGS_R: Allows the user to obtain “FIGS” subsets by filtering method . Alternatively the user may use ELC maps (from “ELC mapas” tool) in order to balance the germplasm selection.Version 1.2 includes the following eight tools.
  • Version 2.0 includes two additional auxiliary tools:
  1. SelecVar:  It performs four different statistical analysis (Random forest, clustvarsel, bivariate correlations and principal component analysis) which can help to select ecogeographical variables in a objective way (without expert knowledge contribution). The list of selected variables should be subject of expert’s review (subjective-objective process) and the final list can be used in the ELC mapas tool.
  2. rLayer: This tool generates a new set of ecogeographical variables for geographic areas which can exceed countries boundaries (for the 105 available variables in CAPFITOGEN), cropping each “world” layer using the extent of the collecting/occurrence sites distribution (entered as passport data). Since layers set to be cropped is “world”, then available resolutions for the new set are 10×10 or 20×20 km. New set of layers will be available to work in other tools.
  • CAPFITOGEN tools v 2.0 will include three new in situ tool: Complementa (30/03/2015), Modela (19/01/2016) and Criteria (to be released in 2016) and two complementary auxiliary tools: Bfuture (19/01/2016) and Mcompare(19/01/2016):
  1. Complementa: Obtains coverage and complementarity analysis by cell or protected areas networks for a given territory. It also can combine ELC categories (from ELC map) with taxonomic information to perform ecogeographic-taxonomic complementarity analysis.
  2. SelecVIF (Beta version): This tool is designed to obtain the Variance Inflation Factor (VIF) values from a set of ecogeographical variables for modelling processes. SelecVIF is also able to perform a stepwise filtering process to identify a subset of variables with VIF values under a cutoff fixed by the user. Available from 02/10/2017. User manual will be realeased soon.
  3. Modela: Obtains Species Distribution Models (SDM) for presence only and presence –absence data, using about 11 different algorithms (including Random Forest, MaxEnt, GLM, GAM, etc.), 10 different evaluators (including Kappa, ROC, TSS, etc.), four ways to obtain pseudo-absences, six ways to assembly projections and offering model projections for present and future conditions in the same process. Modela is also capable to perform FIGS analysis (calibration method).
  4. Bfuture: Obtains bioclimatic projected layers for future conditions (under climate change scenarios) from worldclim portal, cropped according to the user’s presence data distribution/country and adapt them to CAPFITOGEN layer format.
  5. Mcompare: Compares SDM projections for present and future conditions (from Modela) to determine threats and/or new opportunities for the target species.
  6. Tzones (Beta version): This tool projects Ecogeographical Land Characterization (ELC) maps obtained using current (1950-2000) bioclimatic variables into ELC maps for future scenarios mantaining categories correspondency between current and future ELC maps. To do this, the tool uses a model (Random Forest) and bioclimatic variables projected under climate change conditions.  It also allows to perform germplasm transfer zone (GTZ) analysis in order to determine populations under threat because changes in their future ELC categories (adaptive scenarios) and other populations as potential sources of germplasm for replacement of those threatened populations. Avalilable from 06/10/2017. User manual will be realeased soon.
  • The tools are available in over 160 countries, two regions (Mesoamerica and South America), one single continent (Europe) and at global (“world”) scale.
  • User manual is included (with chapters for each tool) in Spanish and English and partially in Portuguese, with more complete and detailed documentation about the set of tools.
  • Excel formats for passport, external sources and characterization data, now completely in English (updated on 04/07/2014).

Please keep in mind that CAPFITOGEN tools work on Windows (Microsoft) operating system, as this is the most common operative system among technicians in Latin America.

Taking into account that these are large files to be downloaded, it is important to have access to broadband internet or at least a connection time long enough to complete the download. We expect from this download procedure to help speed up the distribution process and reach countries, programs, centers and/or universities much faster than via USB memory distributed by regular mail. This distribution procedure will be exclusively used to give support to users with no network access.

The instructions for the correct download and implementation of the tools’ installer are as follows:

1. Make sure you have ALZip file compression software, or similar software that can unzip files with .alz extension. Installer for ALZip software can be downloaded from the following address:

http://www.altools.com/ALTools/ALZip.aspx

(after the installation of ALZip, use the “trial version” option to have free access)

2. Go to the following websites to download the main package of the tools’ installer (no need to start session in Google to proceed with the download):

For CAPFITOGEN version 1.2:

https://drive.google.com/file/d/0B7JxjDasV98BaENjekZKcjRfSlk/edit?usp=sharing

(updated 27/11/2014)

Otherwise, if you want to install CAPFITOGEN version 2.0:

https://goo.gl/vsbVMZ

(updated 06/10/2017)

These files are about 2.6 Gb (each one), then download them may takes long times depending on the internet connection. There is available a lighter version which does not includes GEOQUAL tool and is only about  731 Mb. This version can be downloaded from this link:

Version 1.2:

https://drive.google.com/file/d/0B7JxjDasV98BTDRFbE9KSm1kVm8/edit?usp=sharing

(updated 27/11/2014)

Version 2.0:

https://goo.gl/Xa6QsB

(updated 06/10/2017)

3. Download the main package of the tools’ installer called CAPFITOGEN.alz / CAPFITOGEN2.alz for the complete toolkit version or CAPFITOGEN.zip / CAPFITOGEN2.zip for light version without GEOQUAL tool, on your hard or flash drive with enough free space. Please consider that CAPFITOGEN.alz / CAPFITOGEN2.alz or CAPFITOGEN.zip / CAPFITOGEN2.zip  files are  5.5 or 0.9 Gb decompressed respectively. To complete the downloading process, click on the “File” menu, then click “Download”. Sometimes a download interface might appear, in this case click on “Download anyway”.

