Marc-Olivier Beausoleil 0 Posted March 17 Share Posted March 17 I'm compiling a list of relevant R packages in ornithology. I was wondering if you can provide one or more packages that you find relevant in these categories. Communication and acoustic analysis Conservation Genetics Mark-recapture analysis Movement ecology, navigation, telemetry, GPS, habitat use Phylogeny Physiology, phenology and life histories Population dynamics I welcome packages not only on CRAN. Thanks! Link to post Share on other sites
Chris Merkord 28 Posted March 29 Share Posted March 29 Some population related packages: Distance dsm marked mrds nimbleSCR oSCR PresenceAbsence Rcapture RMark scrbook secr unmarked Some packages for accessing bird observation citizen science data: auk (and ebirdst) rinat rgbif Lots of general modeling packages: MuMIn AICcmodavg You might also check out some of the CRAN task views such as, Analysis of Ecological and Environmental Data Analysis of Spatial Data Multivariate Statistics Phylogenetics, Especially Comparative Methods Cluster Analysis & Finite Mixture Models Handling and Analyzing Spatio-Temporal Data Link to post Share on other sites
Marc-Olivier Beausoleil 0 Posted March 30 Author Share Posted March 30 Thanks this is really helpful! Link to post Share on other sites
Ian Ausprey 0 Posted April 1 Share Posted April 1 For regression models I regularly use emmeans/emtrends: https://aosmith.rbind.io/2019/03/25/getting-started-with-emmeans/ visreg: https://pbreheny.github.io/visreg/ rr2 to plot partial residual plots, calculate model coefficients and effect sizes, and extract pseudo R-squared values for anything that is not least squares. This is especially useful for regression models with lots of variables, especially multiple categorical variables and/or interactions. Link to post Share on other sites
Marc-Olivier Beausoleil 0 Posted April 3 Author Share Posted April 3 Thanks! Well, if you are interested, I'm actually building a Cran task View (or maybe just a Task view) for ornithologists. If anyone wants to join, we can discuss on how to move forward :D Link to post Share on other sites
Alex R 0 Posted April 20 Share Posted April 20 For acoustic data I use Seewave warbleR tuneR I also recommend Sound Analysis and Synthesis With R by Jerome Sueur Link to post Share on other sites
Marc-Olivier Beausoleil 0 Posted April 20 Author Share Posted April 20 Thanks! This is still a work in progress, and I included all of the packages suggested here. This is an example of the reference that I'm building (see Cran task views for comparison) https://beausoleilmo.github.io/Ornithometrics-ctv/Ornithometrics.html Link to post Share on other sites
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