QCPA-r-script

Tailored R script guiding novice R users in the extraction and compilation of batch QCPA output data into .csv tables that can be used for downstream analysis in R. This R script is a companion script for:

van den Berg, C.P. et al. 2024 Automated workflows using Quantitative Colour Pattern Analysis (QPCA): a guide to batch processing and downstream data analysis. Evolutionary Ecology. View

Data

Data used in this example is accessible here from UQ eSpace. To account for varying data download capacities, particularly for users with limited data caps, bandwidth, or unstable connections, we offer two options for downloading data.

Option 1

For users that do not have limited downloading abilities and/or have skipped the QCPA batch scripting step:

1. Download the Worked_example_data_Processed.zip (301.66 MB)
2. Extract the data into your working folder
3. Rename the unzipped folder to “Worked_example_data”

Option 2

For users with limited data, we recommend downloading the unprocessed data and implementing the batch QCPA workflow. Take these steps:

1. Download the Worked_example_data_Unprocessed.zip (150.61 MB)
2. Implement the QCPA-batch-script following the QCPA-batch-script pdf manual
3. Rename the folder to “Worked_example_data”

Using QCPA-r-script

We would recommend downloading and using the QCPA_r-script.R script in R. You can then follow either the QCPA_R pdf manual or the QCPA_R html manual.

Markdown version

For users using the R Markdown version of QCPA-r-script, the dependency scripts are:

• QCPA_r-script.Rmd bibliography uses the QCPA_r_bib.bib
• pdf_document uses legend_fix.tex to fix figure and table legends
• html_document uses styles.css to modify the table of contents and manual headers

Authors

Cara Conradsen, Cedric van den Berg, Tom White