Marc-Olivier Beausoleil Posted March 17, 2021 Share Posted March 17, 2021 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 comment Share on other sites More sharing options...
Chris Merkord Posted March 29, 2021 Share Posted March 29, 2021 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 comment Share on other sites More sharing options...
Marc-Olivier Beausoleil Posted March 30, 2021 Author Share Posted March 30, 2021 Thanks this is really helpful! Link to comment Share on other sites More sharing options...
Ian Ausprey Posted April 1, 2021 Share Posted April 1, 2021 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 comment Share on other sites More sharing options...
Marc-Olivier Beausoleil Posted April 3, 2021 Author Share Posted April 3, 2021 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 comment Share on other sites More sharing options...
Alex R Posted April 20, 2021 Share Posted April 20, 2021 For acoustic data I use Seewave warbleR tuneR I also recommend Sound Analysis and Synthesis With R by Jerome Sueur Link to comment Share on other sites More sharing options...
Marc-Olivier Beausoleil Posted April 20, 2021 Author Share Posted April 20, 2021 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 comment Share on other sites More sharing options...
pnassivera Posted April 21, 2021 Share Posted April 21, 2021 For ringing data, I have already used ringR. http://ringr.gryllosoft.hu/ Link to comment Share on other sites More sharing options...
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