Plot number of introduced taxa for CBD pathways level 1

Function to plot bar graph with number of taxa introduced by different pathways at level 1. Possible breakpoints: taxonomic (kingdoms + vertebrates/invertebrates) and temporal (lower limit year). Facets can be added (see argument facet_column).

Usage

visualize_pathways_level1(
  df,
  category = NULL,
  from = NULL,
  facet_column = NULL,
  pathways = NULL,
  pathway_level1_names = "pathway_level1",
  taxon_names = "key",
  kingdom_names = "kingdom",
  phylum_names = "phylum",
  first_observed = "first_observed",
  cbd_standard = TRUE,
  title = NULL,
  x_lab = "Number of introduced taxa",
  y_lab = "Pathways"
)

Arguments

df

A data frame.

category

NULL or character. One of the kingdoms as given in GBIF and Chordata (the phylum), Not Chordata (all other phyla of Animalia): 1. Plantae 2. Animalia 3. Fungi 4. Chromista 5. Archaea 6. Bacteria 7. Protozoa 8. Viruses 9. incertae sedis 10. Chordata 11. Not Chordata Default: NULL.

from

NULL or numeric. Year trade-off: select only pathways related to taxa introduced during or after this year. Default: NULL.

facet_column

NULL (default) or character. The column to use to create additional facet wrap bar graphs underneath the main graph. When NULL, no facet graph are created. One of family, order, class, phylum, locality, native_range, habitat. If column has another name, rename it before calling this function. Facet phylum is not allowed in combination with category equal to "Chordata" or "Not Chordata". Facet kingdom is allowed only with category equal to NULL.

pathways

character. Vector with pathways level 1 to visualize. The pathways are displayed following the order as in this vector.

pathway_level1_names

character. Name of the column of df containing information about pathways at level 1. Default: pathway_level1.

taxon_names

character. Name of the column of df containing information about taxa. This parameter is used to uniquely identify taxa.

kingdom_names

character. Name of the column of df containing information about kingdom. Default: "kingdom".

phylum_names

character. Name of the column of df containing information about phylum. This parameter is used only if category is one of: "Chordata", "Not Chordata". Default: "phylum".

first_observed

character. Name of the column of df containing information about year of introduction. Default: "first_observed".

cbd_standard

logical. If TRUE the values of pathway level 1 are checked based on CBD standard as returned by pathways_cbd(). Error is returned if unmatched values are found. If FALSE, a warning is returned. Default: TRUE.

title

NULL or character. Title of the graph. Default: NULL.

x_lab

NULL or character. x-axis label. Default: "Number of introduced taxa".

y_lab

NULL or character. Title of the graph. Default: "Pathways".

Value

A list with three slots:

• plot: ggplot2 object (or egg object if facets are used). NULL if there are no data to plot.

• 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. NULL is returned if facet_column is NULL.

Examples

if (FALSE) {
library(readr)
datafile <- paste0(
  "https://raw.githubusercontent.com/trias-project/indicators/master/data/",
  "interim/data_input_checklist_indicators.tsv"
)
data <- read_tsv(datafile,
  na = "NA",
  col_types = cols(
    .default = col_character(),
    key = col_double(),
    nubKey = col_double(),
    speciesKey = col_double(),
    acceptedKey = col_double(),
    first_observed = col_double(),
    last_observed = col_double()
  )
)
# All taxa
visualize_pathways_level1(data)

# Animalia
visualize_pathways_level1(data, category = "Animalia")

# Chordata
visualize_pathways_level1(data, category = "Chordata")

# facet phylum
visualize_pathways_level1(
  data,
  category = "Animalia",
  facet_column = "phylum"
)

# facet habitat
visualize_pathways_level1(data, facet_column = "habitat")

# Only taxa introduced from 1950
visualize_pathways_level1(data, from = 1950)

# Only taxa with pathways "corridor" and "escape"
visualize_pathways_level1(data, pathways = c("corridor", "escape"))

# Add a title
visualize_pathways_level1(
  data,
  category = "Plantae",
  from = 1950,
  title = "Plantae - Pathway level 1 from 1950"
)

# Personalize axis labels
visualize_pathways_level1(data, x_lab = "Aantal taxa", y_lab = "pathways")
}