Package 'letsR' reference manual

Title:	Data Handling and Analysis in Macroecology
Description:	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]
Maintainer:	Bruno Vilela <[email protected]>
License:	GPL-2
Version:	5.0
Built:	2024-09-13 06:42:25 UTC
Source:	https://github.com/macroecology/letsr

Tools for Data Handling and Analysis in Macroecology.

Description

The letsR package is being developed to help researchers in the handling, processing, and analysis of macroecological data. Its purpose is to integrate these methodological processes into a single software platform for macroecological analyses. The package's main functions allow users to build presence-absence matrices, the basic analytical tool in macroecology, from species' geographical distributions and merge them with species' traits, conservation information (downloadable using functions from this package) and spatial environmental layers. In addition, other package's functions enable users to summarize and visualize information from presence-absence matrices.

Details

All functions in this package use a prefix and a suffix separated by a dot. The prefix refers to the package's name and the suffix to the actual function. This is done to avoid confusion with potentially similarly-named functions from other R packages. For instance, the letsR function used to create presence-absence matrices is called lets.presab (but see also lets.presab.birds and lets.presab.points) whereas the one used to add variables to a presence-absence matrix is called lets.addvar. The package's basic functions create and work on a particular S3 object class called PresenceAbsence. Such PresenceAbsence object class allows storing information beyond presence-absence data (e.g. user-defined grid-cell system) and using the generic plot, summary and print functions of R. Also, some package's functions allow the user to input customary R objects (e.g. vector, matrix, data.frame).

Another set of functions in this package allow the user to download species' information related to their description and conservation status as provided by the IUCN's REdList database (lets.iucn, lets.iucn.ha, lets.iucn.his). For this, such functions use the IUCN's RedList API to retrieve information from its webpage.

If you are looking for the most recent version of the package, you can get the development version of letsR on github (https://github.com/macroecology/letsR).

Package:	lestR
Type:	Package
Version:	3.1
Date:	2018-01-24
License:	GPL-2

Author(s)

Bruno Vilela
(email: [email protected]; Website: https://bvilela.weebly.com/)

Fabricio Villalobos
(email: [email protected]; Website: https://fabro.github.io)

References

Vilela, B., & Villalobos, F. (2015). letsR: a new R package for data handling and analysis in macroecology. Methods in Ecology and Evolution.

IUCN evaluation for frogs of the genus Phyllomedusa

Description

Result of the (deprecated) function lets.iucn applied to South American frog genus Phyllomedusa in 2014.

Usage

IUCN
IUCN

Format

A data frame with 32 rows and 7 columns:

Species: Scientific name
Family: Family
Status: Red List Status
Criteria: Criteria for listing as threatened
Population: Population trend per IUCN
Description_Year: Year described
Country: Presence in country

Source

IUCN - https://www.iucnredlist.org/. 2014.

Add polygon coverage to a PresenceAbscence object

Description

Add polygon coverage within cells of a PresenceAbsence object.

Usage

lets.addpoly(x, y, z, onlyvar = FALSE, count = FALSE)
lets.addpoly(x, y, z, onlyvar = FALSE, count = FALSE)

Arguments

`x`	A `PresenceAbsence` object.
`y`	Polygon of interest.
`z`	A character indicating the column name of the polygon containing the attributes to be used.
`onlyvar`	If `TRUE` only the matrix object will be returned.
`count`	Logical, if `TRUE` a progress bar indicating the processing progress will be shown.

Value

The result is a presence-absence matrix of species with the polygons' attributes used added as columns at the right-end of the matrix. The Values represent the percentage of the cell covered by the polygon attribute used.

Author(s)

Bruno Vilela

Examples

## Not run: 
data(PAM)  # Phyllomedusa presence-absence matrix
data(wrld_simpl)  # World map
Brazil <- wrld_simpl[wrld_simpl$NAME == "Brazil", ]  # Brazil (polygon)

# Check where is the variable name 
# (in this case it is in "NAME" which will be my z value)
names(Brazil)

PAM_pol <- lets.addpoly(PAM, Brazil, "NAME", onlyvar = TRUE)

## End(Not run)

## Not run: 
data(PAM)  # Phyllomedusa presence-absence matrix
data(wrld_simpl)  # World map
Brazil <- wrld_simpl[wrld_simpl$NAME == "Brazil", ]  # Brazil (polygon)

# Check where is the variable name 
# (in this case it is in "NAME" which will be my z value)
names(Brazil)

PAM_pol <- lets.addpoly(PAM, Brazil, "NAME", onlyvar = TRUE)

## End(Not run)

Add variables (in raster format) to a PresenceAbscence object

Description

Add variables (in raster format), usually environmental, to a PresenceAbsence object. Variables are included as additional columns containing the aggregate/summarize value of the variable(s) in each cell of the presence-absence matrix.

Usage

lets.addvar(x, y, onlyvar = FALSE, fun = mean)
lets.addvar(x, y, onlyvar = FALSE, fun = mean)

Arguments

`x`	A `PresenceAbsence` object.
`y`	Variables to be added in `SpatRaster` format.
`onlyvar`	If `TRUE` only the `matrix` object will be returned.
`fun`	Function used to aggregate the variables(s) values over each cell. Note that this will only work for variables with a resolution value smaller (i.e. higher resolution) than the PAM.

Value

The result is a presence-absence matrix of species with the variables added as columns at the right-end of the matrix (but see the 'onlyvar' argument).

Note

The PresenceAbsence and the Raster variable must be in the same projection.

Author(s)

Bruno Vilela

Examples

## Not run: 
data(temp)  # Global mean temperature
temp <- terra::unwrap(temp)
data(PAM)  # Phyllomedusa presence-absence matrix
# Mean temperature
PAM_temp_mean <- lets.addvar(PAM, temp)
# Standard deviation of temperature
PAM_temp_sd <- lets.addvar(PAM, temp, fun = sd, onlyvar = TRUE)
# Mean and SD in the PAM
PAM_temp_mean_sd <- cbind(PAM_temp_mean, PAM_temp_sd)

## End(Not run)

## Not run: 
data(temp)  # Global mean temperature
temp <- terra::unwrap(temp)
data(PAM)  # Phyllomedusa presence-absence matrix
# Mean temperature
PAM_temp_mean <- lets.addvar(PAM, temp)
# Standard deviation of temperature
PAM_temp_sd <- lets.addvar(PAM, temp, fun = sd, onlyvar = TRUE)
# Mean and SD in the PAM
PAM_temp_mean_sd <- cbind(PAM_temp_mean, PAM_temp_sd)

## End(Not run)

Frequency distribution of a variable within a species' range

Description

Based on a species Presence-Absence matrix including variables of interest (see lets.addvar), the function divides a continuous variable into classes and counts the frequency of each class within each species' range.

Usage

lets.classvar(x, groups = "default", pos, xy)
lets.classvar(x, groups = "default", pos, xy)

Arguments

`x`	Presence-absence `matrix` with a single variable added (see `lets.addvar`).
`groups`	The number of classes into which the variable will be divided. Default calculates the number of classes as the default for a histogram (`hist`).
`pos`	Column number containing the variable of interest.
`xy`	Logical, if `TRUE` the input matrix contains the geographic coordinates in the first two columns.

Value

A matrix with species in the rows and the variable's classes in the columns.

Author(s)

Bruno Vilela

References

Morales-Castilla et al. 2013. Range size patterns of New World oscine passerines (Aves): insights from differences among migratory and sedentary clades. Journal of Biogeography, 40, 2261-2273.

Examples

## Not run: 
data(PAM)
data(temp)
pamvar <- lets.addvar(PAM, temp)
resu <- lets.classvar(x = pamvar, pos = ncol(pamvar), xy = TRUE)

## End(Not run)
  
## Not run: 
data(PAM)
data(temp)
pamvar <- lets.addvar(PAM, temp)
resu <- lets.classvar(x = pamvar, pos = ncol(pamvar), xy = TRUE)

## End(Not run)

Compute correlogram based on the Moran's I index

Description

Computes the Moran's I correlogram of a single or multiple variables.

