README.md

In rijaf-iri/CDT: Climate Data Tools

Climate Data Tools

Climate Data Tools CDT is a set of utility functions for meteorological data quality control, homogenization and merging station data with satellite and others proxies such as reanalysis, all functions are available in the GUI mode.

CDT installation on Windows

1) Install R

Go to the CRAN website CRAN. Then click on the link Download R for Windows and base. Download the latest version of R. Install the downloaded file (example: R-4.3.0-win.exe). Perform a default installation (Just click on Next).

CDT requires R version 4.0.0 or higher. It is recommend to have the latest version of R.

2) Install Rtools

Go to the CRAN website CRAN. Then click on the link Download R for Windows and Rtools. Download the recommended version of Rtools compatible with your R version. Install the downloaded file. Follow the installation instructions displayed on the page.

3) Install CDT

Open R and install devtools package with:

install.packages("devtools")

Now, you can install the the development version of CDT from GitHub with:

library(devtools)
install_github("rijaf-iri/CDT")

CDT installation on MacOS X

1) Install XQuartz

Type XQuartz in Apple's search, if you don't find it, that means XQuartz is not installed yet. It's better to update XQuartz to the latest version if it is already installed.

Download and install it from https://www.xquartz.org.

Restart your computer.

2) Install Tcl/Tk

Check Tcl/Tk installation

Check if the Tcl/Tk libraries are already installed in your computer. Open a terminal and run the following command:

echo 'puts $tcl_library;exit 0' | tclsh

If Tcl/Tk libraries are installed in your computer, you should get the path to the Tcl library like this: /usr/local/lib/tcl8.6.

If Tcl/Tk libraries are not yet installed in your computer, you can install ActiveTcl®. Go directly to the ActiveTcl® installation below.

Check Tktable package

Check if the package Tktable is installed. Run the following command from terminal:

echo 'puts [package require Tktable];exit 0' | tclsh

If the package is installed, you should have the version number of the package. If Tktable is not installed, you can download it from here.

Change to the directory where you downloaded Tktable archive file.

cd ~/path/to/Tktable/archive

Uncompressed the archive file.

tar -zxvf Tktable2.10.tar.gz

This will create a subdirectory Tktable2.10 with all the files in it. Change to this directory.

cd Tktable2.10

The default installation path of Tktable is under /usr/local. If the Tcl Library Path directory is under this directory, you can install Tktable by default using the following commands:

./configure
make install

If Tcl Library Path directory is anywhere else. Check the auto_path global variable using the following command

echo 'puts $auto_path;exit 0' | tclsh

You should have a list of directories like this: /usr/local/lib/tcl8.6 /usr/local/lib. You need to set the --prefix option of configure

./configure --prefix=/usr/local
make install

Check BWidget package

Check if the package BWidget is installed. Run the following command from terminal:

echo 'puts [package require BWidget];exit 0' | tclsh

If the package is installed, you should have the version number of the package. If BWidget is not installed, you can download it from here. Unzipped the file bwidget-1.9.12.zip and copy it under the Tcl Library Path directory. Copy the bwidget directory bwidget-1.9.12 under one of the auto_path global variable directories.

Note If you install Tktable and BWidget anywhere else, remember the path you put the packages, you will need it when you install CDT.

Install ActiveTcl®

Download ActiveTcl® from https://www.activestate.com/products/activetcl/downloads/.

ActiveTcl® executables will be installed (wish, tclsh and tkcon) in /usr/local/bin and the library will be put in /usr/local/lib/tcl8.6 or /usr/local/lib/tcl8.5 depending on the version.

Tktable will be put in /Library/Tcl/teapot/package/macosx10.5-i386-x86_64/lib/Tktable2.11 and BWidget in /Library/Tcl/teapot/package/tcl/lib/BWidget1.9.8.

3) Install GDAL/GEOS/PROJ.4

Download and install GDAL binaries from http://www.kyngchaos.com/software/frameworks. Install the latest version of GDAL Complete.

GDAL will be installed in /Library/Frameworks/GDAL.framework,

GEOS in /Library/Frameworks/GEOS.framework

and PROJ in /Library/Frameworks/PROJ.framework.

