R code and output supporting: Time series sightability modeling of animal populations

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Collection period

2005
2016

Date completed

Date updated

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Geographic coverage

Northeastern Minnesota

Source information

This work represents original analysis and interpretation of Minnesota Department of Natural Resources moose survey (sightability trials and operational surveys) data.

Journal Title

Journal ISSN

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Title

R code and output supporting: Time series sightability modeling of animal populations

Published Date

2017-03-29

Group

Author Contact

ArchMiller, Althea A
althea.archmiller@gmail.com

Type

Dataset

Abstract

The goal of our study was to expand a previously developed model-based approach to include random effects and a temporal spline for time series modeling of multiple years of operational survey data. We developed a Bayesian hierarchical model as our framework to build and compare fixed-effects and temporal model-based sightability models applied to 12 years of MN moose operational survey data. Here, we share the Program R code and data necessary to replicate the manuscript results that demonstrate how our time series sightability modeling approach can increase the precision of population estimators and predict population dynamics with smoother (and thus more realistic trends) through time.

Description

Referenced by

ArchMiller, Dorazio, St. Clair, Fieberg. 2018. Time series sightability modeling of animal populations. PLOS ONE.
https://doi.org/10.1371/journal.pone.0190706

Related to

Replaces

This is an updated version of the dataset. The g_plots_results.html, programs_R.zip, and model_diagram.pdf files have been updated to reflect changes in the final PLOS ONE publication of the corresponding manuscript. The updates are to reformat the axis labels for the figures in the final publication. Version 1 can be found here:
http://hdl.handle.net/11299/185411.1

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Publisher

Funding information

Minnesota Department of Natural Resources
Wildlife Restoration (Pittman-Robertson) Program
Minnesota Agricultural Experimental Station

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Previously Published Citation

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Suggested citation

ArchMiller, Althea A; Fieberg, John R; Dorazio, Robert M; St. Clair, Katherine. (2017). R code and output supporting: Time series sightability modeling of animal populations. Retrieved from the Data Repository for the University of Minnesota (DRUM), https://doi.org/10.13020/D6N30B.

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Description
Size
a_define_sightability_model.html
JAGS model definition: sightability model
(15.55 KB)

a_define_FE_model.html
JAGS model definition: fixed-effect model
(17.83 KB)

a_define_TS_model.html
JAGS model definition: temporal spline model
(18.64 KB)

a_define_joint_model.html
JAGs model definition: joint models
(26.7 KB)

b_augment_data.html
Augment data for analysis
(24.77 KB)

c_run_sight_model.html
Code to run sightability model
(18.2 KB)

d_run_FE_model.html
Code to run fixed-effect model
(38.01 KB)

d_run_TS_model.html
Code to run temporal spline model
(38.78 KB)

d_run_joint_models.html
Code to run joint models
(38.22 KB)

e_calculate_mHT_abundance.html
Code to calculate abundance with mHT
(22.69 KB)

e_calculate_FE_model_abundance.html
Code to calculate abundance with fixed-effect model
(24.98 KB)

e_calculate_TS_model_abundance.html
Code to calculate abundance with temporal spline model
(24.63 KB)

e_calculate_joint_abundance.html
Code to calculate abundance with joint models
(40.05 KB)

f_process_results.html
Code to process raw results for plotting
(34.23 KB)

g_plot_results.html
Code to make plots for manuscript
(413.43 KB)

h_appendix_traceplot.html
Code to make trace plot for supplementary figure 1
(26.93 KB)

ex0507.csv
Sightability trial data
(1.7 KB)

moose0416.csv
Annual operational survey data
(41.73 KB)

plots_and_strata2016.csv
Data with stratum identifiers for each year and plot
(13.14 KB)

model_diagram.pdf
Hierarchical model overview
(550.6 KB)

programs_R.zip
Zipped file containing all R programs
(39.78 KB)

stratification_schema.pdf
Example MN DNR stratification schema
(261.81 KB)

README.txt
Readme
(14.69 KB)

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