benmR: benmR: A package for estimating ecological niches through a...
In LauraJim/benmR: Implementation of a Bayesian Method for Estimating Niches from Presence Data
Description
Visualization functions
Modeling functions
Analysis functions
Description
The underlying Bayesian model that is used to estimate ecological niches with
this package is presented in Jimenez et al (2018?). The main
benmR package is to provide code to apply this methodology of niche
purpose of the estimation. It package provides three categories of functions
grouped together according to their main purpose: visualization, modeling and
estimation, and analysis of results.
Visualization functions
The package contains a function called plotdata which displays the
data to be used to estimate the ecological niche of a species.
Once the Bayesian estimation is done for the parameters of interest,
PlotIterations plots the fitted ellipsoids that come from the
simulations of the posterior distribution on top of the background data in
environmental space.
The function UncertaintyPlot calculates an uncertainty index for each
cell in the environmental space were the niche is being estimated and
displays these values as a color map.
Modeling functions
The modeling functions are those specifically designed to define the
components of the posterior distribution. priorpar fixes the parameters
of the a priori distributions using tolerance ranges of the species.
Supp, Initth, and Energy are the functions needed to
simulate from the posterior distribution by using the t-walk algorithm,
being the last function the one that contains the expression for the posterior.
The function postsample is the one used to simulate from the posterior
and depends on all the other functions mentioned in this section.
Analysis functions
These are functions that help processing the results of the t-walk sampling.
plot_iter takes the output of the function Runtw and plots the
resulting ellipses in the environmental space.
uncer_plot combines all the simulated values to produce an uncertainty
map.
LauraJim/benmR documentation built on May 16, 2019, 11:11 p.m.
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Description Visualization functions Modeling functions Analysis functions
Description
The underlying Bayesian model that is used to estimate ecological niches with
this package is presented in Jimenez et al (2018?). The main
benmR package is to provide code to apply this methodology of niche
purpose of the estimation. It package provides three categories of functions
grouped together according to their main purpose: visualization, modeling and
estimation, and analysis of results.
Visualization functions
The package contains a function called plotdata which displays the
data to be used to estimate the ecological niche of a species.
Once the Bayesian estimation is done for the parameters of interest,
PlotIterations plots the fitted ellipsoids that come from the
simulations of the posterior distribution on top of the background data in
environmental space.
The function UncertaintyPlot calculates an uncertainty index for each
cell in the environmental space were the niche is being estimated and
displays these values as a color map.
Modeling functions
The modeling functions are those specifically designed to define the
components of the posterior distribution. priorpar fixes the parameters
of the a priori distributions using tolerance ranges of the species.
Supp, Initth, and Energy are the functions needed to
simulate from the posterior distribution by using the t-walk algorithm,
being the last function the one that contains the expression for the posterior.
The function postsample is the one used to simulate from the posterior
and depends on all the other functions mentioned in this section.
Analysis functions
These are functions that help processing the results of the t-walk sampling.
plot_iter takes the output of the function Runtw and plots the
resulting ellipses in the environmental space.
uncer_plot combines all the simulated values to produce an uncertainty
map.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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