Recolorize examples

A repository with example files and code illustrating how to use the recolorize package (https://github.com/hiweller/recolorize). Before running these examples, I recommend installing the development version of the package:

install.packages("devtools")
devtools::install_github("hiweller/recolorize")

Alternatively, you can install the release version of the package from CRAN (just know that this will lag behind the development version):

install.packages("recolorize")

Examples included

• 01_neolamprologus:

Wild Neolamprologus cichlid images are all courtesy Ad Konings.

• 02_wasps:

Polistes fuscatus social wasp images are courtesy James Tumulty, excerpted with permission from this paper.

• 03_birds:

All flowerpiercer (Diglossa spp.) birds were photographed by Anna E. Hiller.

• Two examples running single images.

Running these examples

1. Clone the GitHub repository, either by clicking the green 'Code' button and downloading/unzipping the zip file, or by cloning the repository:

git clone https://github.com/hiweller/recolorize_examples.git

2. If you are using RStudio, open on the recolorize_examples.Rproj file in this directory to open R in the home directory of this repository. Otherwise, open R and use setwd() to set the working directory to this directory (setwd([path/to/folder]/recolorize_examples)).
3. Execute all scripts in each folder from this directory, not the subdirectories.
4. For examples 3-5, it is recommended to execute the scripts in their alphabetic order, e.g. 01_a_alignment.R, then 01_b1_recolorize.R, 01_b2_kmeans_fits.R, then 01_c_PCA.R to understand how the examples go from input images to final output. However, for each example, the intermediate files generated by each step are saved as RDS files in an rds_files folder, so you can also run them out of order and they should still work.