Data from: A multistate dynamic site occupancy model for spatially aggregated sessile communities

Fukaya K, Royle JA, Okuda T, Nakaoka M, Noda T

Date Published: November 8, 2016

DOI: http://dx.doi.org/10.5061/dryad.30mb4

 

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Title Site occupancy data from rocky intertidal communities
Downloaded 14 times
Description Data file written in the Rdump format. This is a sort of text file and can be loaded into R by source("dumpdata.R"), defining the following objects: * Y : a 3-dimensional array of observation of site occupancy state. Each dimension represents: [Quadrat, Site, Time]. * x : a matrix in which each row representing spatial coordinate of a site. * I : an integer representing the number of sites per quadrat. * J : an integer representing the number of quadrats. * S : a vector indicating the number of states modeled in each quadrat. * T : an integer representing the number of time points. * state_list : a list of vectors representing ecological states modeled in each quadrat.
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Title R script for data analyses
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Description An R script to estimate transition probabilities by using the naive estimator, nonspatial and spatial model. It also includes codes for estimating and plotting some properties of community dynamics as well as those for drawing estimated local community structure.
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Title Model file for the nonspatial model
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Description JAGS model file for the nonspatial model.
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Title Model file for the spatial model
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Description JAGS model file for the spatial model.
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Title Parameter estimates
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Description This compressed file contains R binary files including estimates of transition probabilities and others, obtained for each quadrat by using the naive estimator, nonspatial and spatial model. They are obtained as outputs from the codes in the "Rscript.R" file.
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Title Posterior samples
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Description This compressed file contains R binary files including JAGS output (i.e., posterior samples) for each quadrat. They are obtained as outputs from the codes in the "Rscript.R" file, and are also used to produce files contained in the "results.zip" file.
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When using this data, please cite the original publication:

Fukaya K, Royle JA, Okuda T, Nakaoka M, Noda T (2016) A multistate dynamic site occupancy model for spatially aggregated sessile communities. Methods in Ecology and Evolution 8(6): 757–767. http://dx.doi.org/10.1111/2041-210x.12690

Additionally, please cite the Dryad data package:

Fukaya K, Royle JA, Okuda T, Nakaoka M, Noda T (2016) Data from: A multistate dynamic site occupancy model for spatially aggregated sessile communities. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.30mb4
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