Usage

lets.correl(x, y, z, equidistant = FALSE, plot = TRUE)
lets.correl(x, y, z, equidistant = FALSE, plot = TRUE)

Arguments

`x`	A single numeric variable in vector format or multiple variables in matrix format (as columns).
`y`	A distance matrix of class `matrix` or `dist`.
`z`	The number of distance classes to use in the correlogram.
`equidistant`	Logical, if `TRUE` the classes will be equidistant. If `FALSE` the classes will have equal number of observations.
`plot`	Logical, if `TRUE` the correlogram will be ploted.

Value

Returns a matrix with the Moran's I Observed value, Confidence Interval (95 and Expected value. Also the p value of the randomization test, the mean distance between classes, and the number of observations. quase tudo

Author(s)

Bruno Vilela, Fabricio Villalobos, Lucas Jardim & Jose Alexandre Diniz-Filho

References

Sokal, R.R. & Oden, N.L. (1978) Spatial autocorrelation in biology. 1. Methodology. Biological Journal of the Linnean Society, 10, 199-228.

Sokal, R.R. & Oden, N.L. (1978) Spatial autocorrelation in biology. 2. Some biological implications and four applications of evolutionary and ecological interest. Biological Journal of the Linnean Society, 10, 229-249.

Examples

## Not run: 
data(PAM)
data(IUCN)

# Spatial autocorrelation in description year (species level)
midpoint <- lets.midpoint(PAM)
distan <- lets.distmat(midpoint[, 2:3])
moran <- lets.correl(IUCN$Description, distan, 12,
                     equidistant = FALSE, 
                     plot = TRUE)
                     

## End(Not run)

## Not run: 
data(PAM)
data(IUCN)

# Spatial autocorrelation in description year (species level)
midpoint <- lets.midpoint(PAM)
distan <- lets.distmat(midpoint[, 2:3])
moran <- lets.correl(IUCN$Description, distan, 12,
                     equidistant = FALSE, 
                     plot = TRUE)
                     

## End(Not run)

Compute a geographic distance matrix

Description

Calculates a geographic distance matrix based on a PresenceAbsence or a two column matrix of x(longitude) and y(latitude).

Usage

lets.distmat(xy, asdist = TRUE)
lets.distmat(xy, asdist = TRUE)

Arguments

`xy`	A `PresenceAbsence` object or a `matrix` with two columns (longitude, latitude).
`asdist`	Logical, if `TRUE` the result will be an object of class `dist`, if `FALSE` the result will be an object of class `matrix`.

Details

This function basically facilitates the use of terra::distance on a PresenceAbsence object, allowing also the user to have directly a dist object. The distance is always expressed in meter if the coordinate reference system is longitude/latitude, and in map units otherwise. Map units are typically meter, but inspect crs(x) if in doubt.

Value

The user can choose between dist and matrix class object to be returned. The resulting values are in kilometres (but see the argument 'unit' in rdist.earth).

Author(s)

Bruno Vilela & Fabricio Villalobos

Examples

## Not run: 
data(PAM)
distPAM <- lets.distmat(PAM)

## End(Not run)

## Not run: 
data(PAM)
distPAM <- lets.distmat(PAM)

## End(Not run)

Create species' values based on the species co-occurrence within focal ranges

Description

Create single species' values based on the attributes of species co-occurring within individual ranges.

Usage

lets.field(x, y, z, weight = TRUE, xy = NULL, count = FALSE)
lets.field(x, y, z, weight = TRUE, xy = NULL, count = FALSE)

Arguments

`x`	A `PresenceAbsence` object or a presence-absence in `matrix` format (see xy argument for matrix use) with the species named in the columns.
`y`	Species attribute to be considered. It must be a numeric attribute.
`z`	Species names in the same order as the attributes and exactly the same as named in the `matrix` or in the `PresenceAbsence` object.
`weight`	If `TRUE` the value is weighted by species' range size, if `FALSE` the value is the mean of all species that co-occur within the focal species.
`xy`	If `TRUE` the presence-absence `matrix` contains the cell coordinates in the first two columns.
`count`	Logical, if `TRUE` a counting window will open.

Details

If the species do not co-occur with any other species NaN will be returned.

Author(s)

Bruno Vilela & Fabricio Villalobos

References

Villalobos, F. and Arita, H.T. 2010. The diversity field of New World leaf-nosed bats (Phyllostomidae). Global Ecology and Biogeography. 19, 200-211.

Villalobos, F., Rangel, T.F., and Diniz-Filho, J.A.F. 2013. Phylogenetic fields of species: cross-species patterns of phylogenetic structure and geographical coexistence. Proceedings of the Royal Society B. 280, 20122570.

Examples

## Not run: 
data(PAM)
range <- lets.rangesize(x = PAM, units = "cell")
field <- lets.field(PAM, range, PAM$S, weight = TRUE)

## End(Not run)

## Not run: 
data(PAM)
range <- lets.rangesize(x = PAM, units = "cell")
field <- lets.field(PAM, range, PAM$S, weight = TRUE)

## End(Not run)

Fits a grid into a PresenceAbsence object

Description

This function creates a grid in shapefile format and adds its cells' IDs to the presence-absence matrix. The function was created to facilitate the use of the PresenceAbsence object for the ones who prefer to work with a grid in shapefile format.

Usage

lets.gridirizer(x)
lets.gridirizer(x)

Arguments

`x`	A `PresenceAbsence` object.

Value

The result is a list of two objects. The first is a grid in shapefile format; the second is a presence-absence matrix with an aditional column called SP_ID (shapefile cell identifier).

Author(s)

Bruno Vilela

Examples

## Not run: 
data(PAM)
PAM.grid <- lets.gridirizer(PAM)
names(PAM.grid)
# Grid in polygon format (can be saved in shapefile)
PAM.grid$Grid
# Presence-absence matrix (beggining only)
head(PAM.grid$Presence[, 1:5])


## End(Not run)

## Not run: 
data(PAM)
PAM.grid <- lets.gridirizer(PAM)
names(PAM.grid)
# Grid in polygon format (can be saved in shapefile)
PAM.grid$Grid
# Presence-absence matrix (beggining only)
head(PAM.grid$Presence[, 1:5])


## End(Not run)

Download species' information from the IUCN RedList online database (No longer supported)

Description

Get species' information from the IUCN website(https://www.iucnredlist.org/) for one or more species.

Usage

lets.iucn(input, count = FALSE)
lets.iucn(input, count = FALSE)

Arguments

`input`	Character vector with one or more species names, or an object of class `PresenceAbsence`.
`count`	Logical, if `TRUE` a counting window will open.

Details

Note that you must be connected to the internet to use this function.

Value

Returns a data frame with the Species Name, Family, Conservation Status, Criteria used to estabilish the conservation status, Population Status, Year of Description (only for animals), and the Countries where it occurs. If species do not have information (i.e. have not been evaluated), the result is: NE (Not evaluated).

Author(s)

Bruno Vilela

Examples

## Not run: 
# Single species
lets.iucn("Pongo pygmaeus")

# Multiple species
sp <- c("Musonycteris harrisoni", "Ailuropoda melanoleuca",
        "Cebus flavius")
lets.iucn(sp)

## End(Not run)

## Not run: 
# Single species
lets.iucn("Pongo pygmaeus")

# Multiple species
sp <- c("Musonycteris harrisoni", "Ailuropoda melanoleuca",
        "Cebus flavius")
lets.iucn(sp)

## End(Not run)

Download species' habitat information from the IUCN RedList online database (No longer supported)

Description

Get species' habitat information from the IUCN RedList website(https://www.iucnredlist.org/) for one or more species.

Usage

lets.iucn.ha(input, count = FALSE)
lets.iucn.ha(input, count = FALSE)

Arguments

`input`	Character vector with one or more species names, or an object of the `PresenceAbsence` class.
`count`	Logical, if `TRUE` a counting window will open.

Details

Note that you must be connected to the internet to use this function.

Value

A data frame with species names in the first column and the habitats where it occurs in the remaining columns, '1' if species is present in that habitat and '0' otherwise.

