portal-rodent-dispersal

Research on rodent dispersal patterns near Portal AZ. Contains code for reproducing the results of analyses using individual-level tag data for common rodent species at the Portal Project site. Collaborators on this project include Sarah R. Supp, David N. Koons, and S. K. Morgan Ernest. Code was written by Sarah R. Supp and D. N. Koons.

The code and data in this repository all for the analyses and figures to be fully replicated using a subset of the published Portal dataset which includes individual-level rodent data from 1980-2009. Species evaluated include granivores, folivores and insectivores: Peromyscus eremicus (PE), Peromyscus maniculatus (PM), Peromyscus leucopus (PL), Onychomys torridus (OT), Onychomys leucogaster (OL), Dipodomys merriami (DM), Dipodomys ordii (DO), Dipodomys spectabilis (DS), Chaetodipus baileyi (PB), Chaetodipus penicillatus (PP), Perognathus flavus (PF), Chaetodipus intermedius (PI), Chaetodipus hispidus (PH), Sigmodon hispidus (SH), Sigmodon fulviventer (SF), Sigmodon ochrognathus (SO), Neotoma albigula (NAO), Baiomys taylori (BA), Reithrodontomys megalotis (RM), Reithrodontomys fulvescens (RF), and Reithrodontomys montanus (RM).

NOTE: The project and code in this repository is still under development.

Requirements: R 2.x, Python 2.7 or higher, Program MARK (http://www.phidot.org/software/mark/) and the files containing data and functions specific to this code, movement_fxns.R. R Packages: ape, calibrate, fields, geiger, ggbiplot, ggmap, ggplot2, gridExtra, picante, PhyloOrchard, plyr, reshape2, RMark

The analyses can be replicated by changing the working directory at the top of the file rodent_wrapper.R to the location on your computer where you have stored the .R and .csv files.

Code should take approximately 30 minutes to run start to finish in rodent_wrapper.R and may take days or weeks to run start to finish in MARK_analyses.R. Figures should output as pdfs to your working directory or print to the screen.

Data use: Data is provided in this supplement for the purposes of replication. If you wish to use the data for additional research, they should be obtained from the published source (Ecological Archives E090-118-D1; S. K. Morgan Ernest, Thomas J. Valone, and James H. Brown. 2009. Long-term monitoring and experimental manipulation of a Chihuahuan Desert ecosystem near Portal, Arizona, USA. Ecology 90:1708. doi:10.1890/08-1222.1)

Included Files

• rodent_wrapper.R script -- runs through all the analyses, starting with the 30 year dataset. -USE
• movement_fxns.R script -- holds the relevant functions for executing the stake_movement.R script. -USE
• MARK_analyses.R script -- code to run Program MARK models. Should be run on a server - takes a long time to finish! -USE
• stake_movment.R script -- cleans up the data, runs the statistical analyses, and outputs figures. - IGNORE
• rodent_data. R -- old code that explores only 2 species - IGNORE
• additional_movement_fxns.R -- code that I'm not currently using for the main product, but would like to keep around - IGNORE
• RodentQueries.ipynb script -- ipython notebook code to query the main server for Portal data.
• rawdata -- folder containing data queried from the published Portal database
  • cricetids_2000-2009.csv -- individual level data for granivores in the family Cricetidae. Includes the species Peromyscus eremicus, Peromyscus maniculatus, and Reithrodontomys megalotis
  • folivores_2000-2009.csv -- individual level data for folivores in the family Cricetidae. Includes the species Sigmodon hispidus, Sigmodon fulviventer, and Neotoma albigula.
  • heteromyids_2000-2009.csv -- individual level data for granivores in the family Heteromyidae. Includes the species Dipodomys merriami, Dipodomys ordii, Chaetodipus baileyi, Chaetodipus penicillatus, and Perognathus flavus.
  • onychomys_2000-2009.csv -- individual level data for carnivores in the family Cricetidae. Includes the species Onychomys leucogaster and Onychomys torridus.
  • all_1980-2009.txt -- individual level data for all the species from 1980-2009.
• mark_datafiles -- folder to store .inp files for the MARK_analyses.r code
• mark_output -- folder to store the output files generated by RMark and Program Mark. Also stores outfile.txt which holds text generated from the code to mark where the code is located.
• output -- folder that stores past versions of the figures and text generated for this project

License This code is available under a BSD 2-Clause License.

Copyright (c) 2013 Weecology. All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Contact information Sarah Supp's email: sarah@weecology.org and sarah.supp@stonybrook.edu

Sarah's website: http://weecology.org/people/sarahsupp/Sarah_Supp/