The configuration files are located in

GEOS: /Library/Frameworks/GEOS.framework/unix/bin/geos-config

GDAL: /Library/Frameworks/GDAL.framework/unix/bin/gdal-config

And PROJ include and lib are located in /Library/Frameworks/PROJ.framework/unix/include and /Library/Frameworks/PROJ.framework/unix/lib respectively.

Remember these paths, you will need them when you install the package rgdal and rgeos on R.

4) Install R

Download and install R binary for your MacOS X version from https://cran.r-project.org/bin/macosx

CDT requires R version 4.0.0 or higher. We recommend that you have the latest version of R.

5) Install CDT

Open R and install devtools package with:

install.packages("devtools")

Now, you can install the development version of CDT from GitHub with:

library(devtools)
install_github("rijaf-iri/CDT")

If you get a warning message telling you that Tktable or BWidget not found, you need to edit CDT's local configuration for Tcl: ~/Library/Application Support/CDT/config/Tcl_config.json. Go to the MacOS configuration and change Tktable.auto or Bwidget.auto to false, then set the full path to Tktable or BWidget directory with Tktable.path or Bwidget.path, as shown in the following example:

"MacOS": {
    "Tktable.auto": false,
    "Tktable.path": "/Library/Tcl/teapot/package/macosx10.5-i386-x86_64/lib/Tktable2.11",
    "Bwidget.auto": false,
    "Bwidget.path": "/Library/Tcl/teapot/package/tcl/lib/BWidget1.9.8"
  },

After editing Tcl_config.json, save it. Open a new R session and load and start CDT.

CDT installation on Ubuntu

1) Install Tcl/Tk

Check if the Tcl/Tk libraries are already installed in your computer, make sure that the *-dev packages are installed. If not, you can install it with:

sudo apt-get install tk-dev tcl-dev

Check if the Tcl package Tktable is installed. If it is not installed, you can download it from here.

Check if the Tcl package BWidget is installed. If it is not installed, you can download it from here.

Note See MacOS X Tktable and BWidget installation.

2) Install GDAL/OGR

Add the PPA to your sources

sudo add-apt-repository ppa:ubuntugis/ppa
sudo apt-get update && sudo apt-get upgrade

Install GDAL

sudo apt-get install gdal-bin libgdal-dev

Verify the installation with

ogrinfo

Get the installation path of gdal-config and geos-config. Save these paths somewhere, you will need it later when installing the R packages rgdal and rgeos.

3) Install NetCDF

sudo apt-get install netcdf-bin libnetcdf-dev

4) Install R

Install R if not installed yet. Add the R repository to your sources

CDT requires R version 4.0.0 or higher. We recommend that you have the latest version of R, this implies that you have to install R from source.

sudo add-apt-repository "deb http://cran.rstudio.com/bin/linux/ubuntu $(lsb_release -sc)/"
sudo apt-get update

Add GPG key

sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9

Install R

sudo apt-get install r-base r-base-dev

5) Install R package ncdf4

sudo apt-get install r-cran-ncdf4

You can install ncdf4 package with:

## edit the path
nc_config <- '/usr/bin/nc-config'

install.packages('ncdf4', type = "source",
        configure.args = paste0('--with-nc-config=', nc_config))

6) Install CDT

Open R and install devtools package with:

install.packages("devtools")

Now, you can install the development version of CDT from GitHub with:

devtools::install_github("rijaf-iri/CDT")

If you get a warning message telling you that Tktable or BWidget not found, you need to edit CDT’s local configuration for Tcl: ~/.local/CDT/config/Tcl_config.json Go to the Linux configuration and change Tktable.auto or Bwidget.auto to false, then set the full path to Tktable or BWidget directory with Tktable.path or Bwidget.path.

Usage

# Load  CDT library
library(CDT)

# Starting CDT
startCDT()

Updating CDT

To only update CDT without updating all dependencies packages, enter the following command on R console

if(packageVersion("devtools") >= "2.0.0"){
    devtools::install_github("rijaf-iri/CDT", dependencies = FALSE,
                              upgrade = FALSE, force = TRUE)
}else{
    devtools::install_github("rijaf-iri/CDT", dependencies = FALSE, 
                              upgrade_dependencies = FALSE, force = TRUE)
}

To update CDT and all dependencies packages, use

update.packages(ask = FALSE)
devtools::install_github("rijaf-iri/CDT")

rijaf-iri/CDT documentation built on July 3, 2024, 2:54 a.m.