Package: xsdm 1.0.1

Angel Luis Robles Fernandez

xsdm: Demographic Approach to Species Distribution Model

Integrates concepts of stochastic demography into species distribution modelling. The main approach maximizes a likelihood function based on environmental information and presence/absence records. This is used to reconstruct species' fundamental ecological niches and to project their potential geographic range. Data requirements include species presence/absence records and a timeseries of environmental data.

Authors:Emilio Berti [aut], Daniel C. Reuman [aut], Angel Luis Robles Fernandez [aut, cre]

xsdm_1.0.1.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
xsdm/json (API)

# Install 'xsdm' in R:
install.packages('xsdm', repos = c('https://xsdm-project.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/xsdm-project/xsdm-devel/issues

Pkgdown/docs site:https://xsdm-project.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • example_1 - Consolidated example data for the xsdm package
  • example_2 - Consolidated example data for the xsdm. This is environmental data array and an occurrence presence absence vector of Ophisaurus ventralis. A named list containing all example datasets used in the package's documentation and examples.
  • example_3 - Consolidated example data for the xsdm. This is environmental data array and an occurrence presence absence vector Blarina carolinensis A named list containing all example datasets used in the package's documentation and examples.

On CRAN:

Conda:

cpp

4.81 score 62 scripts 277 downloads 26 exports 34 dependencies

Last updated from:93eaa5c52f. Checks:15 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK204
linux-devel-x86_64OK231
source / vignettesOK221
linux-release-arm64OK155
linux-release-x86_64OK191
macos-release-arm64OK172
macos-release-x86_64OK461
macos-oldrel-arm64OK197
macos-oldrel-x86_64OK440
windows-devel-arm64OK423
windows-devel-x86_64OK233
windows-release-arm64OK416
windows-release-x86_64OK206
windows-oldrel-x86_64OK174
wasm-releaseOK168

Exports:bio_to_mathbuild_orthogonal_matrixconvert_equivalence_classcreate_maskcreate_param_vector_maskeddist_between_paramsenv_data_arrayexpitextract_orthogonal_matrix_parametershabitat_suitabilityinterpret_parameterslike_ltsglike_neg_ltsgrlog_prob_detectlog1mexplog1pexploglik_biologlik_mathmake_mask_namesmath_to_bionum_env_varnum_paroptimize_likelihoodprofile_likelihoodstart_parmsvsp

Dependencies:backportscallrcheckmateclicodetoolsdigestexpmfurrrfuturefuture.callrglobalsgluelatticelifecyclelistenvmagrittrMatrixotelparallellypillarpkgconfigprocessxpspurrrR6RcppRcppParallelrlangsobolterratibbleucminfcpputf8vctrs

Readme and manuals

Help Manual

Help pageTopics
xsdm: Demographic Approach to Species Distribution Modelxsdm-package xsdm
Converts parameters from the biological scale to the math (unconstrained) scalebio_to_math
Build an orthogonal matrix from a real-parameter vectorbuild_orthogonal_matrix
Converts a set of parameters to other representatives of the same equivalence classconvert_equivalence_class
Create a parameter mask aligned with `make_mask_names()`create_mask
Create a complete parameter vector with canonical names (no NAs allowed)create_param_vector_masked
Distance in parameter space between two sets of parametersdist_between_params
Get an array of environmental data from presence-absence points.env_data_array
Consolidated example data for the xsdm packageexample_1
Consolidated example data for the xsdm. This is environmental data array and an occurrence presence absence vector of Ophisaurus ventralis. A named list containing all example datasets used in the package's documentation and examples.example_2
Consolidated example data for the xsdm. This is environmental data array and an occurrence presence absence vector Blarina carolinensis A named list containing all example datasets used in the package's documentation and examples.example_3
Functions to take the expit of numerical vectors. expit exp(x)/(1 + exp(x))expit
Extract a math-scale real-parameter vector corresponding to a special orthogonal matrixextract_orthogonal_matrix_parameters
Tiled habitat-suitability map from environmental raster stackshabitat_suitability
Tool to help interpret xsdm model parametersinterpret_parameters
Compute likelihood for LTSG modellike_ltsg
Long-term stochastic growth rate worker function for the xsdm modellike_neg_ltsgr
Probability of detection of the species in each locationlog_prob_detect
Compute log detection probabilities from a flat environmental data vectorlog_prob_detect_cpp
Numerically stable `log(1 - exp(-a))`log1mexp
Numerically stable `log(1 + exp(x))`log1pexp
Log-likelihood function for the xsdm model, parameters on the biological scale.loglik_bio
Pure-C++ log-likelihood for the xsdm model (biological-scale parameters)loglik_bio_cpp
Log-likelihood function for the xsdm model, parameters on the math scale.loglik_math
Pure-C++ log-likelihood for the xsdm model (math-scale parameters)loglik_math_cpp
Function to facilitate the creation of the argument 'mask' to the function 'loglik_math'make_mask_names
Convert parameters from the math scale to the biological scalemath_to_bio
Get the number of environmental variables given the number of parametersnum_env_var
Get the number of parameters of the main xsdm model given the number of environmental variables to be considerednum_par
Optimize the xsdm log-likelihood from multiple starts (ucminfcpp)optimize_likelihood
Basic (non-adaptive) tool for profiling the likelihoodprofile_likelihood
Starting parameters for the optimizationstart_parms
Generate a virtual species probability map with presence/absence samplingvsp