Package: letsR 6.1

Bruno Vilela

letsR: Data Handling and Analysis in Macroecology

Handling, processing, and analyzing geographic data on species' distributions and environmental variables. Read Vilela & Villalobos (2015) <doi:10.1111/2041-210X.12401> for details.

Authors:Bruno Vilela [aut, cre], Fabricio Villalobos [aut]

letsR_6.1.tar.gz
letsR_6.1.zip(r-4.7)letsR_6.1.zip(r-4.6)letsR_6.1.zip(r-4.5)
letsR_6.1.tgz(r-4.6-any)letsR_6.1.tgz(r-4.5-any)
letsR_6.1.tar.gz(r-4.7-any)letsR_6.1.tar.gz(r-4.6-any)
letsR_6.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
letsR/json (API)

# Install 'letsR' in R:

install.packages('letsR', repos = c('https://macroecology.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/macroecology/letsr/issues

Pkgdown/docs site:https://brunovilela.github.io

Datasets:

IUCN - IUCN evaluation for frogs of the genus Phyllomedusa
PAM - PresenceAbsence object for frogs of the genus Phyllomedusa
Phyllomedusa - Phyllomedusa
prec - Annual Precipitation raster for the world.
temp - Mean temperature raster for the world.
wrld_simpl - Simplified world country polygons

On CRAN:

9.93 score 29 stars 150 scripts 640 downloads 9 mentions 37 exports 14 dependencies

Last updated from:ab886f6e38. Checks:9 OK. Indexed: yes.

Target	Result	Time	Files	Syslog
linux-devel-x86_64	OK	255
source / vignettes	OK	283
linux-release-x86_64	OK	227
macos-release-arm64	OK	268
macos-oldrel-arm64	OK	254
windows-devel	OK	216
windows-release	OK	186
windows-oldrel	OK	215
wasm-release	OK	147

Exports:lets.addpoly lets.addvar lets.attrcells lets.attrpam lets.classvar lets.correl lets.distmat lets.envcells lets.envpam lets.field lets.gridirizer lets.iucncont lets.load lets.maplizer lets.maplizer.attr lets.maplizer.env lets.midpoint lets.overlap lets.pamcrop lets.plot.attrcells lets.plot.attrpam lets.plot.envcells lets.plot.envpam lets.presab lets.presab.birds lets.presab.grid lets.presab.grid.points lets.presab.points lets.rangesize lets.save lets.shFilter lets.subsetPAM lets.subsetPAMatt lets.subsetPAMenv lets.summarizer lets.summaryze.cells lets.transf

Dependencies:class classInt DBI e1071 geosphere KernSmooth MASS proxy Rcpp s2 sf terra units wk

Mapping species richness in attribute space

Overview | Simulating trait data and building the attribute space PAM | Visualizing richness in attribute space | Computing attribute-space descriptors | Summarizing descriptors by species | Linking attribute space to geographic space | References

Rendered fromMapping-species-richness-in-attribute-space.Rmdusingknitr::rmarkdown

Last update: 2026-03-27
Started: 2025-10-17

Mapping species richness in environmental space

Loading data | Creating a PAM in environmental space | Visualizing environmental richness | Highlighting a single species | Mapping traits in environmental space | Describing environmental–geographical structure | Summarize descriptors per environmental cell | Plot the descriptors | Diagnosing centrality vs. richness (optional) | References

Rendered fromMapping-species-richness-in-environmental-space.Rmdusingknitr::rmarkdown

Last update: 2026-03-27
Started: 2025-07-07

Cross-mapping biodiversity metrics across spaces

Overview | Data and environmental PAM (example with Phyllomedusa) | Environmental descriptors per environmental cell | Attribute-space PAM for Phyllomedusa species | Cross-mapping an environmental metric into geographic and attribute spaces | A. Into geographic space | B. Into attribute space | Cross-mapping attribute metrics back to geography

Rendered fromCross-mapping-biodiversity-metrics-Phyllomedusa.Rmdusingknitr::rmarkdown

Last update: 2026-03-25
Started: 2025-10-17

A guide to transform species distributions into a presence absence matrix based on a user-defined grid in R

IUCN shapefiles | Quick start | Using different projections | Other features | Occurrence data (e.g. GBIF) | Using your own grid

Rendered fromA-guide-to-transform-species-distributions-into-a-presence-absence-matrix-based.Rmdusingknitr::rmarkdown

