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.
00_submitted-pdfs
: Submitted PDF files. Knitted from the bookdown template located in05_writing
.01_data
: Data directory. The processed data is provided in the repo. The raw data, however, needs to be copied separetly to01_data/activity_raw/
.02_data_processing
: Data processing scripts used to process and merge acelerometer and luximiter raw data. These scripts generates the file01_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 usedhttps://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.
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
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.
Some actograms were plotted using forked scripts from ggetho.