Author(s)

Bruno Vilela

Examples

## Not run: 
# Single species
lets.iucn.ha("Pongo pygmaeus")

# Multiple species
sp <- c("Musonycteris harrisoni", "Ailuropoda melanoleuca",
        "Cebus flavius")
lets.iucn.ha(sp)

## End(Not run)

## Not run: 
# Single species
lets.iucn.ha("Pongo pygmaeus")

# Multiple species
sp <- c("Musonycteris harrisoni", "Ailuropoda melanoleuca",
        "Cebus flavius")
lets.iucn.ha(sp)

## End(Not run)

Download species' temporal trend in conservation status from the IUCN RedList online database (No longer supported)

Description

Get species conservation status over time (i.e. from 1980 to the present date available) from the IUCN website(https://www.iucnredlist.org/) for one or more species.

Usage

lets.iucn.his(input, count = FALSE)
lets.iucn.his(input, count = FALSE)

Arguments

`input`	character vector with one or more species names, or an object of class `PresenceAbsence`.
`count`	Logical, if `TRUE` a counting window will open.

Details

Note that you must be connected to the internet to use this function.

Value

A data frame with the species names in the first column rows and the years (1980 - present) in the remaining columns, the code represents the species' conservation status (see the IUCN RedList website for details). If species do not have information (i.e. have not been evaluated), the result is: NE (Not evaluated).

Codes and categories:

EX: Extinct

EW: Extinct in the Wild

VU: Vulnerable

EN: Endangered

CR: Critically Endangered

LC: Least Concern

NT: Near Threatened

DD: Data Deficient

CT: Commercially Threatened

IN: Indeterminate

IK: Insufficiently Known

LR: Lower Risk

RA: Rare

Author(s)

Bruno Vilela

Examples

## Not run: 
# Single species
lets.iucn.his("Panthera onca")

# Multiple species
sp <- c("Rhincodon typus", "Ailuropoda melanoleuca")
lets.iucn.his(sp)

## End(Not run)

## Not run: 
# Single species
lets.iucn.his("Panthera onca")

# Multiple species
sp <- c("Rhincodon typus", "Ailuropoda melanoleuca")
lets.iucn.his(sp)

## End(Not run)

Transform IUCN RedList conservation status to continuous values

Description

Transform IUCN RedList conservation status to continuous values ranging from 0 to 5.

Usage

lets.iucncont(x, dd = NA, ne = NA)
lets.iucncont(x, dd = NA, ne = NA)

Arguments

`x`	A vector or a matrix containing IUCN codes to be transformed.
`dd`	The value to be attributed to DD (data-deficient) species, the default option is NA.
`ne`	The value to be attributed to NE (not-evaluated) species, the default option is NA.

Value

Returns a vector/matrix with continuos values from 0 to 5.

EX and EW = 5

CR = 4

EN = 3

VU = 2

NT = 1

LC = 0

DD = NA

NE = NA

Author(s)

Bruno Vilela

References

Purvis A et al., 2000. Predicting extinction risk in declining species. Proceedings of the Royal Society of London. Series B: Biological Sciences, 267.1456: 1947-1952.

Examples

## Not run: 
#Vector transformation
status <- sample(c("EN","VU", "NT", "CR", "DD", "LC", "EX"), 
                 30, replace = TRUE) 
transV <- lets.iucncont(status)

#matrix transformation
data(IUCN)
transM <- lets.iucncont(IUCN)


## End(Not run)

## Not run: 
#Vector transformation
status <- sample(c("EN","VU", "NT", "CR", "DD", "LC", "EX"), 
                 30, replace = TRUE) 
transV <- lets.iucncont(status)

#matrix transformation
data(IUCN)
transM <- lets.iucncont(IUCN)


## End(Not run)

Load a PresenceAbsence object

Description

Reload PresenceAbsence objects written with the function lets.save.

Usage

lets.load(file)
lets.load(file)

Arguments

file

a character string giving the name of the file to load.

Author(s)

Bruno Vilela

Examples

## Not run: 
data(PAM)
lets.save(PAM, file = "PAM.RData")
PAM <- lets.load(file = "PAM.RData")

## End(Not run)

## Not run: 
data(PAM)
lets.save(PAM, file = "PAM.RData")
PAM <- lets.load(file = "PAM.RData")

## End(Not run)

Create a matrix summarizing species' attributes within cells of a PresenceAbsence object

Description

Summarize species atributes per cell in a presence-absence matrix.

Usage

lets.maplizer(x, y, z, func = mean, ras = FALSE)
lets.maplizer(x, y, z, func = mean, ras = FALSE)

Arguments

`x`	A `PresenceAbsence` object.
`y`	Species attribute to be considered. It must be a numeric attribute.
`z`	Species names in the same order as the attributes and exactly the same as named in the `PresenceAbsence` object.
`func`	A function to summarize the species' atribute in each cell (the function must return only one value).
`ras`	If `TRUE` the raster object will be returned together with the matrix.

Value

The result can be both a matrix or a list cointaining the follow objects:

Matrix: a matrix object with the cells' geographic coordinates and the summarized species' attributes within them.

Raster: The summarized species'attributed maped in a SpatRaster object.

Author(s)

Bruno Vilela

Examples

## Not run: 
data(PAM)
data(IUCN)
trait <- IUCN$Description_Year
resu <- lets.maplizer(PAM, trait, PAM$S, ras = TRUE)
head(resu$Matrix)
plot(resu$Raster, xlab = "Longitude", ylab = "Latitude", 
main = "Mean description year per site")


## End(Not run)

## Not run: 
data(PAM)
data(IUCN)
trait <- IUCN$Description_Year
resu <- lets.maplizer(PAM, trait, PAM$S, ras = TRUE)
head(resu$Matrix)
plot(resu$Raster, xlab = "Longitude", ylab = "Latitude", 
main = "Mean description year per site")


## End(Not run)

Compute the midpoint of species' geographic ranges

Description

Calculate species distribution midpoint from a presence-absence matrix using several methods.

Usage

lets.midpoint(pam, planar = FALSE, method = "PC", inside = FALSE)
lets.midpoint(pam, planar = FALSE, method = "PC", inside = FALSE)

Arguments

`pam`	A presence-absence `matrix` (sites in the rows and species in the columns, with the first two columns containing the longitudinal and latitudinal coordinates, respectively), or an object of class `PresenceAbsence`.
`planar`	Logical, if `FALSE` the coordinates are in Longitude/Latitude. If `TRUE` the coordinates are planar.
`method`	Default option, "PC" (polygon centroid) will generate a polygon from the raster, and calculate the centroid of this polygon based on the function `terra::centroids`. Note that for the "PC" method, users can only use PresenceAbsence objects. Note also that this method will not be the best for PresenceAbsence objects made from occurrence records, or that have multiple disjoint distributions. Users can also choose the geographic midpoint, using the option "GM". "GM" will create a bounding box across the extremes of the distribution and calculate the centroid. Alternatively, the midpoint can be calculated as the point that minimize the distance between all cells of the PAM, using the method "CMD"(centre of minimum distance). The user can also calculate the midpoint, based on the centroid of the minimum convex polygon of the distribution, using the method "MCC". This last method is useful when using a PresenceAbsence object made from occurrence records.
`inside`	logical. If TRUE the points returned are guaranteed to be inside the polygons or on the lines, but they are not the true centroids. True centroids may be outside a polygon, for example when a polygon is "bean shaped", and they are unlikely to be on their line

Value

A data.frame containing the species' names and geographic coordinates (longitude [x], latitude [y]) of species' midpoints.

