BeeBDC (version 1.2.0)

plotFlagSummary: Generate a plot summarising flagged data

Description

Creates a compound bar plot that shows the proportion of records that pass or fail each flag (rows) and for each data source (columns). The function can also optionally return a point map for a user-specified species when plotMap = TRUE. This function requires that your dataset has been run through some filtering functions - so that is can display logical columns starting with ".".

Usage

plotFlagSummary(
  data = NULL,
  flagColours = c("#127852", "#A7002D", "#BDBABB"),
  fileName = NULL,
  outPath = OutPath_Figures,
  width = 15,
  height = 9,
  units = "in",
  dpi = 300,
  bg = "white",
  device = "pdf",
  speciesName = NULL,
  saveFiltered = FALSE,
  filterColumn = ".summary",
  nameColumn = NULL,
  plotMap = FALSE,
  mapAlpha = 0.5,
  xbuffer = c(0, 0),
  ybuffer = c(0, 0),
  ptSize = 1,
  saveTable = FALSE,
  jitterValue = NULL,
  returnPlot = FALSE,
  ...
)

Value

Exports a compound bar plot that summarises all flag columns. Optionally can also return a point map for a particular species in tandem with the summary plot.

Arguments

data

A data frame or tibble. Occurrence records as input.

flagColours

A character vector. Colours in order of pass (TRUE), fail (FALSE), and NA. Default = c("#127852", "#A7002D", "#BDBABB").

fileName

Character. The name of the file to be saved, ending in ".pdf". If saving as a different file type, change file type suffix - See device.

outPath

A character path. The path to the directory in which the figure will be saved. Default = OutPath_Figures.

width

Numeric. The width of the output figure in user-defined units Default = 15.

height

Numeric. The height of the output figure in user-defined units Default = 9.

units

Character. The units for the figure width and height passed to ggplot2::ggsave() ("in", "cm", "mm", or "px"). Default = "in".

dpi

Numeric. Passed to ggplot2::ggsave(). Plot resolution. Also accepts a string input: "retina" (320), "print" (300), or "screen" (72). Applies only to raster output types. Default = 300.

bg

Character. Passed to ggplot2::ggsave(). Background colour. If NULL, uses the plot.background fill value from the plot theme. Default = "white."

device

Character. Passed to ggplot2::ggsave(). Device to use. Can either be a device function (e.g. png), or one of "eps", "ps", "tex" (pictex), "pdf", "jpeg", "tiff", "png", "bmp", "svg" or "wmf" (windows only). Default = "pdf". If not using default, change file name suffix in fileName argument.

speciesName

Optional. Character. A species name, as it occurs in the user-input nameColumn. If provided, the data will be filtered to this species for the plot.

saveFiltered

Optional. Logical. If TRUE, the filtered data will be saved to the computer as a .csv file.

filterColumn

Optional. The flag column to display on the map. Default = .summary.

nameColumn

Optional. Character. If speciesName is not NULL, enter the column to look for the species in. A User might realise that, combined with speciesName, figures can be made for a variety of factors.

plotMap

Logical. If TRUE, the function will produce a point map. Tested for use with one species at a time; i.e., with speciesName is not NULL.

mapAlpha

Optional. Numeric. The opacity for the points on the map.

xbuffer

Optional. Numeric vector. A buffer in degrees of the amount to increase the min and max bounds along the x-axis. This may require some experimentation, keeping in mind the negative and positive directionality of hemispheres. Default = c(0,0).

ybuffer

Optional. Numeric vector. A buffer in degrees of the amount to increase the min and max bounds along the y-axis. This may require some experimentation, keeping in mind the negative and positive directionality of hemispheres. Default = c(0,0).

ptSize

Optional. Numeric. The size of the points as passed to ggplot2. Default = 1.

saveTable

Optional. Logical. If TRUE, the function will save the data used to produce the compound bar plot.

jitterValue

Optional. Numeric. The value to jitter points by in the map in decimal degrees.

returnPlot

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

...

Optional. Extra variables to be fed into forcats::fct_recode() to change names on plot. For example... 'B. Mont.' = "BMont", 'B. Minkley' = "BMin", Ecd = "Ecd", Gaiarsa = "Gai"

Examples

# import data
data(beesFlagged)
OutPath_Figures <- tempdir()
 # Visualise all flags for each dataSource (simplified to the text before the first underscore)
plotFlagSummary(
  data = beesFlagged,
  # Colours in order of pass (TRUE), fail (FALSE), and NA
  flagColours = c("#127852", "#A7002D", "#BDBABB"),
  fileName = paste0("FlagsPlot_TEST_", Sys.Date(),".pdf"),
  outPath = OutPath_Figures,
  width = 15, height = 9,
  # OPTIONAL:
  #\   #  # Filter to species
  #\   speciesName = "Holcopasites heliopsis",
  #\   # column to look in
  #\   nameColumn = "species",
  #\   # Save the filtered data
  #\   saveFiltered = TRUE,
  #\   # Filter column to display on map
  #\   filterColumn = ".summary",
  #\   plotMap = TRUE,
  #\   # amount to jitter points if desired, e.g. 0.25 or NULL
  #\   jitterValue = NULL,
  #\   # Map opacity value for points between 0 and 1
  #\   mapAlpha = 1,
  # 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. Minkley' = "BMin", Ecd = "Ecd",
  Gaiarsa = "Gai", EPEL = "EPEL"
)