indicator_introduction_year: Plot number of new introductions per year.

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

Plot number of new introductions per year.

Description

Calculate how many new species has been introduced in a year.

Usage

indicator_introduction_year(
  df,
  start_year_plot = 1920,
  smooth_span = 0.85,
  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 = "Number of introduced alien species"
)

Arguments

df	A data frame.
start_year_plot	Year where the plot starts from. Default: 1920.
smooth_span	(numeric) Parameter for the applied loess smoother. For more information on the appropriate value, see ggplot2::geom_smooth(). Default: 0.85.
x_major_scale_stepsize	(integer) Parameter that indicates the breaks of the x axis. Default: 10.
x_minor_scale_stepsize	(integer) Parameter that indicates the minor breaks of the x axis. Default: 5.
facet_column	NULL or character. The column to use to create additional facet wrap plots underneath the main graph. When NULL, no facet graph are created. Valid facet options: "family", "order", "class", "phylum", "kingdom", "pathway_level1", "locality", "native_range" 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 set or remove the x-axis label.
y_lab	NULL or character. to set or remove the y-axis label.

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()
  )
)
# without facets
indicator_introduction_year(data)
# specify start year and smoother parameter
indicator_introduction_year(data,
  start_year_plot = 1940,
  smooth_span = 0.6
)
# with facets
indicator_introduction_year(data, facet_column = "kingdom")
# specify columns with year of first observed
indicator_introduction_year(data,
  first_observed = "first_observed"
)
# specify axis labels
indicator_introduction_year(data, x_lab = "YEAR", y_lab = NULL)

## End(Not run)

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