Author(s)

Fabricio Villalobos & Bruno Vilela

Examples

## Not run: 
data(PAM)
mid <- lets.midpoint(PAM, method = "PC")
mid2 <- lets.midpoint(PAM, method = "GM")
mid3 <- lets.midpoint(PAM, method = "CMD")
mid4 <- lets.midpoint(PAM, method = "MCC")
mid5 <- lets.midpoint(PAM, method = "PC", planar = TRUE)
mid6 <- lets.midpoint(PAM, method = "GM", planar = TRUE)
mid7 <- lets.midpoint(PAM, method = "CMD", planar = TRUE)
mid8 <- lets.midpoint(PAM, method = "MCC", planar = TRUE)

for (sp in seq_len(nrow(mid))) {
 #sp = 4 # Or choose a line or species
 plot(PAM, name = mid[sp, 1])
 points(mid[sp, -1], col = adjustcolor("blue", .8), pch = 20, cex = 1.5)
 points(mid2[sp, -1], col = adjustcolor("green", .8), pch = 20, cex = 1.5)
 points(mid3[sp, -1], col = adjustcolor("yellow", .8), pch = 20, cex = 1.5)
 points(mid4[sp, -1], col = adjustcolor("purple", .8), pch = 20, cex = 1.5)
 points(mid5[sp, -1], col = adjustcolor("orange", .8), pch = 20, cex = 1.5)
 points(mid6[sp, -1], col = adjustcolor("black", .8), pch = 20, cex = 1.5)
 points(mid7[sp, -1], col = adjustcolor("gray", .8), pch = 20, cex = 1.5)
 points(mid8[sp, -1], col = adjustcolor("brown", .8), pch = 20, cex = 1.5)
 Sys.sleep(1)
}

## End(Not run)

## Not run: 
data(PAM)
mid <- lets.midpoint(PAM, method = "PC")
mid2 <- lets.midpoint(PAM, method = "GM")
mid3 <- lets.midpoint(PAM, method = "CMD")
mid4 <- lets.midpoint(PAM, method = "MCC")
mid5 <- lets.midpoint(PAM, method = "PC", planar = TRUE)
mid6 <- lets.midpoint(PAM, method = "GM", planar = TRUE)
mid7 <- lets.midpoint(PAM, method = "CMD", planar = TRUE)
mid8 <- lets.midpoint(PAM, method = "MCC", planar = TRUE)

for (sp in seq_len(nrow(mid))) {
 #sp = 4 # Or choose a line or species
 plot(PAM, name = mid[sp, 1])
 points(mid[sp, -1], col = adjustcolor("blue", .8), pch = 20, cex = 1.5)
 points(mid2[sp, -1], col = adjustcolor("green", .8), pch = 20, cex = 1.5)
 points(mid3[sp, -1], col = adjustcolor("yellow", .8), pch = 20, cex = 1.5)
 points(mid4[sp, -1], col = adjustcolor("purple", .8), pch = 20, cex = 1.5)
 points(mid5[sp, -1], col = adjustcolor("orange", .8), pch = 20, cex = 1.5)
 points(mid6[sp, -1], col = adjustcolor("black", .8), pch = 20, cex = 1.5)
 points(mid7[sp, -1], col = adjustcolor("gray", .8), pch = 20, cex = 1.5)
 points(mid8[sp, -1], col = adjustcolor("brown", .8), pch = 20, cex = 1.5)
 Sys.sleep(1)
}

## End(Not run)

Compute pairwise species' geographic overlaps

Description

Creates a species geographic overlap matrix from a Presence-absence matrix.

Usage

lets.overlap(pam, method = "Chesser&Zink", xy = NULL)
lets.overlap(pam, method = "Chesser&Zink", xy = NULL)

Arguments

`pam`	A presence-absence matrix (sites in rows and species in columns, with the first two columns containing the longitudinal and latitudinal coordinates, respectively), or an object of class `PresenceAbsence`.
`method`	The method used to calculate the overlap matrix. "Chesser&Zink" calculates the degree of overlap as the proportion of the smaller range that overlaps within the larger range (Chesser & Zink 1994). "Proportional" calculates the proportion of a range that overlaps another range, the resultant matrix is not symmetric. "Cells" will show the number of overlapping grid cells between a pair of species' ranges (same for both species in a pair), here the resultant matrix is symmetric.
`xy`	Logical, if `TRUE` the input matrix contains geographic coordinates in the first two columns.

Author(s)

Fabricio Villalobos & Bruno Vilela

References

Chesser, R. Terry, and Robert M. Zink. "Modes of speciation in birds: a test of Lynch's method." Evolution (1994): 490-497.

Barraclough, Timothy G., and Alfried P. Vogler. "Detecting the geographical pattern of speciation from species-level phylogenies." The American Naturalist 155.4 (2000): 419-434.

Examples

## Not run: 
data(PAM)
CZ <- lets.overlap(PAM, method = "Chesser&Zink")
prop <- lets.overlap(PAM, method = "Proportional")
cells <- lets.overlap(PAM, method = "Cells")

## End(Not run)

## Not run: 
data(PAM)
CZ <- lets.overlap(PAM, method = "Chesser&Zink")
prop <- lets.overlap(PAM, method = "Proportional")
cells <- lets.overlap(PAM, method = "Cells")

## End(Not run)

Crop a PresenceAbsence object based on an input shapefile

Description

Crop a PresenceAbsence object based on a shapefile provided by the user.

Usage

lets.pamcrop(x, shp, remove.sp = TRUE, remove.cells = FALSE)
lets.pamcrop(x, shp, remove.sp = TRUE, remove.cells = FALSE)

Arguments

`x`	A `PresenceAbsence` object.
`shp`	Object of class SpatVector (see function `terra::vect`) to crop the PresenceAbsence object.
`remove.sp`	Logical, if `TRUE` the final matrix will not contain species that do not match any cell in the grid.
`remove.cells`	Logical, if `FALSE` the final matrix will not contain cells in the grid with a value of zero (i.e. sites with no species present).

Value

The result is an object of class PresenceAbsence croped.

Author(s)

Bruno Vilela

Examples

## Not run: 
data(PAM)
data("wrld_simpl")

# PAM before crop
plot(PAM, xlab = "Longitude", ylab = "Latitude",
     main = "Phyllomedusa species richness")

# Crop PAM to Brazil
data(wrld_simpl)  # World map
Brazil <- wrld_simpl[wrld_simpl$NAME == "Brazil", ]  # Brazil (polygon)
PAM_crop <- lets.pamcrop(PAM, Brazil, remove.sp = TRUE)
plot(PAM_crop, xlab = "Longitude", ylab = "Latitude",
     main = "Phyllomedusa species richness (Brazil crop)")
plot(sf::st_geometry(wrld_simpl), add = TRUE)

## End(Not run)

## Not run: 
data(PAM)
data("wrld_simpl")

# PAM before crop
plot(PAM, xlab = "Longitude", ylab = "Latitude",
     main = "Phyllomedusa species richness")

# Crop PAM to Brazil
data(wrld_simpl)  # World map
Brazil <- wrld_simpl[wrld_simpl$NAME == "Brazil", ]  # Brazil (polygon)
PAM_crop <- lets.pamcrop(PAM, Brazil, remove.sp = TRUE)
plot(PAM_crop, xlab = "Longitude", ylab = "Latitude",
     main = "Phyllomedusa species richness (Brazil crop)")
plot(sf::st_geometry(wrld_simpl), add = TRUE)

## End(Not run)

Create a presence-absence matrix of species' geographic ranges within a grid

Description

Convert species' ranges (in shapefile format) into a presence-absence matrix based on a user-defined grid system

Usage

lets.presab(
  shapes,
  xmn = NULL,
  xmx = NULL,
  ymn = NULL,
  ymx = NULL,
  resol = NULL,
  remove.cells = TRUE,
  remove.sp = TRUE,
  show.matrix = FALSE,
  crs = "+proj=longlat +datum=WGS84",
  crs.grid = crs,
  cover = 0,
  presence = NULL,
  origin = NULL,
  seasonal = NULL,
  count = FALSE
)
lets.presab(
  shapes,
  xmn = NULL,
  xmx = NULL,
  ymn = NULL,
  ymx = NULL,
  resol = NULL,
  remove.cells = TRUE,
  remove.sp = TRUE,
  show.matrix = FALSE,
  crs = "+proj=longlat +datum=WGS84",
  crs.grid = crs,
  cover = 0,
  presence = NULL,
  origin = NULL,
  seasonal = NULL,
  count = FALSE
)