Last update: 2026-03-25
Started: 2023-11-15

Adding variables to a PresenceAbsence object

Adding variables in raster format | Adding variables in polygon format

Rendered fromAdding-variables-to-a-presenceabsence-object.Rmdusingknitr::rmarkdown

Last update: 2026-03-25
Started: 2023-11-15

Cropping and subseting your presence absence matrix

Rendered fromcropping-and-subseting-your-presence-absence-matrix.Rmdusingknitr::rmarkdown

Last update: 2026-03-25
Started: 2023-11-15

Mapping species traits: community level analysis

Community level analysis

Rendered frommapping-species-traits.Rmdusingknitr::rmarkdown

Last update: 2026-03-25
Started: 2023-11-15

How to save and load a PresenceAbsence object

Rendered fromsave-load-presenceabsence.Rmdusingknitr::rmarkdown

Last update: 2026-03-25
Started: 2023-11-15

Macroecological analysis at the species level

Example 1: Species level test of Rapoport's rule on Phyllomedusa frogs. | Example 2: Extinction risk correlation with temperature

Rendered fromspecies-level-macroecological-analysis.Rmdusingknitr::rmarkdown

Last update: 2026-03-25
Started: 2023-11-15

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Tools for Data Handling and Analysis in Macroecology.	letsR-package letsR
IUCN evaluation for frogs of the genus Phyllomedusa	IUCN
Add polygon coverage to a PresenceAbscence object	lets.addpoly
Add variables (in raster format) to a PresenceAbscence object	lets.addvar
Descriptors of position, centrality, and isolation in attribute space	lets.attrcells
Attribute-space Presence–Absence Matrix (attrPAM)	lets.attrpam
Frequency distribution of a variable within a species' range	lets.classvar
Compute correlogram based on the Moran's I index	lets.correl
Compute a geographic distance matrix	lets.distmat
Environmental descriptors for Presence–Absence in environmental space	lets.envcells
Create a presence–absence matrix in environmental space	lets.envpam
Create species' values based on the species co-occurrence within focal ranges	lets.field
Fits a grid into a PresenceAbsence object	lets.gridirizer
Transform IUCN RedList conservation status to continuous values	lets.iucncont
Load a PresenceAbsence object	lets.load
Create a matrix summarizing species' attributes within cells of a PresenceAbsence object	lets.maplizer
Map species-level attributes over the attribute-space grid	lets.maplizer.attr
Map species attributes in both environmental and geographic spaces	lets.maplizer.env
Compute the midpoint of species' geographic ranges	lets.midpoint
Compute pairwise species' geographic overlaps	lets.overlap
Crop a PresenceAbsence object based on an input shapefile	lets.pamcrop
Map AttrPAM descriptor layers	lets.plot.attrcells
Plot attrPAM results	lets.plot.attrpam
Map envPAM descriptors	lets.plot.envcells
Plot species richness in environmental and geographical space	lets.plot.envpam
Create a presence-absence matrix of species' geographic ranges within a grid	lets.presab
Create a presence-absence matrix of species' geographic ranges within a grid for the Birdlife spatial data	lets.presab.birds
Create a presence-absence matrix of species' geographic ranges within a user's grid shapefile (beta version)	lets.presab.grid
Create a presence-absence matrix based on species' point occurrences within a user's grid shapefile (beta version)	lets.presab.grid.points
Create a presence-absence matrix based on species' point occurrences	lets.presab.points
Compute species' geographic range sizes	lets.rangesize
Save a PresenceAbsence object	lets.save
Filter species' shapefiles based on its presence, origin, and season	lets.shFilter
Subset a PresenceAbsence object based on species names	lets.subsetPAM
Subset an attribute PAM by species names	lets.subsetPAMatt
Subset an environmental PAM by species names	lets.subsetPAMenv
Summarize variable(s) values in a presence-absence matrix within species' ranges	lets.summarizer
Aggregate cell-wise metrics across occupied cells per species	lets.summaryze.cells
Transform values of a vector	lets.transf
PresenceAbsence object for frogs of the genus Phyllomedusa	PAM
Phyllomedusa	Phyllomedusa
Plot an object of class PresenceAbsence	plot.PresenceAbsence
Annual Precipitation raster for the world.	prec
PresenceAbsence Class	PresenceAbsence PresenceAbsence-class
Print for object of class PresenceAbsence	print.PresenceAbsence
Print summary for object of class PresenceAbsence	print.summary.PresenceAbsence
Summary for object of class PresenceAbsence	summary.PresenceAbsence
Mean temperature raster for the world.	temp
Simplified world country polygons	wrld_simpl

Usage by other packages (reverse dependencies)