jtsilverio / mestrado_tuco-tucos_chronobiology

Masters' thesis in Biology. Changes in daily activity patterns throughout the year in free-living tuco-tucos (Ctenomys sp.). It can also be downloaded from: https://doi.org/10.11606/D.41.2022.tde-12052022-151830

Annual changes in daily activity patterns in free-living tuco-tucos

This is a repository for my masters' thesis. This thesis was presented to departamento de fisiologia - IB-USP. It was done using R v4.1.2.

Main directories

• 00_submitted-pdfs: Submitted PDF files. Knitted from the bookdown template located in 05_writing.
• 01_data: Data directory. The processed data is provided in the repo. The raw data, however, needs to be copied separetly to 01_data/activity_raw/.
• 02_data_processing: Data processing scripts used to process and merge acelerometer and luximiter raw data. These scripts generates the file 01_data/activity_processed/tuco_processed.rds.
• 03_analysis: Analysis scripts used to run EDA, HMM models, statistical tests and generate the appendix plots (e.g. actograms, weather, vegetation, daylength).
• 04_figures: Figures generated by the analysis scripts plus other images such as the introduction diagram, maps and tuco-tuco's photo.
• 05_writing: Bookdown based structured to write and generate the final thesis document using markdown, pandoc and LaTeX. I used https://github.com/COPPE-UFRJ/coppedown as a base bookdown template and modified specific details to follow the IB-USP template.
• 06_stats_report: Statistical report that analysed some parameter we used in the main paper analysis such as the downsampling factor and summary window.
• requirements.txt: Script with all necessary packages used in the markdown and analysis documents.
• tuco-tuco-activity.Rproj: Rstudio project.

Installing the R-package momentuHMM on linux

Some external dependencies are needed in order to compile and install the momentuHMM package:

On Ubuntu based distros:
---
sudo apt install libssl-dev
sudo apt install libnode-dev
sudo apt install libprotobuf-dev
sudo apt install libjq-dev
sudo apt install protobuf-compiler
sudo apt install libudunits2-dev
sudo apt install libgeos-dev
sudo apt install libudunits2-0
sudo apt install libgdal-dev

On Fedora:
---
sudo dnf install protobuf-devel -y
sudo dnf install jq-devel -y
sudo dnf install libcurl-devel -y
sudo dnf install udunits2-devel -y
sudo dnf install v8-devel -y
sudo dnf install geos-devel -y
sudo dnf install gdal-devel -y
sudo dnf install proj-devel -y
sudo dnf install sqlite-devel -y

How to Knit the PDF files

In Rstudio open 05_writing/index.Rmd and click the knit button on the top bar. Another option is to execute bookdown::render_book("05_writing", "coppedown::thesis_pdf") on the command line.

References

Some actograms were plotted using forked scripts from ggetho.