Arguments

`shapes`	Object of class `SpatVect` or `Spatial` (see packages `terra` and `sf` to read these files) containing the distribution of one or more species. Species names should be stored in the object as BINOMIAL/binomial or SCINAME/sciname.
`xmn`	Minimum longitude used to construct the grid in which the matrix will be based (i.e. the [gridded] geographic domain of interest). If NULL, limits will be calculated based on the limits of the shapes object.
`xmx`	Maximum longitude used to construct the grid in which the matrix will be based (i.e. the [gridded] geographic domain of interest). If NULL, limits will be calculated based on the limits of the shapes object.
`ymn`	Minimum latitude used to construct the grid in which the matrix will be based (i.e. the [gridded] geographic domain of interest). If NULL, limits will be calculated based on the limits of the shapes object.
`ymx`	Maximum latitude used to construct the grid in which the matrix will be based (i.e. the [gridded] geographic domain of interest). If NULL, limits will be calculated based on the limits of the shapes object.
`resol`	Numeric vector of length 1 or 2 to set the grid resolution. If NULL, resolution will be equivalent to 1 degree of latitude and longitude.
`remove.cells`	Logical, if `TRUE` the final matrix will not contain cells in the grid with a value of zero (i.e. sites with no species present).
`remove.sp`	Logical, if `TRUE` the final matrix will not contain species that do not match any cell in the grid.
`show.matrix`	Logical, if `TRUE` only the presence-absence matrix will be returned.
`crs`	Character representing the PROJ.4 type description of a Coordinate Reference System (map projection) of the polygons.
`crs.grid`	Character representing the PROJ.4 type description of a Coordinate Reference System (map projection) for the grid. Note that when you change this options you may probably change the extent coordinates and the resolution.
`cover`	Percentage of the cell covered by the shapefile that will be considered for presence (values between 0 and 1).
`presence`	A vector with the code numbers for the presence type to be considered in the process (for IUCN spatial data https://www.iucnredlist.org/resources/spatial-data-download, see metadata).
`origin`	A vector with the code numbers for the origin type to be considered in the process (for IUCN spatial data).
`seasonal`	A vector with the code numbers for the seasonal type to be considered in the process (for IUCN spatial data).
`count`	Logical, if `TRUE` a progress bar indicating the processing progress will be shown.

Details

This function creates the presence-absence matrix based on a raster object. Depending on the cell size, extension used and number of species it may require a lot of memory, and may take some time to process it. Thus, during the process, if count argument is set TRUE, a counting window will open to display the progress (i.e. the polygon/shapefile that the function is working on). Note that the number of polygons is not the same as the number of species (i.e. a species may have more than one polygon/shapefiles).

Value

The result is a list object of class PresenceAbsence with the following objects: Presence-Absence Matrix: A matrix of species' presence(1) and absence(0) information. The first two columns contain the longitude (x) and latitude (y) of the cells' centroid (from the gridded domain used); Richness Raster: A raster containing species richness data; Species name: A character vector with species' names contained in the matrix. *But see the optional argument show.matrix.

Author(s)

Bruno Vilela & Fabricio Villalobos

Examples

## Not run: 
# Spatial distribution polygons of South American frogs
# of genus Phyllomedusa.
data(Phyllomedusa)
PAM <- lets.presab(Phyllomedusa)
summary(PAM)
# Species richness map
plot(PAM, xlab = "Longitude", ylab = "Latitude",
     main = "Phyllomedusa species richness")
# Map of individual species
plot(PAM, name = "Phyllomedusa nordestina")

## End(Not run)

## Not run: 
# Spatial distribution polygons of South American frogs
# of genus Phyllomedusa.
data(Phyllomedusa)
PAM <- lets.presab(Phyllomedusa)
summary(PAM)
# Species richness map
plot(PAM, xlab = "Longitude", ylab = "Latitude",
     main = "Phyllomedusa species richness")
# Map of individual species
plot(PAM, name = "Phyllomedusa nordestina")

## End(Not run)

Create a presence-absence matrix of species' geographic ranges within a grid for the Birdlife spatial data

Description

Convert species' ranges (in shapefile format and stored in particular folders) into a presence-absence matrix based on a user-defined grid. This function is specially designed to work with BirdLife Intl. shapefiles (https://www.birdlife.org). (Notice that new versions of birds spatial data are in a similar format to other groups and should be run using the lets.presab function. We will keep this function in case someone needs to use on the previous data format.)

Usage

lets.presab.birds(
  path,
  xmn = NULL,
  xmx = NULL,
  ymn = NULL,
  ymx = NULL,
  resol = NULL,
  remove.cells = TRUE,
  remove.sp = TRUE,
  show.matrix = FALSE,
  crs = "+proj=longlat +datum=WGS84",
  crs.grid = crs,
  cover = 0,
  presence = NULL,
  origin = NULL,
  seasonal = NULL,
  count = FALSE
)
lets.presab.birds(
  path,
  xmn = NULL,
  xmx = NULL,
  ymn = NULL,
  ymx = NULL,
  resol = NULL,
  remove.cells = TRUE,
  remove.sp = TRUE,
  show.matrix = FALSE,
  crs = "+proj=longlat +datum=WGS84",
  crs.grid = crs,
  cover = 0,
  presence = NULL,
  origin = NULL,
  seasonal = NULL,
  count = FALSE
)

Arguments

`path`	Path location of folders with one or more species' individual shapefiles. Shapefiles with more than one species will not work on this function. To use multi-species shapefiles see `lets.presab`.
`xmn`	Minimum longitude used to construct the grid in which the matrix will be based (i.e. the [gridded] geographic domain of interest). If NULL, limits will be calculated based on the limits of the shapes object.
`xmx`	Maximum longitude used to construct the grid in which the matrix will be based (i.e. the [gridded] geographic domain of interest). If NULL, limits will be calculated based on the limits of the shapes object.
`ymn`	Minimum latitude used to construct the grid in which the matrix will be based (i.e. the [gridded] geographic domain of interest). If NULL, limits will be calculated based on the limits of the shapes object.
`ymx`	Maximum latitude used to construct the grid in which the matrix will be based (i.e. the [gridded] geographic domain of interest). If NULL, limits will be calculated based on the limits of the shapes object.
`resol`	Numeric vector of length 1 or 2 to set the grid resolution. If NULL, resolution will be equivalent to 1 degree of latitude and longitude.
`remove.cells`	Logical, if `TRUE` the final matrix will not contain cells in the grid with a value of zero (i.e. sites with no species present).
`remove.sp`	Logical, if `TRUE` the final matrix will not contain species that do not match any cell in the grid.
`show.matrix`	Logical, if `TRUE` only the presence-absence matrix will be returned.
`crs`	Character representing the PROJ.4 type description of a Coordinate Reference System (map projection) of the polygons.
`crs.grid`	Character representing the PROJ.4 type description of a Coordinate Reference System (map projection) for the grid. Note that when you change this options you may probably change the extent coordinates and the resolution.
`cover`	Percentage of the cell covered by the shapefile that will be considered for presence (values between 0 and 1).
`presence`	A vector with the code numbers for the presence type to be considered in the process (for IUCN spatial data https://www.iucnredlist.org/resources/spatial-data-download, see metadata).
`origin`	A vector with the code numbers for the origin type to be considered in the process (for IUCN spatial data).
`seasonal`	A vector with the code numbers for the seasonal type to be considered in the process (for IUCN spatial data).
`count`	Logical, if `TRUE` a progress bar indicating the processing progress will be shown.

Details

The function creates the presence-absence matrix based on a raster file. Depending on the cell size, extension used and number of species it may require a lot of memory, and may take some time to process it. Thus, during the process, if count argument is set TRUE, a counting window will open so you can see the progress (i.e. in what polygon the function is working). Note that the number of polygons is not the same as the number of species that you have (i.e. a species may have more than one polygon/shapefiles).

