Description Usage Arguments References Examples
View source: R/generate_fig5.r
This takes the posterior estimates for each species and the species trend estimates
downloaded from the repository, calculates the average occupancy across the time frame
of each species for whihch data were available and generates figure 5 of the
associated paper.
generage_fig5
function estimates species level average occupancy and generates figure 5.
1 2 | generate_fig5(postdir, outdir, sp_trends, status = TRUE,
save_plot = TRUE)
|
postdir |
A filepath specifying where the species level posteriors have been saved. If outputs have not been moved, this will be in a directory "/POSTERIOR_SAMPLES". |
outdir |
A filepath specifying where the outputs of the function are to be saved. |
sp_trends |
A dataframe, downloaded from the repository which details the species level trends in occupancy and the years for which data were avaialble for each species. |
status |
Logical. If TRUE the species name being worked on will be printed to the console. |
save_plot |
Logical. If 'TRUE', the plot will be saved as a PDF file within the 'outdir'. Default is 'TRUE'. |
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
1 2 3 4 5 6 7 8 9 10 11 | ## Not run:
# Run generate_fig5 function to produce plot of average occupancy against
# trend in occupancy.
# datadir should be the filepath of where the posterior samples are saved.
generate_fig5(postdir = "/POSTERIOR_SAMPLES", outdir = getwd(),
sp_trends = read.csv(paste0(datadir, "/Species_Trends.csv")))
## End(Not run)
|
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