R code and output supporting: Time series sightability modeling of animal populations
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2016
2016
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Northeastern Minnesota
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This work represents original analysis and interpretation of Minnesota Department of Natural Resources moose survey (sightability trials and operational surveys) data.
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Title
R code and output supporting: Time series sightability modeling of animal populations
Published Date
2017-03-29
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Author Contact
ArchMiller, Althea A
althea.archmiller@gmail.com
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.
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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
https://doi.org/10.1371/journal.pone.0190706
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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
http://hdl.handle.net/11299/185411.1
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Funding information
Minnesota Department of Natural Resources
Wildlife Restoration (Pittman-Robertson) Program
Minnesota Agricultural Experimental Station
Wildlife Restoration (Pittman-Robertson) Program
Minnesota Agricultural Experimental Station
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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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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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