Create graphics of species discoveries accumulation and nomenclatural changes

Produces graphics of the dynamics of species description and historical nomenclature changes within any family or genus provided. It is designed to create graphics based on the dataframe resulted from powoSpecies. The graph type can be selected by two arguments (spp_acc and spp_changes) and then multiple graphs for any different taxonomic groups within the input data can be produced automatically in a single run.

Usage

accGraph(inputdf = NULL,
         verbose = TRUE,
         spp_acc = TRUE,
         spp_changes = TRUE,
         spp_changes_col = NULL,
         genus_plots = TRUE,
         save = FALSE,
         dir = "results_accGraph",
         filename = "cumulative_discovery_",
         format = "pdf")

Arguments

inputdf: A dataframe generated using powoSpecies function using the argument synonyms set as TRUE and containing the genus and species column and the associated information about the protologue of each species. The species name must be binomial, i.e. must contain both the genus name and specific epithet.
verbose: Logical, if FALSE, a message showing each step during the POWO search will not be printed in the console in full.
spp_acc: Logical. Setting to FALSE means that you do not want to create individual accumulation graphs for each genus present in your dataset. The default is TRUE.
spp_changes: Logical. Setting to FALSE means that you do not want to create a violin plot with all data provided. The default is TRUE.
spp_changes_col: Define the name of a column in the main input data for which the species changes will be considered. For example, if densities and jitters should be presented for each genus in the same graphic, then set spp_changes_col = "genus". If you are plotting the dynamics of nomenclatural changes across the entire dataset in a single density graphic, then you must add a new column in your input data containing the same character inside all rows. In this case, ensure that you also keep genus_plots = TRUE.
genus_plots: Logical. If FALSE, a single density and jitter plot graphic will be produced for the entire input data. The default is TRUE, which will result in a graphic where multiple densities and jitters will be created inside the graphic, depending on the chosen column.
save: Logical, if TRUE, the search results will be saved on disk.
dir: Pathway to the computer's directory, where the file will be saved provided that the argument save is set up in TRUE. The default is to create a directory named results_accGraph 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 cumulative_discovery_.
format: A character vector related to the file format of the graph to be saved. The default is "pdf" to save the output in Portable Document Format (.pdf), but you can also choose "jpg" to save in Joint Photographic Experts Group (.jpg), "tiff" to save in Tag Image File Format (.tiff) or "png" to save in Portable Network Graphics (.png).

Value

Objects of class c("gg", "ggplot") and saves the output on disk.

Author

Debora Zuanny & Domingos Cardoso

Examples

if (FALSE) {

library(expowo)

accGraph(inputdf = "output",
         verbose = TRUE,
         spp_acc = TRUE,
         spp_changes = TRUE,
         spp_changes_col = "genus",
         genus_plots = TRUE,
         save = FALSE,
         dir = "results_accGraph",
         filename = "cumulative_discovery_Cyperaceae",
         format = "pdf")
}