| bin_tables0 {nichevol} | R Documentation |
Bin tables of environmental conditions in M and for occurrences from data
Description
bin_tables0 helps in creating bin tables of environmental conditions in accessible areas (M) and species occurrence records (i.e., table of characters). This is done using data read directly from a local directory, and can be applied to various species and multiple variables.
Usage
bin_tables0(M_folder, M_format, occ_folder, longitude,
latitude, var_folder, var_format, round = FALSE,
round_names, multiplication_factor = 1,
percentage_out = 5, n_bins = 20, bin_size, save = FALSE,
output_directory, overwrite = FALSE, verbose = TRUE)
Arguments
M_folder |
(character) name of the folder containing files representing the accessible area (M) for all species to be analyzed. See details. |
M_format |
format of files representing the accessible area (M) for the
species. Names of M files must match the ones for occurrence files in
|
occ_folder |
(character) name of the folder containing csv files of
occurrence data for all species. Names of csv files must match the ones of M
files in |
longitude |
(character) name of the column in occurrence files containing values of longitude. |
latitude |
(character) name of the column in occurrence files containing values of latitude. |
var_folder |
(character) name of the folder containing layers to represent environmental variables. |
var_format |
format of layers to represent environmental variables.
Format options are all the ones supported by |
round |
(logical) whether or not to round the values of one or more
variables after multiplying them times the value in |
round_names |
(character) names of the variables to be rounded.
Default = NULL. If |
multiplication_factor |
(numeric) value to be used to multiply the
variables defined in |
percentage_out |
(numeric) percentage of extreme environmental data in M to be excluded in bin creation for further analyses. See details. Default = 5. |
n_bins |
(numeric) number of bins to be created from the range of environmental values considered when creating each character in bin tables. Default = 20. See details. |
bin_size |
(numeric) argument deprecated, use n_bins instead. |
save |
(logical) whether or not to save the results in working directory. Default = FALSE. |
output_directory |
(character) name of the folder in which results will be written. |
overwrite |
(logical) whether or not to overwrite existing results in
|
verbose |
(logical) whether messages should be printed. Default = TRUE. |
Details
Coordinates in csv files in occ_folder, SpatVector-like files in
M_folder, and raster layers in var_folder must coincide in the
geographic projection in which they are represented. WGS84 with no planar
projection is recommended.
Accessible area (M) is understood as the geographic area that has been accessible for a species for relevant periods of time. Defining M is usually a hard task, but also a very important one, because it allows identifying uncertainties about the ability of a species to maintain populations in certain environmental conditions. For further details on this topic, see Barve et al. (2011) doi:10.1016/j.ecolmodel.2011.02.011 and Machado-Stredel et al. (2021) doi:10.21425/F5FBG48814.
Rounding variables may be useful when multiple variables are considered and
the values of some or all of them are too small (e.g., when using principal
components). To round specific variables arguments round,
round_names, and multiplication_factor, must be used accordingly.
The percentage to be defined in percentage_out excludes a percentage
of extreme environmental values to prevent from considering extremely rare
environmental values in the accessible area for the species (M). Being too
rare, these values may have never been explored by the species; therefore,
including them in the process of preparation of the table of characters
(bin table) is risky.
The argument n_bins helps to define how many characters (bins) will be
considered for the range of values in each variable. This is, a value of 20
determines that a range of temperature (5-25) will be split approximately
every 1 degree. The argument bin_size has been deprecated.
Value
A list named as the variables present in var_folder, containing all
tables of characters. A folder named as in output_directory containing
all resultant csv files with the tables of characters will be created if
save is set as TRUE.
Potential values for characters are:
"1" = the species is present in those environmental conditions.
"0" = the species is not present in those environmental conditions. This is, those environmental conditions inside the accessible area (M) are more extreme than the ones used for the species.
"?" = there is no certainty about the species presence in those environmental conditions. This happens in environmental combinations more extreme than the ones found in the accessible area (M), when environmental conditions in species records are as extreme as the most extreme ones in M.
Examples
# preparing data and directories for example
## directories
tempdir <- file.path(tempdir(), "nevol_test")
dir.create(tempdir)
cvariables <- paste0(tempdir, "/variables")
dir.create(cvariables)
records <- paste0(tempdir, "/records")
dir.create(records)
m_areas <- paste0(tempdir, "/M_areas")
dir.create(m_areas)
## data
data("occ_list", package = "nichevol")
temp <- system.file("extdata", "temp.tif", package = "nichevol")
m_files <- list.files(system.file("extdata", package = "nichevol"),
pattern = "m\\d.gpkg", full.names = TRUE)
## writing data in temporal directories
spnames <- sapply(occ_list, function (x) as.character(x[1, 1]))
ocnames <- paste0(records, "/", spnames, ".csv")
occs <- lapply(1:length(spnames), function (x) {
write.csv(occ_list[[x]], ocnames[x], row.names = FALSE)
})
to_replace <- paste0(system.file("extdata", package = "nichevol"), "/")
otemp <- gsub(to_replace, "", temp)
file.copy(from = temp, to = paste0(cvariables, "/", otemp))
file.copy(from = m_files, to = paste0(m_areas, "/", spnames, ".gpkg"))
# preparing tables
tabs <- bin_tables0(M_folder = m_areas, M_format = "gpkg", occ_folder = records,
longitude = "x", latitude = "y", var_folder = cvariables,
var_format = "tif")