mghaderizefreh/rivalidation

R and sh scripts for simulation and analysis of 1D trajectory resilience indicators

This repository provides the simulation and analysis tool developed for the paper "Validating statistical resilience indicators derived from longitudinal performance measures of animals"¹

running simulations and getting results

To simulate and analyse a scenario run Rscript.R with 4 inputs where function is 1:cte (known), 2:linear, 3:wood, study is 1:pairwise, 2:amplitude change, 3:phase change, 4:change of onset, 5:frequency change and 6:change in observation period, fittingMethod is 1: QR, 2:RR, 3:AVF but if function is 1 this input ignored (not needed if function is constant or known) and repNumber is any positive integer

Plots

For getting the plots, concatenate similar files (for a specific <function>, <study> and <fittingMethod>) and remove redundant headers. Then run the file plots.R. The data used for the paper are compressed and put in the folder results.

Tables

Table 2 and 3 can be reproduced from the uploaded datasets in this repo. Run RocTables.R

References

The scripts use several packages in R Programming Language², including quantreg³, plyr⁴, mvtnorm^{5, 6}, readr⁷, dplyr⁸, magrittr⁹, tidyr¹⁰, purrrr¹¹, stringr¹², tibble¹³, ggplot2¹⁴ ,ggpubr¹⁵, Rmisc ¹⁶ and pROC¹⁷. The data for the paper were simulated and analysed using the Edinburgh Computing Cluster "Eddie"¹⁸.

[1] Ghaderi Zefreh M, Pong-Wong R, Doeschl-Wilson A, Validating statistical resilience indicators derived from longitudinal performance measures of animals, submitted ...

[2] R Core Team (2023). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/.

[3] Koenker R (2023). quantreg: Quantile Regression. R package version 5.95, https://CRAN.R-project.org/package=quantreg.

[4] Hadley Wickham (2011). The Split-Apply-Combine Strategy for Data Analysis. Journal of Statistical Software, 40(1), 1-29. https://www.jstatsoft.org/v40/i01.

[5] Alan Genz, Frank Bretz, Tetsuhisa Miwa, Xuefei Mi, Friedrich Leisch, Fabian Scheipl, Torsten Hothorn (2021). mvtnorm: Multivariate Normal and t Distributions. R package version 1.1-3. http://CRAN.R-project.org/package=mvtnorm.

[6] Alan Genz, Frank Bretz (2009), Computation of Multivariate Normal and t Probabilities. Lecture Notes in Statistics, Vol. 195., Springer-Verlag, Heidelberg. ISBN 978-3-642-01688-2.

[7] Wickham H, Hester J, Bryan J (2023). readr: Read Rectangular Text Data. R package version 2.1.4, https://CRAN.R-project.org/package=readr.

[8] Wickham H, François R, Henry L, Müller K, Vaughan D (2023). dplyr: A Grammar of Data Manipulation. R package version 1.1.2, https://CRAN.R-project.org/package=dplyr.

[9] Bache S, Wickham H (2022). magrittr: A Forward-Pipe Operator for R. R package version 2.0.3, https://CRAN.R-project.org/package=magrittr.

[10] Wickham H, Vaughan D, Girlich M (2023). tidyr: Tidy Messy Data. R package version 1.3.0, https://CRAN.R-project.org/package=tidyr.

[11] Wickham H, Henry L (2023). purrr: Functional Programming Tools. R package version 1.0.1, https://CRAN.R-project.org/package=purrr.

[12] Wickham H (2022). stringr: Simple, Consistent Wrappers for Common String Operations. R package version 1.5.0, https://CRAN.R-project.org/package=stringr.

[13] Müller K, Wickham H (2023). tibble: Simple Data Frames. R package version 3.2.1, https://CRAN.R-project.org/package=tibble.

[14] H. Wickham. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York, 2016 https://ggplot2.tidyverse.org.

[15] Kassambara A (2023). ggpubr: 'ggplot2' Based Publication Ready Plots. R package version 0.6.0, https://CRAN.R-project.org/package=ggpubr.

[16] Hope RM (2022). Rmisc: Ryan Miscellaneous. R package version 1.5.1, https://CRAN.R-project.org/package=Rmisc.

[17] Xavier Robin, Natacha Turck, Alexandre Hainard, Natalia Tiberti, Frédérique Lisacek, Jean-Charles Sanchez and Markus Müller (2011). pROC: an open-source package for R and S+ to analyze and compare ROC curves. BMC Bioinformatics, 12, p. 77. DOI: 10.1186/1471-2105-12-77 http://www.biomedcentral.com/1471-2105/12/77/.

[18] Edinburgh Compute and Data Facility web site. 1 December 2021. U of Edinburgh https://www.ecdf.ed.ac.uk.