Codes to reproduce the results in the paper "Modeling animal movement with directional persistence and attractive points"
Models estimates can be obtained running the Julia script "PosteriorEstimates.jl". Inside the script, a value must be given to the objects "IndModel", "NAME" and "DIR".
- "DIR" is the directory where all the relevant codes and folders are saved;
- "IndModel" is a vector with 1 element, that has value 1 if we want to estimate the STAP-HMM, value 2 for the BRW-HMM, and 3 for the CRW-HMM.
- The results, depending on the value of "IndModel", are saved in an R object called "NAME_STAP.Rdata", "NAME_BRW.Rdata" or "NAME_CRW.Rdata" in the directory "DIR/out/".
To automatically load the exact versions of the Julia packages, the file "DIR/Juliapackagesversions/Manifest.toml" should be loaded and activated before running the code. Inside the file, "XXX" on line 32 must be replace with "DIR/BayesianAnimalMovementModels.jl"
All figures and tables can be reproduced running the script "Plots.R". Inside the script, a value must be given to the objects "PLOT_DIRDATA", "NAME" and "PLOT_DIRPLOT", "MOD_STAP_NAME", "MOD_BRW_NAME" and "MOD_CRW_NAME".
- "PLOT_DIRDATA" is the directory where the results of the script "PosteriorEstimates.jl" are saved ("DIR/out/"),
- "PLOT_DIRPLOT" is the directory where we want to save the figures,
- "MOD_STAP_NAME", "MOD_BRW_NAME" and "MOD_CRW_NAME" are the names of the R objects that contain the posterior samples of the respective model.
Tables are printed on the R console. To have a clearer output, the file "PlotsAndTables.R" should be run in R using the command "source("DIR/PlotsAndTables.R")"
Notice that there are inconsistencies between the names of the parameters in the paper and in the scripts: \mu and \nu in the paper are, respectively, \mu_0 and \psi in the scripts.
The folder "BayesianAnimalMovementModels.jl" contains the Julia package needed to estimate the models.
The folder "Data" contains the dataset saved in a ".Rdata" format (R workspace); coordinates of several dogs and sheep are present. The one used in the paper are "Long_Bindi_Canis" (Longitude) and "Lat_Bindi_Canis" (Latitude).
The ".csv" data can be downloaded at "https://www.datarepository.movebank.org/handle/10255/move.395".