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Create an interactive plot for the number of alien species per native region and year of introduction

Source: R/indicator_native_range_year.R
indicator_native_range_year.Rd

Based on countYearProvince plot from reporting - rshiny - grofwildjacht

Usage

indicator_native_range_year(
  df,
  years = NULL,
  type = c("native_range", "native_continent"),
  x_major_scale_stepsize = 10,
  x_lab = "year",
  y_lab = "alien species",
  response_type = c("absolute", "relative", "cumulative"),
  relative = lifecycle::deprecated(),
  taxon_key_col = "key",
  first_observed = "first_observed"
)

Arguments

df

input data.frame.

years

(numeric) vector years we are interested to. If NULL (default) all years from minimum and maximum of years of first observation are taken into account.

type

character, native_range level of interest should be one of c("native_range", "native_continent"). Default: "native_range". A column called as the selected type must be present in df.

x_major_scale_stepsize

(integer) Parameter that indicates the breaks of the x axis. Default: 10.

x_lab

character string, label of the x-axis. Default: "year".

y_lab

character string, label of the y-axis. Default: "number of alien species".

response_type

(character) summary type of response to be displayed; should be one of c("absolute", "relative", "cumulative"). Default: "absolute". If "absolute" the number per year and location is displayed; if "relative" each bar is standardised per year before stacking; if "cumulative" the cumulative number over years per location.

relative

(logical) if TRUE each bar is standardised before stacking. Deprecated, use response_type = "relative" instead.

taxon_key_col

character. Name of the column of df containing taxon IDs. Default: "key".

first_observed

(character) Name of the column in data containing temporal information about introduction of the alien species. Expressed as years.

Value

list with:

  • static_plot: ggplot object, for a given species the observed number per year and per native range is plotted in a stacked bar chart.

  • interactive_plot: plotly object, for a given species the observed number per year and per native range is plotted in a stacked bar chart.

  • data: data displayed in the plot, as a data.frame with:

    • year: year at which the species were introduced.

    • native_range: native range of the introduced species.

    • n: number of species introduced from the native range for a given year.

    • total: total number of species, from all around the world, introduced. during a given year.

    • perc: percentage of species introduced from the native range for a given year, n/total*100.

Examples

if (FALSE) { # \dontrun{
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()
  )
)
indicator_native_range_year(data, "native_continent", years = c(2010,2013))
} # }