This repository contains statistical code related to Havmoller et al. (2021) Arboreal monkeys facilitate foraging of terrestrial frugivores. Biotropica

Data used in all analyses for this project are hosted on Open Science Framework. Original movement data are hosted on Movebank (Processed data: Movebank ID 1120749252; Unprocessed data: Movebank ID 468460067)

There are various packages with complex dependencies used accross the scripts used in this study. In order to install every package, Windows users must first ensure that the latest version of rtools is properly installed. Mac users must ensure that the latest version of Xcode is properly installed. This step cannot be skipped .

The following script installs all of the required packages and their dependencies:

install.packages(c("devtools","miniCRAN","pacman"), dependencies = TRUE, type="source") 
devtools::install_github("wrathematics/getPass")

#Check if required packages and their dependencies need installation or updates
list_of_required_packages <- c("mgcv", "plyr", "dplyr", "readr", "stringr", 
"lme4", "Matrix", "maditr", "reshape2", "magrittr", "ggplot2", "ggpubr", "fitdistrplus", "tidyr", 
"mgcv", "gganimate", "scales", "tweenr", "lubridate", "spacetime", "sp", 
"plotKML", "rgdal", "raster", "rgeos", "move", "recurse","RStoolbox", "ggspatial", "gapminder", "gifski", 
"StanHeaders", "rstan")

check_if_needs_install=as.character(miniCRAN::pkgDep(list_of_required_packages, suggests = TRUE, enhances = TRUE))
check_if_needs_update=as.character(pacman::p_update(FALSE))

new_packages <- check_if_needs_install[!(check_if_needs_install %in% installed.packages()[,"Package"])]
packages_to_update=check_if_needs_install[check_if_needs_install %in% check_if_needs_update]

packages_to_install=c(new_packages,packages_to_update)


install.packages(packages_to_install, type="source")

Be sure to change the working directory to an appropriate one on your system. Also be sure to modify where write.csv() saves all outputs.

For Dyadic_dist16.R, Dyadic_dist18.R, KMLs.R, and KMLs16.R, please replace the movebank login information with your user information. If you are unable to download the data from movebank, you may need to log in from your browser and request access to the project.

Dyadic_dist16.R: Isolates segments of the 2015-16 data where there are encounters (animals within 20m of each other). Generates data to be used in KLM.R

Dyadic_dist18.R: Isolates segments of the 2017-18 data where there are encounters (animals within 20m of each other). Generates data to be used in KLM.R

KMLs.R: Animates the 2017-18 data as KML files to be reviewed in google earth pro and examine encounter outcomes.

KMLs16.R: Animates the 2015-16 data as KML files to be reviewed in google earth pro and examine encounter outcomes.

Randomizations.R: Permutes GPS tracks at daily timescale, to test encounter rates and durations against random.

2020_04_20_functions.R: Contains functions that are called in Randomizations.R, which are necessary for cleaning the data for permutation, permuting the tracks, and plotting the results.

Playback_Analysis.R: To statistically test experimental treatments against controls for the playback experiments.

Playback_posthoc_analysis_SupplementaryFigure.R: Same as Playback_Analysis.R except treatments and controls have been combined per the suggestion of the subject editor to confirm that statistical trends are real and lack of significance a function of sample size

CoatiDipVisitDuration_monkey_presenceVSabsence.R: Script to make statistical comparisons of coati Dipteryx visit durations with and without the presence of collared monkeys.

ftt recurse dip.R: Calculates tree entry and exit times for collared monkeys, data are used in cam_gps_merge.R

cam_gps_merge.R: Integrates data from camera traps and from GPS collars to determine both the time lag between fruit tree visits (using the camera trap data) and whether a collared monkey was in the tree during the visit. This script produces waiting_times.csv which is then supplied to mixture_model_for_Biotropica.R

mixture_model_for_Biotropica.stan: Stan script specifying the stan model to be used in mixture_model_for_Biotropica.R

mixture_model_for_Biotropica.R: Script to statically test the effect of monkey presence on terrestrial frugivore visit lag times. Calls on mixture_model_for_Biotropica.stan

mix.stan.rds: exported STAN model resulting from mixture_model_for_Biotropica.R

animate_SupplementaryFigure.R generates supplementary videos S1 and S2 BCI_HR_dip_SupplementaryFigure.R generates supplementary figure S1.