ausplotsR (version 2.0.5)

ausplots_visual: Graphical illustration of sample TERN AusPlots data

Description

Generates a set of graphical displays representing TERN AusPlots data based on geographic locations and vegetation attributes from the plot-based point intercepts (as generated by get_ausplots and other pre-processing functions).

Usage

ausplots_visual(my.ausplots.object = NULL, map = TRUE, map.attribute = TRUE, 
fraction.pie = TRUE, growthform.pie = TRUE, cumulative.cover = TRUE, 
whittaker = TRUE, outfile=NULL, max.plots = 5)
map_ausplots(my.ausplots.object)

Value

Plots are written to a pdf file to ensure consistent formatting, saved by default in the working directory.

Arguments

my.ausplots.object

Optional (but required for map_ausplots) input raw data object as generated in a call from the get_ausplots function. The default graphical outputs require $site.info (for locations) and $veg.PI (for vegetation attributes) to be included in the AusPlots data extract.

map

Logical, whether to include a basic map of site locations in the context of Australia.

map.attribute

Logical, whether to include a map depicting site locations in Australia coded by cover of trees over 5 m high.

fraction.pie

Logical, whether to include pie charts depicting fractional_cover.

growthform.pie

Logical, whether to include pie charts depicting relative cover of plant growth forms.

cumulative.cover

Logical, whether to include graphs of cumulative cover estimates by species as point intercepts are taken across each AusPlot.

whittaker

Logical, whether to include Whittaker plots depicting species abundance distributions.

outfile

Optional file path and name to which the output pdf file is written.

max.plots

Maximum number of sites for which to display individual graphics panels. By default, max.plots sites are selected randomly. If you provide existing AusPlots data, max.plots sites are processed (in order) whenever fractional.pie or cumulative.cover are selected, because those calculations can be slow across a large number of plots.

Author

Greg Guerin, Bernardo Blanco-Martin

Details

By default, extracts sample data, allowing the user to explore the dataset in a single call, or to easily visualise an extracted AusPlots dataset. Included in the default demonstration plots are maps of plot locations with and without coding by tree cover, and then a set of four panels for a smaller sample of AusPlots, depicting data from the main vegetation tables in the package, i.e., fractional cover, growth form cover, species cover and species relative abundance. This function is intended as a simple demonstration of the data available. Refer to TERN tutorials for many other ways to visualise and explore AusPlots.

References

Blanco-Martin, B. (2019) Tutorial: Understanding and using the 'ausplotsR' package and AusPlots data. Terrestrial Ecology Research Network. Version 2019.04.0, April 2019. https://github.com/ternaustralia/TERN-Data-Skills/

Guerin, G.R., Sparrow, B., Tokmakoff, A., Smyth, A., Leitch, E., Baruch, Z., Lowe, A.J. (2017) Opportunities for integrated ecological analysis across inland Australia with standardised data from AusPlots Rangelands. PLoS ONE 12, e0170137.

Whittaker, R.H. (1965) Dominance and diversity in land plant communities: numerical relations of species express the importance of competition in community function and evolution. Science, 147, 250-260.

See Also

get_ausplots

fractional_cover

growth_form_table

single_cover_value

species_table

ausplots_trajectory

Examples

if (FALSE) {
#Default output
#Plot locations; visualisations for 5 random plots (including revisits):
ausplots_visual()

#Map tree cover only for all sites:

#Extract data first:
my.data <- get_ausplots(veg.PI=TRUE)

#Set maximum number of plots to all available in the veg.PI data:
ausplots_visual(my.data, map = FALSE, map.attribute = TRUE, 
fraction.pie = FALSE, growthform.pie = FALSE, cumulative.cover = FALSE, 
whittaker = FALSE, outfile = "AusPlots_treeCover.pdf", 
max.plots=length(unique(my.data$veg.PI$site_location_name))) 
}