LANDCLIMII project r-scripts
code used for preparation and analysis in LANDCLIMII project

Code is prepared in blocks

RV.file.format.LANDCLIMII.r prepares unformatted pollen count data in csv files to an LRAready csv format
requires:
-LANDCLIM.ALLEUROPE.taxa.LUT.080219.csv (synonym table for harmonising taxonomy)
-bins.csv (used to define start and end points of time windows for aggregating samples)
-run.all.taxa.100219.csv (used to add rows for RPP taxa where not present)
-TWlookup.csv (used to add columns for timewindows where not present)
-site.metadata.csv (used to add site size and type to count data)
-pollen count data (in csv file format, example datasets provided in folder "input")

Kunes_REVEALS_iterate_across_sitelist.r controls the application of the REVEALS in R function (Abraham et al 2014: REF1) to LRA ready files, by iterating across groups of sites (grouped into 1 degree grid cells for LANDCLIMII project). Selection of grid cells controlled by a list of all grid cells.
requires (all in the working directory):
-LRA-REVEALS-release.R (Kunes' REVEALS-in-R script, available at REF2)
-LRAready_sitename.csv files (product of RV.file.format.LANDCLIMII.r script)
-site.list.xxx.csv files (one per grid cell, xxx as grid cell name/code)
-GC.list.csv (list of all site.list.xxx.csv files)
-taxa.csv (list of RPP taxa for formatting output files)
-av-RPP.all.landclimII.csv (RPP and fall speed of pollen for taxa)
-avar-RPP.all.landclimII.csv (variance-covariance matrix of RPP values)

outputs csv files for
(a) grid cells where rows = taxa and cols = time windows (mean and standard errors separately)
(b) time windows where rows = grid cells and cols = taxa REVEALS estimates (mean and standard error separately)

REFERENCES
REF1: Abraham, V., Oušková, V., & Kuneš, P. 2014. Present-day vegetation helps quantifying past land cover in selected regions of the Czech Republic. PLoS ONE 9: e100117.
REF2: https://github.com/petrkunes/LRA