• Thesis and articles template
• Export word and html document
• Word improved template
• Bibliography citation
• R workflow for data analysis
• Scientific graphic quality

Example: https://flavjack.github.io/rticles/

It is recommended install and create an account if is needed for the following apps, all are free and can be complemented with reproducible research.

• R https://cran.rstudio.com/
• Rstudio https://rstudio.com/products/rstudio/download/
• Git https://git-scm.com/
• Zotero https://www.zotero.org/download/
• Google account: Gsuit

• You can use "rticles" as template from GitHub: https://github.com/Flavjack/rticles

or

• You can clone the "rticles" repository using the terminal in Rstudio, for windows user using bash (install Git)

bash
prj="project_name"
info="project info"
gituser="Flavjack"
repo="https://github.com/Flavjack/rticles"
cd
mkdir git
cd git
git clone $repo.git $prj
cd $prj
mv 'rticles.Rproj' $prj.Rproj
curl -u $gituser https://api.github.com/user/repos -d "{\"name\":\"$prj\", \"description\": \"$info\", \"private\": \"true\"}"
git remote rm origin
git commit -m "starting rticles"
git remote add origin https://github.com/$gituser/$prj.git
git push -u origin master
open $prj.Rproj
open .

1. Run the first chunk in the "index.Rmd" called "setup" and all the packages will be installed automatically.

2. If all packages are installed correctly shoul be appear the "Build" button in the Rstudio IDE (Integrated Development Environment).

3. Play the "Build" button and wait until compile the document and if all is okay pop-up window will be appeare with the html version of the document.

4. You can modify the document changing the text and code in the "index.Rmd" file.

5. Now you are ready to go and produce your first document!

The document is building with Lorem Ipsum text, and the dataset, examples and tables used are from GerminaR package.

The dataset is a germination data example* with a completely randomized design with four replications per treatment under laboratory conditions. The first factor corresponds to five levels of sodium chloride (NaCl) (0, 0.5, 1.0, 1.5 and 2 MPa), and the second factor corresponds to four levels of temperature (25°C, 30°C, 35°C and 40°C).

Source: https://docs.google.com/spreadsheets/d/1QziIXGOwb8cl3GaARJq6Ez6aU7vND_UHKJnFcAKx0VI/edit#gid=137089581

*Lozano-Isla, Flavio, Omar E. Benites-Alfaro, and Marcelo F. Pompelli, 'GerminaR: An R Package for Germination Analysis with the Interactive Web Application "GerminaQuant for R"', Ecological Research, 34.2 (2019), 339--46 https://doi.org/10.1111/1440-1703.1275

{r chunk_name, child = 'file.Rmd'}

<embed src="files/file_name.pdf" width="100%" height="500" alt="pdf" pluginspage="http://www.adobe.com/products/acrobat/readstep2.html">

<iframe width="100%" height="450" src="https://www.youtube.com/embed/video_id" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

# Import changes from origen
git pull

# Push changes to origen
git add .
git commit -m "message"
git push 

# re-write local files from origen
git fetch --all
git reset --hard origin/master
git pull origin master

# Force push to origen
git push -f origin master

# Undoing Multiple Commits
git reset --hard <commit>