Package: tenm 0.5.1

tenm: Temporal Ecological Niche Models

Implements methods and functions to calibrate time-specific niche models (multi-temporal calibration), letting users execute a strict calibration and selection process of niche models based on ellipsoids, as well as functions to project the potential distribution in the present and in global change scenarios.The 'tenm' package has functions to recover information that may be lost or overlooked while applying a data curation protocol. This curation involves preserving occurrences that may appear spatially redundant (occurring in the same pixel) but originate from different time periods. A novel aspect of this package is that it might reconstruct the fundamental niche more accurately than mono-calibrated approaches. The theoretical background of the package can be found in Peterson et al. (2011)<doi:10.5860/CHOICE.49-6266>.

Authors:Luis Osorio-Olvera [aut, cre], Miguel Hernández [aut], Rusby G. Contreras-Díaz [aut], Xavier Chiappa-Carrara [aut], Fernanda Rosales-Ramos [aut], Mariana Munguía-Carrara [aut], Oliver López-Corona [aut], Townsend Peterson [ctb], Jorge Soberón [ctb]

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tenm.pdf |tenm.html✨
tenm/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/luismurao/tenm/issues

Datasets:
  • abronia - Occurrence records of Abronia graminea
  • colors - Colors for plotting

On CRAN:

5.97 score 5 stars 34 scripts 166 downloads 18 exports 65 dependencies

Last updated 4 months agofrom:e96e93e276. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 21 2024
R-4.5-winOKNov 21 2024
R-4.5-linuxOKNov 21 2024
R-4.4-winOKNov 21 2024
R-4.4-macOKNov 21 2024
R-4.3-winOKNov 21 2024
R-4.3-macOKNov 21 2024

Exports:bg_by_datecells2sampclean_dupclean_dup_by_datecorrelation_findercov_centerellipsoid_omrellipsoid_projectionellipsoid_selectionex_by_dateinEllipsoidmetarasplot_ellipsoidpredictpROCsp_temporal_datatdf2swdtenm_selection

Dependencies:base64encbslibcachemclassclassIntclicodetoolscpp11DBIdigestdplyre1071evaluatefansifastmapfontawesomefsfurrrfuturegenericsglobalsgluehighrhtmltoolshtmlwidgetsjquerylibjsonliteKernSmoothknitrlifecyclelistenvlubridatemagrittrMASSmemoisemimeparallellypillarpkgconfigproxypurrrR6rappdirsRcpprglrlangrmarkdowns2sasssfstringistringrterratibbletidyrtidyselecttimechangetinytexunitsutf8vctrswithrwkxfunyaml

Introduction to tenm package

Rendered fromtenm-vignette.Rmdusingknitr::rmarkdownon Nov 21 2024.

Last update: 2024-07-19
Started: 2023-01-23

Readme and manuals

Help Manual

Help pageTopics
Occurrence records of Abronia gramineaabronia
Function to obtain environmental background organized by datebg_by_date
Helper function to randomly select cell IDs for generating environmental background data.cells2samp
Function to thin longitude and latitude dataclean_dup
Function to thin occurrence data Cleans up duplicated longitude and latitude data by year using a specified distance threshold. The distance can be specified as a geographic distance or, if a raster_mask is provided, as a pixel distance.clean_dup_by_date
Colors for plottingcolors
Function to find strong correlations within environmental predictorscorrelation_finder
Function to compute the covariance matrix of an ellipsoid niche model.cov_center
Compute omission rate and statistical metrics for ellipsoid models.ellipsoid_omr
ellipsoid_projection: function to project an ellipsoid modelellipsoid_projection
ellipsoid_selection: Performs models selection for ellipsoid modelsellipsoid_selection
Extract environmental data by dateex_by_date
inEllipsoid: Determine if a point is inside or outside an ellipsoidinEllipsoid
Helper function to obtain layer name from a raster layermetaras
Function to plot ellipsoid models in E-spaceplot_ellipsoid
Predict the potential distribution of species based on environmental conditionspredict predict,sp.temporal.selection-method
Partial ROC calculation for Niche ModelspROC
Function to create a Species Temporal Data object (STD object).sp_temporal_data
S3 classes to organize data and results of 'tenm' objectssp.temporal.bg-class
S3 classes to organize data and results of 'tenm' objectssp.temporal.env-class
S3 classes to organize data and results of 'tenm' objectssp.temporal.modeling-class
S3 classes to organize data and results of 'tenm' objectssp.temporal.selection-class
Temporal data.frame to Samples With Data formattdf2swd
Function to find the best n-dimensional ellipsoid modeltenm_selection