Value

Author(s)

Bruno Vilela & Fabricio Villalobos

Examples

## Not run: 
# Constructing a Presence/Absence matrix for birds
# Attention: For your own files, omit the 'system.file'
# and 'package="letsR"', these are just to get the path
# to files installed with the package.
path.Ramphastos <- system.file("extdata", package = "letsR")
PAM <- lets.presab.birds(path.Ramphastos, xmn = -93, xmx = -29,
                         ymn = -57, ymx = 25)

# Species richness map
plot(PAM, xlab = "Longitude", ylab = "Latitude",
     main = "Ramphastos species Richness")


## End(Not run)


## Not run: 
# Constructing a Presence/Absence matrix for birds
# Attention: For your own files, omit the 'system.file'
# and 'package="letsR"', these are just to get the path
# to files installed with the package.
path.Ramphastos <- system.file("extdata", package = "letsR")
PAM <- lets.presab.birds(path.Ramphastos, xmn = -93, xmx = -29,
                         ymn = -57, ymx = 25)

# Species richness map
plot(PAM, xlab = "Longitude", ylab = "Latitude",
     main = "Ramphastos species Richness")


## End(Not run)

Create a presence-absence matrix of species' geographic ranges within a user's grid shapefile (beta version)

Description

Convert species' ranges (in shapefile format) into a presence-absence matrix based on a grid in shapefile format.

Usage

lets.presab.grid(
  shapes,
  grid,
  sample.unit,
  remove.sp = TRUE,
  presence = NULL,
  origin = NULL,
  seasonal = NULL
)
lets.presab.grid(
  shapes,
  grid,
  sample.unit,
  remove.sp = TRUE,
  presence = NULL,
  origin = NULL,
  seasonal = NULL
)

Arguments

`shapes`	Object of class `SpatVect` or `Spatial` (see packages `terra` and `sf` to read these files) containing the distribution of one or more species. Species names should be stored in the object as BINOMIAL/binomial or SCINAME/sciname.
`grid`	Object of class shapefile representing the spatial grid (e.g. regular/irregular cells, political divisions, hexagonal grids, etc). The grid and the shapefiles must be in the same projection.
`sample.unit`	Object of class `character` with the name of the column (in the grid) representing the sample units of the presence absence matrix.
`remove.sp`	Logical, if `TRUE` the final matrix will not contain species that do not match any cell in the grid.
`presence`	A vector with the code numbers for the presence type to be considered in the process (for IUCN spatial data https://www.iucnredlist.org/resources/spatial-data-download, see metadata).
`origin`	A vector with the code numbers for the origin type to be considered in the process (for IUCN spatial data).
`seasonal`	A vector with the code numbers for the seasonal type to be considered in the process (for IUCN spatial data).

Details

This function is an alternative way to create a presence absence matrix when users already have their own grid.

Value

The result is a list containing two objects:

(I) A matrix the species presence (1) and absence (0) values per sample unity.

(II) The original grid.

Author(s)

Bruno Vilela & Fabricio Villalobos

Examples

## Not run: 
# Species polygons
data("Phyllomedusa")
data("wrld_simpl")
# Grid 
sp.r <- terra::as.polygons(terra::rast(resol = 5, 
crs = terra::crs(Phyllomedusa),
xmin = -93, xmax = -29, ymin = -57, ymax = 15))
sp.r$ID <- 1:length(sp.r)
                         

# PAM
resu <- lets.presab.grid(Phyllomedusa, sp.r, "ID")

# Plot
rich_plus1 <- rowSums(resu$PAM[, -1]) + 1
colfunc <- colorRampPalette(c("#fff5f0", "#fb6a4a", "#67000d"))
colors <- c("white", colfunc(max(rich_plus1)))
plot(resu$grid, border = "gray40",
     col = colors[rich_plus1])
plot(sf::st_geometry(wrld_simpl), add = TRUE)

## End(Not run)


## Not run: 
# Species polygons
data("Phyllomedusa")
data("wrld_simpl")
# Grid 
sp.r <- terra::as.polygons(terra::rast(resol = 5, 
crs = terra::crs(Phyllomedusa),
xmin = -93, xmax = -29, ymin = -57, ymax = 15))
sp.r$ID <- 1:length(sp.r)
                         

# PAM
resu <- lets.presab.grid(Phyllomedusa, sp.r, "ID")

# Plot
rich_plus1 <- rowSums(resu$PAM[, -1]) + 1
colfunc <- colorRampPalette(c("#fff5f0", "#fb6a4a", "#67000d"))
colors <- c("white", colfunc(max(rich_plus1)))
plot(resu$grid, border = "gray40",
     col = colors[rich_plus1])
plot(sf::st_geometry(wrld_simpl), add = TRUE)

## End(Not run)

Create a presence-absence matrix based on species' point occurrences

Description

Convert species' occurrences into a presence-absence matrix based on a user-defined grid.

Usage

lets.presab.points(
  xy,
  species,
  xmn = NULL,
  xmx = NULL,
  ymn = NULL,
  ymx = NULL,
  resol = NULL,
  remove.cells = TRUE,
  remove.sp = TRUE,
  show.matrix = FALSE,
  crs = "+proj=longlat +datum=WGS84",
  count = FALSE
)
lets.presab.points(
  xy,
  species,
  xmn = NULL,
  xmx = NULL,
  ymn = NULL,
  ymx = NULL,
  resol = NULL,
  remove.cells = TRUE,
  remove.sp = TRUE,
  show.matrix = FALSE,
  crs = "+proj=longlat +datum=WGS84",
  count = FALSE
)

Arguments

`xy`	A matrix with geographic coordinates of species occurrences, first column is the longitude (or x), and the second latitude (or y).
`species`	Character vector with species names, in the same order as the coordinates.
`xmn`	Minimum longitude used to construct the grid in which the matrix will be based (i.e. the [gridded] geographic domain of interest). If NULL, limits will be calculated based on the limits of the shapes object.
`xmx`	Maximum longitude used to construct the grid in which the matrix will be based (i.e. the [gridded] geographic domain of interest). If NULL, limits will be calculated based on the limits of the shapes object.
`ymn`	Minimum latitude used to construct the grid in which the matrix will be based (i.e. the [gridded] geographic domain of interest). If NULL, limits will be calculated based on the limits of the shapes object.
`ymx`	Maximum latitude used to construct the grid in which the matrix will be based (i.e. the [gridded] geographic domain of interest). If NULL, limits will be calculated based on the limits of the shapes object.
`resol`	Numeric vector of length 1 or 2 to set the grid resolution. If NULL, resolution will be equivalent to 1 degree of latitude and longitude.
`remove.cells`	Logical, if `TRUE` the final matrix will not contain cells in the grid with a value of zero (i.e. sites with no species present).
`remove.sp`	Logical, if `TRUE` the final matrix will not contain species that do not match any cell in the grid.
`show.matrix`	Logical, if `TRUE` only the presence-absence matrix will be returned.
`crs`	Character representing the PROJ.4 type description of a Coordinate Reference System (map projection) of the polygons.
`count`	Logical, if `TRUE` a progress bar indicating the processing progress will be shown.

Details

Value

Author(s)

Bruno Vilela & Fabricio Villalobos

Examples

## Not run: 
species <- c(rep("sp1", 100), rep("sp2", 100),
             rep("sp3", 100), rep("sp4", 100))
x <- runif(400, min = -69, max = -51)
y <- runif(400, min = -23, max = -4)
xy <- cbind(x, y)
PAM <- lets.presab.points(xy, species, xmn = -93, xmx = -29,
                          ymn = -57, ymx = 15)
summary(PAM)
# Species richness map
plot(PAM, xlab = "Longitude", ylab = "Latitude",
     main = "Species richness map (simulated)")

# Map of the specific species
plot(PAM, name = "sp1")

## End(Not run)


## Not run: 
species <- c(rep("sp1", 100), rep("sp2", 100),
             rep("sp3", 100), rep("sp4", 100))
x <- runif(400, min = -69, max = -51)
y <- runif(400, min = -23, max = -4)
xy <- cbind(x, y)
PAM <- lets.presab.points(xy, species, xmn = -93, xmx = -29,
                          ymn = -57, ymx = 15)
summary(PAM)
# Species richness map
plot(PAM, xlab = "Longitude", ylab = "Latitude",
     main = "Species richness map (simulated)")

# Map of the specific species
plot(PAM, name = "sp1")

## End(Not run)

Compute species' geographic range sizes

Description

This function calculates species' range sizes from a PresenceAbsence object or directly from the species' shapefiles.

