barplotRichness: barplotRichness
In NCRN/NCRNbirds: Data analysis and visualization for NPS I&M bird monitoring.

barplotRichness

R Documentation

barplotRichness

Description

Makes a barplot of species richness

Usage

barplotRichness(
  object,
  byPark = F,
  byYear = F,
  byPoint = F,
  byGuild = F,
  includeNA = T,
  colors = "dark green",
  palette = "BuGn",
  plot_title = NA,
  scale = T,
  labels = T,
  output = "total",
  plot = TRUE,
  ...
)

Arguments

`object`	An `NCRNbirds` object a `list` of such objects, or a `data.frame` like that produced by `birdRichness`.
`byPark`	Defaults to `FALSE`. If true the barplot will have on bar for each park.
`byYear`	Defaults to `FALSE`. If true the barplot will have on bar for each year.
`byPoint`	Defaults to `FALSE`. If `TRUE` the barplot will have one bar for each point.
`byGuild`	Defaults to `FALSE`. If `TRUE` the barplot will be stacked by Guild.
`includeNA`	Defaults to `TRUE`. If `byGuild = T` and `includeNA=F` then speices which have a response guild of `NA` will not be included in the bar chart.
`colors`	One or more colors for the bars.
`palette`	Color pallete for the background of the graph. Defaults to "BuGn" (blue green) but will accept any RColorBrewer palette
`plot_title`	Optional, A title for the plot.
`scale`	If `TRUE` will include a scale to the right of the barplot.
`labels`	If`TRUE` will label species richness values on the barplot.Labels are never shown wehen plotting by guild.
`output`	Either "total" (the default) or "list". Only used when `object` is a `list`
`plot`	Logical. Return plot `TRUE` (default) or data.frame `FALSE`.
`...`	Additional arguments passed to `birdRichness`

Details

This function produces a barplot of species richness by Park, Year or Point. It does this by using the output of the birdRichness function. The data is then passed on to ggplot2 for graphing. The user can chose to have byPark=T, byYear=T or byPoint=T, but should only pick one of the three. These can be combined with a guild category using byGuild. The includeNA argument indicates if bird species that are not categorized for a particular guild shoud be included.

Colors:

Colors of the bars are controlled by either colors or palette argumnts. If the barplot is not by guild then the color indicated by colors will be used. If byGuild=T then by default the palette arguement will be used. However, the palette arguement can be overridden simply by giving colors a vector of colors with one color for each guild category shown in the barplot.If includeNA=T than than the first color will correspond to the NA value.