Title: Creates Bivariate Maps
Version: 1.7
Description: Contains functions mainly focused to plotting bivariate maps.
License: GPL-3
Encoding: UTF-8
Imports: classInt, terra, base, graphics, stats, caper, picante, ape, betapart, CommEcol, grDevices
RoxygenNote: 7.2.3
NeedsCompilation: no
Packaged: 2024-10-04 21:38:56 UTC; heavy
Author: Jose Hidasi-Neto [aut, cre]
Maintainer: Jose Hidasi-Neto <hidasineto@gmail.com>
Repository: CRAN
Date/Publication: 2024-10-04 22:10:02 UTC

EcoEDGE: Ecologically and Evolutionarily Distinct and Globally Endangered

Description

Calculates ED, EcoD, EDGE, EcoDGE, and EcoEDGE, from Red List Categories, a phylogenetic tree, and a functional dendrogram.

Usage

EcoEDGE(
  category,
  phylo,
  func,
  funcweight = 0.5,
  phyloweight = 0.5,
  polytomy = "isaac"
)

Arguments

category

data frame where the first column contains the red list categories of species.

phylo

phylogenetic tree of species.

func

functional dendrogram of species.

funcweight

weight of ecological distinctiveness on the calculation of EcoEDGE scores.

phyloweight

weight of evolutionary distinctiveness on the calculation of EcoEDGE scores. Sum of funcweight and phyloweight must be equal to 1.

polytomy

how to handle polytomies in the phylogeny and the functional dendrogram. See "ed.calc" function for details.

Value

A table with calculated values for each variable.

Examples

# https://rfunctions.blogspot.com/2021/03/ecoedge-ecologically-and-evolutionarily.html

GridFilter: Intersect a Shape with a Grid and Exclude Cells Based on Area Coverage

Description

Overlay a shapefile with a grid. Then, excludes grid cells that do not cover a specific amount of the Shape area.

Usage

GridFilter(shape, resol = 1, prop = 0)

Arguments

shape

A shapefile.

resol

The resolution (in degrees) of the grid you want to overlay. The default is 1 degree of longitude and latitude.

prop

The minimum value of area covered by the grid cell. The default is 0 (i.e. it does not delete any grid cell).

Value

A gridded shapefile.

Examples

# https://rfunctions.blogspot.com/2014/12/gridfilter-intersect-grid-with-shape.html

ancestree: Get a Phylogeny that Starts at the Common Ancestor of a Group of Species

Description

Uses a sample of species to get the phylogeny that starts at the common ancestor of the sample.

Usage

ancestree(sample, tree)

Arguments

sample

A data frame with species in columns' names (check out example link).

tree

.tre phylogenetic tree of species.

Value

A phylogeny that starts at the common ancestor of the provided sample.

Examples

# https://rfunctions.blogspot.com/2013/04/ancestree-function-get-phylogeny-that.html

astRaRium: Generate infinite Astrarium minigames.

Description

Generate infinite minigames based on the Astrarium minigame, from "Dragon Age: Inquisition". You have to click on the stars (asterisks) to find a path that that reveals the same image as shown while not repeating connections already made once. When it begins (by typing "astRaRium()" ), it will ask you for the desired number of stars and the number of links between pairs of stars. A good number is 12 and 9, respectively.

Usage

astRaRium()

Value

You play the game. You can succeed or fail.

Examples

# https://rfunctions.blogspot.com/2021/05/astrarium2-r-game-about-linking-stars.html

betagrid: Calculates Beta Diversity for all the Grid Cells in Comparison with Their Nearest Neighbor Cells

Description

Uses a 'gridded' shapefile and its corresponding community data matrix to calculate beta diversity for each focal grid cell in relation to its neighbor cells (for example, 8 nearest neighbors).

Usage

betagrid(
  gridshp,
  comp,
  xfeature,
  yfeature,
  radius,
  phylotree,
  phylobeta = F,
  index = "sorensen"
)

Arguments

gridshp

Gridded Shapefile ("SpatialPolygonsDataFrame").

comp

community data matrix (species occurrence on each grid cell).

xfeature

number of the feature within the gridded shapefile corresponding to the longitude.

yfeature

number of the feature within the grid shapefile corresponding to the latitude.

radius

the radius (in degrees) that define the maximum distance to select neighbor cells (for example, use the resolution of the gridded shapefile).

phylotree

optional phylogenetic tree ("phylo" class). It can also be a "phylo" class functional dendrogram.

phylobeta

Optional boolean whether or not to calculate or not phylogenetic beta diversity (see "phylo.beta.pair" function in "betapart" package) instead of the usual beta diversity (see "beta.pair" function in "betapart" package). Default is F.

index

to calculate "sorensen" or "jaccard". Default is "sorensen".

Value

A data frame with values of mean turnover, mean nestedness, and mean beta diversity for each grid cell.

Examples

# https://rfunctions.blogspot.com/2015/08/calculating-beta-diversity-on-grid.html

bivariate.map: Create a Bivariate Map

Description

Creates a Bivariate Map using two rasters and a color matrix created with colmat() function.

Usage

bivariate.map(
  rasterx,
  rastery,
  colormatrix,
  nquantiles = 10,
  trivariate = F,
  rasterz
)

Arguments

rasterx

raster

rastery

raster

colormatrix

color matrix from colmat() function

nquantiles

number of quantiles in color matrix (same as used when using colmat() function)

trivariate

boolean indicating if should use a third raster for a "trivariate" map where the third variable corresponds to the transparency (alpha) of colors.

rasterz

raster (only if trivariate=T)

Value

A plot with the bivariate map.

Examples

# https://rfunctions.blogspot.com/2015/03/bivariate-maps-bivariatemap-function.html

colmat: Create a Color Matrix

Description

Creates a color matrix to be used in bivariate.map() function.

Usage

colmat(
  nquantiles = 10,
  upperleft = "blue",
  upperright = "red",
  bottomleft = "grey",
  bottomright = "yellow",
  xlab = "x label",
  ylab = "y label"
)

Arguments

nquantiles

numeric variable for number of quantiles in color matrix

upperleft

upperleft color of color matrix

upperright

upperright color of color matrix

bottomleft

bottomleft color of color matrix

bottomright

bottomright color of color matrix

xlab

character variable

ylab

character variable

Value

Two outputs: a color matrix object to be used in bivariate.map() function, and a plot of the color matrix.

Examples

col.matrix<-colmat(nquantiles=10, xlab="My x label", ylab="My y label")

# https://rfunctions.blogspot.com/2015/03/bivariate-maps-bivariatemap-function.html

tempbetagrid: Calculates Temporal Beta Grid Using Species' Occurrences

Description

Uses two occurrence matrices (from different time periods) to calculate temporal beta diversity for each site or grid cell.

Usage

tempbetagrid(oc1, oc2, index = "sorensen", phylotree, phylobeta = F)

Arguments

oc1

Community data matrix (species occurrence on each grid cell).

oc2

Second community data matrix (species occurrence on each grid cell) for another time period.

index

Calculate "sorensen" or "jaccard". Default is "sorensen".

phylotree

Optional phylogenetic tree ("phylo" class). It can also be a functional dendrogram.

phylobeta

Optional boolean indicating whether or not to calculate phylogenetic beta diversity (see "phylo.beta.pair" function in "betapart" package) instead of the usual beta diversity (see "beta.pair" function in "betapart" package). Default is F.

Value

A data frame with values of turnover, nestedness, beta diversity, and turnover/beta for each site or grid cell.

Examples

# https://rfunctions.blogspot.com/2016/10/calculating-temporal-beta-diversity-on.html