4. Go to the following website to select and download the .alz file for the country or region you wish to be analyzed.

https://drive.google.com/folderview?id=0B-4W7NMFAn9cWjZRM0UxUmlBUWM&usp=sharing

(updated 02/04/2014)

Find the country or area you want to work from the available options. Once you find and select it, download the corresponding .alz file. If you click on the folder with the name of the country or region, a black layer will be displayed with the following message “Sorry, no preview is available”, click then on the blue “Download” button.

You can download as many files (countries/regions) as your drive allows. However, keep in mind that these files will eventually have to be decompressed, consequently, for large countries, you might require space enough to accommodate up to 10 Gb of uncompressed content.

Note: in order to use rLayer tool, you should download “world.alz” file and proceed as detailed in paragraph 6.

5. Unzip the file (downloaded in step 3) CAPFITOGEN.alz / CAPFITOGEN2.alz in the root of the hard or USB drive (eg C:\). The drive must have more than 6Gb of free space available.

Note: you might need even more space, depending on the country or area you want to work with.

If you selected the root of the C drive to locate the decompressed files, a new folder named “CAPFITOGEN” (version 1.2) or “CAPFITOGEN2″ (for version 2.0) should be created (if not, please create it manually). Thus the path always should look like:

C:\CAPFITOGEN

or

C:\CAPFITOGEN2

If you go into the decompressed folder (called “CAPFITOGEN” / “CAPFITOGEN2″), you should find several folders and files that form the main package of the installer.

6. Unzip the contents of the compressed files for the selected country or region (step 4) in the “rdatamaps” folder located inside the “CAPFITOGEN” / “CAPFITOGEN2″ folder that was created when you unzip ”CAPFITOGEN.alz” / ”CAPFITOGEN2.alz” file (step 5).

For in situ tools, polygons (packed on .RData files) which represent protected areas for each country or region from the World Database on Protected Areas (WDPA) should be downloaded from the following link:

http://goo.gl/2SWnvg

(updated 30/03/2015)

Once downloaded these .RData files have to be located on the “wdpa” folder in order to be used by Complementa and other in situ tools.

7. Make sure that the content of the compressed files for the selected countries/regions has been properly placed. If, for example, the main package of the tools’ installer (“CAPFITOGEN.alz” file) has been decompressed in C: \ and the selected country/region was Argentina, the resulting route in step 6 should be:

C:\CAPFITOGEN\rdatamaps\argentina

If you click on the “Argentina” folder, you should find two folders (“1×1″ and “5×5″), whose location routes would look as follows:

C:\CAPFITOGEN\rdatamaps\argentina\1×1

and

C:\CAPFITOGEN\rdatamaps\argentina\5×5

8. You can now proceed with the installation of the tools by clicking on CAPFITOGEN.exe file located into the CAPFITOGEN / CAPFITOGEN2 folder.

WARNING: If you have installed the version 1.2 and wish to upgrade to version 2.0, please close all CAPFITOGEN windows (browser and Tomcat virtual server) and any R session. Then please delete “rwin” folder located in your hard disk (usually C:/). After that, you can click on CAPFITOGEN.exe file and follow installing instructions. If you want to return to the previous version, repeat the above process and reinstall version 1.2 using the appropriate CAPFITOGEN.exe file.

Follow the installation instructions in the available user’s manual (CAPFITOGENtools.pdf) included in the folder “User_manual” from the installer or that you can download directly from:

https://goo.gl/Btaihm

(updated 01/19/2016)

Cover of the new user’s manual of the CAPFITOGEN tools version 2.0

Cover of the new user’s manual of the CAPFITOGEN tools version 2.0

9. If you have already downloaded and installed the tools previously (since March 2016) and just wish to upgrade the software, it is not necessary to download the complete tool package, just download the “x86.zip” file from the following link:

Version 1.2

https://drive.google.com/file/d/0B7JxjDasV98BSVR5RTUtUE9BSHc/edit?usp=sharing

(updated 27/11/2014)

Version 2.0

https://goo.gl/znJwK2

(updated 06/10/2017)

Once downloaded, the file should be unzipped in a temporary folder. A folder called “x86″ will then be created, replacing the existing folder in the same location, within the “CAPFITOGEN” / “CAPFITOGEN2″ tools folder. Once the substitution is completed, the user can access the new tools. For any replacement it is recommended to first remove the x86 folder (from CAPFITOGEN\x86 or CAPFITOGEN2/x86) and then paste the “x86″ folder (from the zip file).

The download of the x86 zip file is much faster than that of the tools main package, since “x86.zip” is only about 7% of the size of “CAPFITOGEN.alz” /”CAPFITOGEN2.alz” (175 Mb).

WARNING: Version 1.2 users should not replace x86 folder using x86.zip file for version 2.0. For upgrade the CAPFITOGEN tools version, please re-install following paragraphs 5, 6 and 8.

10. If you wish to use MaxEnt algorithm within Modela tool, you have to download first the “maxent.jar” file from:

https://www.cs.princeton.edu/~schapire/maxent/

and follow the instructions from the user manual.

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