Package: itallic
ITALLIC: A tool for automatically identifying and correcting errors in location based plant breeding dataOne of the challenges of integrating plant breeding data to collectively analyze it with other sources of
data such as genotype, environment, management, and socioeconomic data is errors in location data. Collectively,
this data could be used to inform genetic predictive models for maize, wheat, and other crops. Typical errors in
plant breeding location data include flipped latitude and longitude values, missing negative signs, and, in some
cases, missing data. This tool, anIntegratedTool forAutomaticLatLongImputation
andCleaning (ITALLIC), automatically detects and corrects errors in location data and imputes missing values
for location-dependent data, such as region name.This page contains instructions for installing and uaing ITALLIC. These instructions assume familiarity working on aterminal.Pre-InstallationITALLIC is aPython 3application. In addition to Python 3, wehighly recommendalso installingConda. Clickthis linkfor more information on installingConda.Even though you do not need Conda to use ITALLIC, using Conda has some advantages that will make life easier. It will not only make installation for ITALLIC and other Python packages easy, it also enables use of conda environments. Use of environments is a good way to prevent conflicts that might arise when working on different projects that require different versions of the same software package.This blognicely summarizes some advantages of using environments.Prepare working environmentCreate a conda environment for data cleaning and install ITALLIC in that environment. The command below uses "DataCleaning" as the environment name and Python 3.8 as the Python version to use. You can use a different name for your conda environment but we recommend sticking with Python 3.8. Any Python 3 version should work but since ITALLIC was tested on Python version 3.8, we recommend using the same Python version.Create conda environment.$condacreate--nameDataCleaningpython=3.8-yActivate the environment.$condaactivateDataCleaningInstall Jupter Notebook.
ITALLIC has a visualization tool that works well withJupyer Notebook. Use conda to install Jupter.$condainstall-cconda-forgejupyter-yInstall dependencies needed to use jupyter.$condainstall-cconda-forgeipykernel-yCreate kernel for this environment to use with jupyter notebook. We recommend using the same name for the kernel that was used for the environment.$ipythonkernelinstall--user--name=DataCleaningInstallationNow that you have the environment setup, and installed jupyter, you are ready to install ITALLIC.Install ITALLIC.$condainstall-cconda-forgeitallic-yYou can now deactivate the conda environment and switch to using Jupyter Notebook to get started.$condadeactivateGetting StartedCreate a working directory$mkdirDataCleaningDirNavigate into the directory$cdDataCleaningDirGet compressed folder with country boundary data and a sample dataset to use for testing$wgethttps://github.com/getiria-onsongo/itallic/raw/main/resources/data.tar.gzIf your platform does not have wget, you can install it using conda "conda install -c conda-forge wget"Uncompress data folder$tar-xvfdata.tar.gzYou can also download the compressed folder by clicking onthis linkand then clicking the "Download" button.Download aGetting StartedPython Notebook with basic commands on how to get started.$wgethttps://github.com/getiria-onsongo/itallic/raw/main/resources/GettingStarted.ipynbMore instructions coming soon....