# Bin tables of environmental conditions in M and for occurrences from data 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. ```r 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`. Format options are: "shp", "gpkg", or any of the options supported by `rast` (e.g., "tif" or "asc"). - `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 `M_folder`. - `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 `rast` (e.g., "tif" or "asc"). - `round`: (logical) whether or not to round the values of one or more variables after multiplying them times the value in `multiplication_factor`. Default = FALSE. See details. - `round_names`: (character) names of the variables to be rounded. Default = NULL. If `round` = TRUE, names must be defined. - `multiplication_factor`: (numeric) value to be used to multiply the variables defined in `round_names`. Default = 1. - `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 `output_directory`. Default = FALSE. - `verbose`: (logical) whether messages should be printed. Default = TRUE. ## Returns 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. ## 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](doi:10.1016/j.ecolmodel.2011.02.011) and Machado-Stredel et al. (2021) [doi:10.21425/F5FBG48814](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. ## Examples ```r # 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") ```

bin_tables0 function