Get familiar with R and rstudio at the terminal.
Use http://subliminal.maths.cam.ac.uk:8787/ to access rstudio remotely.
Work through "Dynamical Models in Biology" handout. The extra R files come from the home page for the book.
LaTeX introduction: slides
LaTeX lab material
We will go through assignment 1 (not knitr as planned before).
Note on vectorization: See R news help desk https://cran.r-project.org/doc/Rnews/Rnews_2008-1.pdf
Finished part 1 of the lecture notes at the start of lecture 12. Rest of lecture 12 on differential equations.
I think we will have an extra supervision class to go through the rabbit-sheep example in slower detail. The following Rmd file and example The R journal article will also be useful reading.
Lecture notes for RR. Slides for this lecture were made in markdown.
All available from https://github.com/lgatto/spr/tree/master/estimate
Makefile material from https://github.com/lgatto/spr/tree/master/rr_make
Note: in Rstudio, it is best to set the default Sweave compilation engine to "knitr" rather than "sweave". Do this from the Tools -> Global Options menu.
Wrapping up (the tidyverse: https://blog.rstudio.org/2016/09/15/tidyverse-1-0-0/)
github, Reproducible research, "good enough" practices.
To follow (estimated due date Jan 2017).