hSDM: hierarchical Bayesian species distribution models

hSDM is an R package for estimating parameters of hierarchical Bayesian species distribution models. Such models allow interpreting the observations (occurrence and abundance of a species) as a result of several hierarchical processes including ecological processes (habitat suitability, spatial dependence and anthropogenic disturbance) and observation processes (species detectability). Hierarchical species distribution models are essential for accurately characterizing the environmental response of species, predicting their probability of occurrence, and assessing uncertainty in the model results.

Author
Ghislain Vieilledent, Cory Merow, Jérôme Guélat, Andrew M. Latimer, Marc Kéry, Alan E. Gelfand, Adam M. Wilson, Frédéric Mortier and John A. Silander Jr.
Date of publication
2014-07-02 09:33:09
Maintainer
Ghislain Vieilledent <ghislain.vieilledent@cirad.fr>
License
GPL-3 | file LICENSE
Version
1.4
URLs

View on CRAN

Man pages

altitude
Virtual altitudinal data
cfr.env
Environmental data for South Africa's Cap Floristic Region
datacells.Latimer2006
Data of presence-absence (from Latimer et al. 2006)
data.Kery2010
Count data for the Willow tit (from Kéry and Royle 2010)
hSDM.binomial
Binomial logistic regression model
hSDM.binomial.iCAR
Binomial logistic regression model with CAR process
hSDM.Nmixture
N-mixture model
hSDM.Nmixture.iCAR
N-mixture model with CAR process
hSDM-package
hierarchical Bayesian species distribution models
hSDM.poisson
Poisson log regression model
hSDM.poisson.iCAR
Poisson log regression model with CAR process
hSDM.siteocc
Site occupancy model
hSDM.siteocc.iCAR
Site-occupancy model with CAR process
hSDM.ZIB
ZIB (Zero-Inflated Binomial) model
hSDM.ZIB.iCAR
ZIB (Zero-Inflated Binomial) model with CAR process
hSDM.ZIB.iCAR.alteration
ZIB (Zero-Inflated Binomial) model with CAR process taking...
hSDM.ZIP
ZIP (Zero-Inflated Poisson) model
hSDM.ZIP.iCAR
ZIP (Zero-Inflated Poisson) model with CAR process
hSDM.ZIP.iCAR.alteration
ZIP (Zero-Inflated Poisson) model with CAR process taking...
logit
Generalized logit and inverse logit function
neighbors.Latimer2006
Neighborhood data (from Latimer et al. 2006)
punc10
Occurrence data for _Protea punctata_ Meisn. in the Cap...

Files in this package

hSDM
hSDM/COPYING
hSDM/src
hSDM/src/hSDM.siteocc.c
hSDM/src/hSDM.poisson.c
hSDM/src/hSDM.binomial.iCAR.c
hSDM/src/hSDM.Nmixture.c
hSDM/src/hSDM.ZIB.c
hSDM/src/hSDM.ZIP.c
hSDM/src/hSDM.siteocc.iCAR.c
hSDM/src/hSDM.poisson.iCAR.c
hSDM/src/hSDM.binomial.c
hSDM/src/hSDM.ZIB.iCAR.c
hSDM/src/useful.h
hSDM/src/useful.c
hSDM/src/hSDM.ZIP.iCAR.c
hSDM/src/hSDM.ZIB.iCAR.alteration.c
hSDM/src/hSDM.Nmixture.iCAR.c
hSDM/src/hSDM.ZIP.iCAR.alteration.c
hSDM/NAMESPACE
hSDM/data
hSDM/data/neighbors.Latimer2006.rda
hSDM/data/data.Kery2010.rda
hSDM/data/datacells.Latimer2006.rda
hSDM/data/cfr.env.rda
hSDM/data/altitude.rda
hSDM/data/punc10.rda
hSDM/R
hSDM/R/hSDM.siteocc.R
hSDM/R/hSDM.ZIB.R
hSDM/R/logit.R
hSDM/R/hSDM.ZIP.iCAR.alteration.R
hSDM/R/hSDM.ZIB.iCAR.R
hSDM/R/hSDM.ZIP.R
hSDM/R/hSDM.Nmixture.iCAR.R
hSDM/R/hSDM.poisson.iCAR.R
hSDM/R/hSDM.binomial.iCAR.R
hSDM/R/hSDM.Nmixture.R
hSDM/R/hidden.R
hSDM/R/hSDM.poisson.R
hSDM/R/hSDM.siteocc.iCAR.R
hSDM/R/hSDM.binomial.R
hSDM/R/hSDM.ZIB.iCAR.alteration.R
hSDM/R/hSDM.ZIP.iCAR.R
hSDM/R/zzz.R
hSDM/README.md
hSDM/MD5
hSDM/DESCRIPTION
hSDM/man
hSDM/man/hSDM.binomial.iCAR.Rd
hSDM/man/hSDM.ZIB.iCAR.alteration.Rd
hSDM/man/hSDM.binomial.Rd
hSDM/man/hSDM.poisson.Rd
hSDM/man/hSDM-package.Rd
hSDM/man/hSDM.Nmixture.iCAR.Rd
hSDM/man/cfr.env.Rd
hSDM/man/hSDM.siteocc.Rd
hSDM/man/logit.Rd
hSDM/man/hSDM.siteocc.iCAR.Rd
hSDM/man/data.Kery2010.Rd
hSDM/man/neighbors.Latimer2006.Rd
hSDM/man/hSDM.ZIP.iCAR.alteration.Rd
hSDM/man/altitude.Rd
hSDM/man/hSDM.ZIB.Rd
hSDM/man/hSDM.poisson.iCAR.Rd
hSDM/man/datacells.Latimer2006.Rd
hSDM/man/hSDM.ZIB.iCAR.Rd
hSDM/man/punc10.Rd
hSDM/man/hSDM.ZIP.Rd
hSDM/man/hSDM.Nmixture.Rd
hSDM/man/hSDM.ZIP.iCAR.Rd
hSDM/LICENSE