Usage

lets.rangesize(
  x,
  species_name = NULL,
  coordinates = "geographic",
  units = "cell"
)
lets.rangesize(
  x,
  species_name = NULL,
  coordinates = "geographic",
  units = "cell"
)

Arguments

`x`	A `PresenceAbsence` or an `SpatVector` object.
`species_name`	Species names in the same order as in the `SpatVector` (only needed if x is a `SpatVector`).
`coordinates`	"geographical" or "planar". Indicate whether the shapefile has geographical or planar coordinates(only needed if x is a `SpatVector`).
`units`	"cell" or "squaremeter". Indicate if the size units wanted are in number of cells occupied or in square meters(only needed if x is a `PresenceAbsence` object).

Value

The result is a matrix with the range size of each species. If the range size accounts for the earth curvature (Yes or No) or its size unit may differ for each argument combination:

1) SpatVector & geographical = Square meters. Yes.

2) SpatVector & planar = Square meters. No.

3) PresenceAbsence & cell = number of cells. No.

4) PresenceAbsence & squaremeter = Square meters. Yes.

Author(s)

Bruno Vilela

Examples

## Not run: 
# SpatialPolygonsDataFrame & geographical
data(Phyllomedusa)
rangesize <- lets.rangesize(x = Phyllomedusa,
                            coordinates = "geographic")

# SpatialPolygonsDataFrame & planar
rangesize2 <- lets.rangesize(x = Phyllomedusa,
                             coordinates = "planar")

# PresenceAbsence & cell
data(PAM)
rangesize3 <- lets.rangesize(x = PAM,
                             units = "cell")

# PresenceAbsence & squaremeter
rangesize4 <- lets.rangesize(x = PAM,
                             units = "squaremeter")

## End(Not run)


## Not run: 
# SpatialPolygonsDataFrame & geographical
data(Phyllomedusa)
rangesize <- lets.rangesize(x = Phyllomedusa,
                            coordinates = "geographic")

# SpatialPolygonsDataFrame & planar
rangesize2 <- lets.rangesize(x = Phyllomedusa,
                             coordinates = "planar")

# PresenceAbsence & cell
data(PAM)
rangesize3 <- lets.rangesize(x = PAM,
                             units = "cell")

# PresenceAbsence & squaremeter
rangesize4 <- lets.rangesize(x = PAM,
                             units = "squaremeter")

## End(Not run)

Save a PresenceAbsence object

Description

Save an external representation of a PresenceAbsence object to the specified file. The object can be read back from the file at a later date by using the function lets.load.

Usage

lets.save(pam, ...)
lets.save(pam, ...)

Arguments

`pam`	A PresenceAbsence object.
`...`	other arguments passed to the function `save`

Author(s)

Bruno Vilela

Examples

## Not run: 
data(PAM)
lets.save(PAM, file = "PAM.RData")
PAM <- lets.load(file = "PAM.RData")

## End(Not run)

## Not run: 
data(PAM)
lets.save(PAM, file = "PAM.RData")
PAM <- lets.load(file = "PAM.RData")

## End(Not run)

Filter species' shapefiles based on its presence, origin, and season

Description

Filter species shapefiles by origin, presence, and seasonal type (following IUCN types: https://www.iucnredlist.org/resources/spatial-data-download, see metadata).

Usage

lets.shFilter(shapes, presence = NULL, origin = NULL, seasonal = NULL)
lets.shFilter(shapes, presence = NULL, origin = NULL, seasonal = NULL)

Arguments

`shapes`	Object of class `SpatVect` or `Spatial` (see packages `terra` and `sf` to read these files) containing the distribution of one or more species. Species names should be stored in the object as BINOMIAL/binomial or SCINAME/sciname.
`presence`	A vector with the code numbers for the presence type to be considered in the process (for IUCN spatial data https://www.iucnredlist.org/resources/spatial-data-download, see metadata).
`origin`	A vector with the code numbers for the origin type to be considered in the process (for IUCN spatial data).
`seasonal`	A vector with the code numbers for the seasonal type to be considered in the process (for IUCN spatial data).

Details

Presence codes: (1) Extant, (2) Probably Extant, (3) Possibly Extant, (4) Possibly Extinct, (5) Extinct (post 1500) & (6) Presence Uncertain.

Origin codes: (1) Native, (2) Reintroduced, (3) Introduced, (4) Vagrant & (5) Origin Uncertain.

Seasonal codes: (1) Resident, (2) Breeding Season, (3) Non-breeding Season, (4) Passage & (5) Seasonal Occurrence Uncertain.

More info in the shapefiles' metadata.

Value

The result is the shapefile(s) filtered according to the selected types. If the filters remove all polygons, the result will be NULL.

Author(s)

Bruno Vilela

Subset a PresenceAbsence object based on species names

Description

Subset a PresenceAbsence object based on species character vector provided by the user.

Usage

lets.subsetPAM(x, names, remove.cells = TRUE)
lets.subsetPAM(x, names, remove.cells = TRUE)

Arguments

`x`	A `PresenceAbsence` object.
`names`	Character vector with species names to subset the `PresenceAbsence` object.
`remove.cells`	Logical, if `TRUE` the final matrix will not contain cells in the grid with a value of zero (i.e. sites with no species present).

Value

The result is an object of class PresenceAbsence subseted.

Author(s)

Bruno Vilela

Examples

## Not run: 
data(PAM)
# PAM before subset
plot(PAM, xlab = "Longitude", ylab = "Latitude",
     main = "Phyllomedusa species richness")

# Subset PAM to the first 20 species
PAMsub <- lets.subsetPAM(PAM, PAM[[3]][1:20])
plot(PAMsub, xlab = "Longitude", ylab = "Latitude",
     main = "Phyllomedusa species richness")

## End(Not run)

## Not run: 
data(PAM)
# PAM before subset
plot(PAM, xlab = "Longitude", ylab = "Latitude",
     main = "Phyllomedusa species richness")

# Subset PAM to the first 20 species
PAMsub <- lets.subsetPAM(PAM, PAM[[3]][1:20])
plot(PAMsub, xlab = "Longitude", ylab = "Latitude",
     main = "Phyllomedusa species richness")

## End(Not run)

Summarize variable(s) values in a presence-absence matrix within species' ranges

Description

Based on a Presence-Absence matrix with added variables (see lets.addvar), this function summarizes the values of such variable(s) per species (across the species' occupied cells. i.e. within their ranges).

Usage

lets.summarizer(x, pos, xy = TRUE, fun = mean, ...)
lets.summarizer(x, pos, xy = TRUE, fun = mean, ...)

Arguments

`x`	Presence-absence matrix with variables added.
`pos`	Column position of the variables of interest.
`xy`	Logical, if `TRUE` the input matrix contains geographic coordinates in the first two columns.
`fun`	Function to be used to summarize the variable per species. Default is `mean`.
`...`	Other parameters passed to the function defined in `fun`.

Author(s)

Bruno Vilela & Fabricio Villalobos

References

Villalobos, F. and Arita, H.T. 2010. The diversity field of New World leaf-nosed bats (Phyllostomidae). Global Ecology and Biogeography. 19, 200-211.

Examples

## Not run: 
data(PAM)
data(temp)
temp <- terra::unwrap(temp)
pamvar <- lets.addvar(PAM, temp)
resu <- lets.summarizer(x = pamvar, pos = ncol(pamvar),
                        xy = TRUE)

## End(Not run)

## Not run: 
data(PAM)
data(temp)
temp <- terra::unwrap(temp)
pamvar <- lets.addvar(PAM, temp)
resu <- lets.summarizer(x = pamvar, pos = ncol(pamvar),
                        xy = TRUE)

## End(Not run)

Transform values of a vector

Description

Transform each element of a vector.

Usage

lets.transf(x, y, z, NUMERIC = TRUE)
lets.transf(x, y, z, NUMERIC = TRUE)

Arguments

`x`	A vector to be transformed.
`y`	levels to be transformed.
`z`	The value to be atributed to each level (same order as y).
`NUMERIC`	logical, if `TRUE` z will be considered numbers.

