Create a compound bar graph of duplicate data sources

Source: R/dupePlotR.R

Creates a plot with two bar graphs. One shows the absolute number of duplicate records for each data source while the other shows the proportion of records that are duplicated within each data source. This function requires a dataset that has been run through dupeSummary().

dupePlotR(
  data = NULL,
  outPath = NULL,
  fileName = NULL,
  legend.position = c(0.85, 0.8),
  base_height = 7,
  base_width = 7,
  ...,
  dupeColours = c("#F2D2A2", "#B9D6BC", "#349B90"),
  returnPlot = FALSE
)

Arguments

data

A data frame or tibble. Occurrence records as input.

outPath

Character. The path to a directory (folder) in which the output should be saved.

fileName

Character. The name of the output file, ending in '.pdf'.

legend.position

The position of the legend as coordinates. Default = c(0.85, 0.8).

base_height

Numeric. The height of the plot in inches. Default = 7.

base_width

Numeric. The width of the plot in inches. Default = 7.

...

Other arguments to be used to change factor levels of data sources.

dupeColours

A vector of colours for the levels duplicate, kept duplicate, and unique. Default = c("#F2D2A2","#B9D6BC", "#349B90").

returnPlot

Logical. If TRUE, return the plot to the environment. Default = FALSE.

Value

Outputs a .pdf figure.

Examples


# This example will show a warning for the factor levels taht are not present in the specific 
# test dataset
dupePlotR(
  data = beesFlagged,
  # The outPath to save the plot as
    # Should be something like: #paste0(OutPath_Figures, "/duplicatePlot_TEST.pdf"),
  outPath = tempdir(), 
  fileName = "duplicatePlot_TEST.pdf",
  # Colours in order: duplicate, kept duplicate, unique
  dupeColours = c("#F2D2A2","#B9D6BC", "#349B90"),
  # Plot size and height
  base_height = 7, base_width = 7,
  legend.position = c(0.85, 0.8),
  # Extra variables can be fed into forcats::fct_recode() to change names on plot
  GBIF = "GBIF", SCAN = "SCAN", iDigBio = "iDigBio", USGS = "USGS", ALA = "ALA", 
  ASP = "ASP", CAES = "CAES", 'B. Mont.' = "BMont", 'B. Minckley' = "BMin", Ecd = "Ecd",
  Gaiarsa = "Gai", EPEL = "EPEL", Lic = "Lic", Bal = "Bal", Arm = "Arm"
  )
#> Loading required namespace: forcats
#> Loading required namespace: cowplot
#> Warning: Unknown levels in `f`: CAES, BMont, BMin, Ecd, Gai, EPEL, Lic, Bal, Arm