generate_fig1: Generating Figure 1

In CharlieOuthwaite/UKBiodiversity: Recreates analyses and figures of Outhwaite et al (in revision)

Description

This takes the major group level posterior combinations generated using the combine_posteriors function and generates figure 1 presented within the paper. It also generates the posteriors of average change across species for each group that are also used in the estimation of major group level trends presented within the text of the associated paper and for the generation of figure 3.

Usage

generate_fig1(postdir, status = TRUE, save_plot = TRUE,
  interval = 95)

Arguments

postdir	A filepath specifying where the posterior combinations are saved.
status	Logical. If 'TRUE', group name will be printed to the console as means and indicator values are being estimated. Default is 'TRUE'.
save_plot	Logical. If 'TRUE' plot will be saved as a PDF file as well as being returned to the console.
interval	A number between 0 and 100 indicating the percentiles of the credible intervals to be plotted and reported. Defaults to 95%

References

Outhwaite et al (in prep) Complexity of biodiversity change revealed through long-term trends of invertebrates, bryophytes and lichens.

Outhwaite, C. L., Powney, G. D., August, T. A., Chandler, R. E., Rorke, S., Pescott, O., … Isaac, N. J. B. (2019). Annual estimates of occupancy for bryophytes, lichens and invertebrates in the UK (1970-2015). NERC Environmental Information Data Centre. https://doi.org/10.5285/0ec7e549-57d4-4e2d-b2d3-2199e1578d84

Examples

## Not run: 

# Run generate_fig1 function
# postdir should be the filepath of where the 4 major group level posteriors
# combinations are saved.
generate_fig1(postdir = paste0(getwd(), "/MajorGroups"),
status = TRUE,
save_plot = TRUE,
interval = 90)


## End(Not run)

CharlieOuthwaite/UKBiodiversity documentation built on Jan. 24, 2020, 12:45 p.m.