Value

Return a vector with changed values.

Author(s)

Bruno Vilela

Examples

## Not run: 
status <- sample(c("EN","VU", "NT", "CR", "DD", "LC"), 30, replace=TRUE) 
TE <- "Threatened"
NT <- "Non-Threatened"
new <- c(TE, TE, NT, TE, "Data Deficient", NT)
old <- c("EN","VU", "NT", "CR", "DD", "LC")
statustrans <- lets.transf(status, old, new, NUMERIC=FALSE)


## End(Not run)

## Not run: 
status <- sample(c("EN","VU", "NT", "CR", "DD", "LC"), 30, replace=TRUE) 
TE <- "Threatened"
NT <- "Non-Threatened"
new <- c(TE, TE, NT, TE, "Data Deficient", NT)
old <- c("EN","VU", "NT", "CR", "DD", "LC")
statustrans <- lets.transf(status, old, new, NUMERIC=FALSE)


## End(Not run)

PresenceAbsence object for frogs of the genus Phyllomedusa

Description

PresenceAbsence object obtained using the function lets.presab for the Geographic distribution of the South American frog genus Phyllomedusa.

Usage

PAM
PAM

Format

A PresenceAbsence object

Source

Generated from IUCN Spatial Data - https://www.iucnredlist.org/. 2014.

Phyllomedusa

Description

Geographic distribution of the South American frog genus Phyllomedusa.

Usage

Phyllomedusa
Phyllomedusa

Format

A simple feature collection for 32 species with 46 features and 4 fields.

binomial: Scientific name
presence: IUCN Red List distributional code
origin: IUCN Red List distributional code
seasonal: IUCN Red List distributional code

Details

See the IUCN Red List Attribute Information for Species Ranges.

Source

IUCN - https://www.iucnredlist.org/. 2014.

Plot an object of class PresenceAbsence

Description

Plots species richness map from an object of class PresenceAbsence or a particular species' map.

Usage

## S3 method for class 'PresenceAbsence'
plot(x, name = NULL, world = TRUE, col_rich = NULL, col_name = "red", ...)
## S3 method for class 'PresenceAbsence'
plot(x, name = NULL, world = TRUE, col_rich = NULL, col_name = "red", ...)

Arguments

`x`	An object of class `PresenceAbsence`.
`name`	A character specifying a species to be ploted instead of the complete species richness map.
`world`	If `TURE` a map of political divisions (countries) is added to the plot.
`col_rich`	Color function (e.g. `rainbow`, `heat.colors`, `colorRampPalette`) to be used in the richness map.
`col_name`	The color to use when ploting single species.
`...`	Other parameters pass to the plot function.

Author(s)

Bruno Vilela

Examples

## Not run: 
data(PAM)
plot(PAM)
plot(PAM, xlab = "Longitude", ylab = "Latitude",
     main = "Phyllomedusa species richness")
plot(PAM, name = "Phyllomedusa atelopoides")
plot(PAM, name = "Phyllomedusa azurea")

## End(Not run)

## Not run: 
data(PAM)
plot(PAM)
plot(PAM, xlab = "Longitude", ylab = "Latitude",
     main = "Phyllomedusa species richness")
plot(PAM, name = "Phyllomedusa atelopoides")
plot(PAM, name = "Phyllomedusa azurea")

## End(Not run)

PresenceAbsence Class

Description

The PresenceAbsence is a new S3 object class created and used inside the letsR package. This object class is used to store information on species distribution within a geographic domain in the form of a presence-absence matrix. In addition, the PresenceAbsence object also contains other essential information (e.g. user-defined grid cell system, including resolution, projection, datum, and extent) necessary for other analysis performed with the package's functions.

Details

Creating a PresenceAbsence object
A PresenceAbsence object can be generated using the following functions:
- lets.presab
- lets.presab.birds
- lets.presab.points

The PresenceAbsence information
The result is a list object of class PresenceAbsence that includes the following objects:
- Presence_and_Absence_Matrix: A matrix of species' presence(1) and absence(0) information. The first two columns contain the longitude (x) and latitude (y) of the cells' centroid (from the gridded domain used);
- Richness_Raster: A raster containing species richness information across the geographic domain, which can be used to map the observed geographic gradient in species richness;
- Species_name: A character vector with species' names contained in the matrix.

Each of the objects can be obtained usign the standard subsetting operators that are commonly applied to a list object (i.e. '[[' and '$').

letsR functions applied to a PresenceAbsence object
The following functions from the letsR package can be directly applied to a PresenceAbsence:
- lets.addpoly
- lets.addvar
- lets.distmat
- lets.field
- lets.gridirizer
- lets.iucn
- lets.iucn.ha
- lets.iucn.his
- lets.maplizer
- lets.midpoint
- lets.overlap
- lets.pamcrop
- lets.rangesize

Generic functions applied to a PresenceAbsence object
The following generic functions can be directly applied to the PresenceAbsence object.
- print (print.PresenceAbsence)
- summary (summary.PresenceAbsence)
- plot (plot.PresenceAbsence)

Print for object of class PresenceAbsence

Description

Print for objects of class PresenceAbsence.

Usage

## S3 method for class 'PresenceAbsence'
print(x, ...)
## S3 method for class 'PresenceAbsence'
print(x, ...)

Arguments

`x`	an object of class `PresenceAbsence`.
`...`	Other print parameters.

Author(s)

Bruno Vilela

Print summary for object of class PresenceAbsence

Description

Print summary for objects of class PresenceAbsence.

Usage

## S3 method for class 'PresenceAbsence'
print.summary(x, ...)
## S3 method for class 'PresenceAbsence'
print.summary(x, ...)

Arguments

`x`	an object of class `PresenceAbsence`.
`...`	Other print parameters.

Author(s)

Bruno Vilela

Summary for object of class PresenceAbsence

Description

Summary for objects of class PresenceAbsence.

Usage

## S3 method for class 'PresenceAbsence'
summary(object, ...)
## S3 method for class 'PresenceAbsence'
summary(object, ...)

Arguments

`object`	an object of class `PresenceAbsence`.
`...`	additional arguments affecting the summary produced.

Author(s)

Bruno Vilela

Mean temperature raster for the world.

Description

Mean temperature raster in degrees Celsius (multiplied by 100) for the world in 10 arc min of resolution.

Usage

temp
temp

Format

A PackedStatRaster object.

Source

Data was modified from WorldClim (https://worldclim.com/, downloaded 05/2014).

Hijmans, R.J., S.E. Cameron, J.L. Parra, P.G. Jones and A. Jarvis, 2005. Very high resolution interpolated climate surfaces for global land areas. International Journal of Climatology 25: 1965-1978.

Simplified world country polygons

Description

World map in sf format. Obtained from maptools and converted to sf.

Usage

wrld_simpl
wrld_simpl

Format

A simple feature collection with 246 features and 11 fields.

Source

Originally https://mappinghacks.com/data/TM_WORLD_BORDERS_SIMPL-0.2.zip, now available from https://github.com/nasa/World-Wind-Java/tree/master/WorldWind/testData/shapefiles.

Package 'letsR'

Help Index

Tools for Data Handling and Analysis in Macroecology.

Description

Details

Author(s)

References

See Also

IUCN evaluation for frogs of the genus Phyllomedusa

Description

Usage

Format

Source

Add polygon coverage to a PresenceAbscence object

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

Add variables (in raster format) to a PresenceAbscence object

Description

Usage

Arguments

Value

Note

Author(s)

See Also

Examples

Frequency distribution of a variable within a species' range

Description

Usage

Arguments

Value

Author(s)

References

Examples

Compute correlogram based on the Moran's I index

Description

Usage

Arguments

Value

Author(s)

References

Examples

Compute a geographic distance matrix

Description

Usage

Arguments

Details

Value

Author(s)

Examples

Create species' values based on the species co-occurrence within focal ranges

Description

Usage

Arguments

Details

Author(s)

References

See Also

Examples

Fits a grid into a PresenceAbsence object

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

Download species' information from the IUCN RedList online database (No longer supported)

Description

Usage

Arguments

Details

Value

Author(s)

See Also

Examples