generate_fig3: Generate Figure 3

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

Description

This takes the posterior values of the group level indicators generated within the generage_fig1 function, calculates the quantiles and plots the group level quantiles presented in figure 3.

Usage

generate_fig3(postdir, save_plot = TRUE, interval = 95)

Arguments

postdir	A filepath specifying where the posteior samples that are generated from the combine_posteriors function are saved. are saved. If outputs have not been moved, this will be in a directory "/MajorGroups".
save_plot	Logical. If 'TRUE', the plot will be saved as a PDF file within the 'postdir'. Default is 'TRUE'.
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_fig2 function to produce boxplot.
# datadir should be the filepath of where the posterior indicator values are saved.
# generate_fig2(postdir = paste0(getwd(), "/MajorGroups/geomeans"),
save_plot = TRUE,
interval = 90)


## End(Not run)

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