indicator_total_year: Create cumulative number of alien species indicator plot.

In trias-project/trias: Process Data for the Project Tracking Invasive Alien Species (TrIAS)

Create cumulative number of alien species indicator plot.

Description

This function calculates the cumulative number of taxa introduced per year. To do this, a column of input dataframe containing temporal information about year of introduction is required.

Usage

indicator_total_year(
  df,
  start_year_plot = 1940,
  x_major_scale_stepsize = 10,
  x_minor_scale_stepsize = 5,
  facet_column = NULL,
  taxon_key_col = "key",
  first_observed = "first_observed",
  x_lab = "Year",
  y_lab = "Cumulative number of alien species"
)

Arguments

df	df. Contains the data as produced by the Trias pipeline, with minimal columns.
start_year_plot	numeric. Limit to use as start year of the plot. For scientific usage, the entire period could be relevant, but for policy purpose, focusing on a more recent period could be required. Default: 1940.
x_major_scale_stepsize	integer. On which year interval labels are placed on the x axis. Default: 10.
x_minor_scale_stepsize	integer. On which year interval minor breaks are placed on the x axis. Default: 5.
facet_column	NULL or character. Name of the column to use to create additional facet wrap plots underneath the main graph. When NULL, no facet graph is included. It is typically one of the highest taxonomic ranks, e.g. "kingdom", "phylum", "class", "order", "family". Other typical breakwdowns could be geographically related, e.g. "country", "locality", "pathway" of introduction or "habitat". Default: NULL.
taxon_key_col	character. Name of the column of df containing unique taxon IDs. Default: key.
first_observed	character. Name of the column of df containing information about year of introduction. Default: "first_observed".
x_lab	NULL or character. To personalize or remove the x-axis label. Default: "Year.
y_lab	NULL or character. To personalize or remove the y-axis label. Default: "Cumulative number of alien species".

Value

A list with three slots:

• plot: ggplot2 object (or egg object if facets are used).

• data_top_graph: data.frame (tibble) with data used for the main plot (top graph) in plot.

• data_facet_graph: data.frame (tibble) with data used for the faceting plot in plot. If facet_column is NULL, NULL is returned.

Examples

## Not run: 
library(readr)
datafile <- paste0(
  "https://raw.githubusercontent.com/trias-project/indicators/master/data/",
  "interim/data_input_checklist_indicators.tsv"
)
data <- read_tsv(datafile,
  na = "",
  col_types = cols(
    .default = col_character(),
    key = col_double(),
    nubKey = col_double(),
    speciesKey = col_double(),
    first_observed = col_double(),
    last_observed = col_double()
  )
)
start_year_plot <- 1900
x_major_scale_stepsize <- 25
x_minor_scale_stepsize <- 5
# without facets
indicator_total_year(data, start_year_plot, x_major_scale_stepsize)
# with facets
indicator_total_year(data, start_year_plot, facet_column = "kingdom")
# specify name of column containing year of introduction (first_observed)
indicator_total_year(data, first_observed = "first_observed")
# specify axis labels
indicator_total_year(data, x_lab = "YEAR", y_lab = NULL)

## End(Not run)

trias-project/trias documentation built on Sept. 18, 2024, 11:50 a.m.