powoMap: Create global maps of species richness

In DBOSlab/expowo: An R package for mining global plant diversity and distribution data

Create global maps of species richness

Description

Produces global-scale maps of species richness at political country and botanical country levels. Despite being originally designed to create maps for all input data of any specified taxonomic group (genus or family) from the search results with powoSpecies, the function is also useful for any dataframe-formatted input data that has at least a column with species and one or two columns with associated distribution in the countries and/or botanical regions. Multiple richness maps for any different taxonomic groups within the input data can be produced automatically in a single run by just specifying a column name with the associated taxonomic classification.

Usage

powoMap(inputdf = NULL,
        botctrs = FALSE,
        distcol = NULL,
        taxclas = NULL,
        verbose = TRUE,
        save = FALSE,
        vir_color = "viridis",
        bre_color = NULL,
        leg_title = "SR",
        dpi = 600,
        dir = "results_powoMap",
        filename = "global_richness_map",
        format = "jpg")

Arguments

inputdf	A dataframe with a species column and the associated global distribution at country or botanical country level. The species name must be as a binomial, i.e. must contain both the genus name and specific epithet, but the authorship is optional. Each species must be as a single row with its corresponding full distribution in all countries and/or botanical regions within a single cell of their respective columns, where the country names or botanical regions are separated by a comma. This is, for example, the standard dataframe from the search results with the function powoSpecies.
botctrs	Logical. If TRUE, the species richness maps will be created according to the botanical country subdivisions of the world. Also, a WGSRPD folder including the level 3 shapefile and the associated Brummitt's (2001) book fully describing the World Geographical Scheme for Recording Plant Distributions will be downloaded into the working directory. If you do not remove this folder or rename any of the contents, then the function will not download the same folder again. The default is FALSE.
distcol	Column name with the full global distribution data for each species at political country level or the level 3 of botanical subdivision of the World Geographical Scheme for Recording Plant Distributions. If the species distribution is given with botanical subdivisions, then you must also change the argument botctrs to TRUE. If the distribution is described only by political country names, then set botctrs to FALSE.
taxclas	A character vector with the column name for the corresponding taxonomic classification of each species in any higher taxonomic level. If provided, the function will produce, in a single run, all global richness maps for every distinct group within the input data. The default is NULL, then the function will generate only one global species richness map for the entire input data.
verbose	Logical. If FALSE, a message showing the map creation steps will not be printed in the console in full.
save	Logical, if TRUE, the global maps will be saved on disk.
vir_color	A character vector with the name or code of any of the color palettes from Viridis package.
bre_color	A character vector with the name or code of any of the color palettes from RColorBrewer package.
leg_title	A character vector to be displayed in the output map as a legend. Default is to create a title called SR, an acronym for species richness.
dpi	One number in the range of 72-4000 referring to the image resolution in the format of dots per inch in the output file. Default is to create an output with 600 dpi.
dir	Pathway to the computer's directory, where the map file will be saved provided that the argument save is set up in TRUE. The default is to create a directory named results_powoMap and the search results will be saved within a subfolder named after the current date.
filename	Name of the output file to be saved. The default is to create a file entitled global_richness_map.
format	A character vector related to the file format of the global map to be saved. The default is "jpg" to save the output in Joint Photographic Experts Group (.jpg), but you can also choose "pdf" to save in Portable Document Format (.pdf), "tiff" to save in Tag Image File Format (.tiff) or "png" to save in Portable Network Graphics (.png).

Value

One or a list of objects of class c("gg", "ggplot").

Author(s)

Debora Zuanny & Domingos Cardoso

See Also

megaGen

topGen

powoSpecies

powoFam

powoGenera

Examples

## Not run: 
library(expowo)

mapspdist <- powoSpecies(family = "Martyniaceae",
                         hybridspp = FALSE,
                         country = NULL,
                         verbose = TRUE,
                         save = FALSE,
                         dir = "results_powoSpecies",
                         filename = "Martyniaceae_spp")

# To create multiple maps for each genus within the input data according to
# political countries.
powoMap(inputdf = mapspdist,
        botctrs = FALSE,
        distcol = "native_to_country",
        taxclas = "genus",
        verbose = FALSE,
        save = FALSE,
        vir_color = "viridis",
        bre_color = NULL,
        leg_title = "SR",
        dpi = 600,
        dir = "results_powoMap",
        filename = "global_richness_country_map",
        format = "jpg")

# To create multiple maps for each genus within the input data according to
# botanical country subdivisions.
powoMap(inputdf = mapspdist,
        botctrs = TRUE,
        distcol = "native_to_botanical_countries",
        taxclas = "genus",
        verbose = FALSE,
        save = FALSE,
        vir_color = "viridis",
        bre_color = NULL,
        leg_title = "SR",
        dpi = 600,
        dir = "results_powoMap",
        filename = "global_richness_botcountry_map",
        format = "jpg")

## End(Not run)

DBOSlab/expowo documentation built on Oct. 29, 2024, 6:27 p.m.