# This wrapper script calls the 'create.indices.from.files' function to create ETCCDI, ET-SCI and other indices
# based on the information provided below.
# Note even when using a threshold file, the base.range parameter must still be specified.

library(climdex.pcic.ncdf,lib.loc="/data/local/hadhd/climpact2-master/R/x86_64-redhat-linux-gnu-library/3.3")
# list of one to three input files. e.g. c("a.nc","b.nc","c.nc")

infiles=c("./4.apdaea.par0t9.05216.nc","./4.apdaea.par0t9.3236X.nc","./4.apdaea.par0t9.3236N.nc")

# list of variable names according to above file(s)
vars=c(prec="precipitation_flux",tmax="Tmax", tmin="Tmin")

# output directory
outdir="./output/"

# CMIP5 formatted file name. Must use CMIP5 file name convention.
#file.template="pr_from_fromthreshold_DECCMA_precis_2070-2099.nc"
file.template="var_daily_DECCMA_rcp85_precis_2070-2099.nc

# author data
author.data=list(institution="Met Office", institution_id="UKMO")

# reference period. Even when using a threshold file, specify this variable.
base.range=c(1961,1990)

# number of cores to use (or FALSE).
cores=4 #FALSEpre ppresent.r &
 

# list of indices to calculate, or NULL to calculate all.
indices=NULL

# input threshold file to use, or NULL for none.
thresholds.files="precis.thresholds.1961-1990.nc"



#######################################################
# Esoterics below, do not modify without a good reason.

# definition used for Excess Heat Factor (EHF). "PA13" for Perkins and Alexander (2013), this is the default. "NF13" for Nairn and Fawcett (2013).
EHF_DEF = "PA13"

# axis to split data on. For chunking up of grid, leave this.
axis.name="Y"

# Number of data values to process at once. If you receive "Error: rows.per.slice >= 1 is not TRUE", try increasing this to 20. You might have a large grid.
maxvals=10

# output compatible with FCLIMDEX. Leave this.
fclimdex.compatible=FALSE

# Call the package.
create.indices.from.files(infiles,outdir,file.template,author.data,variable.name.map=vars,base.range=base.range,parallel=cores,axis.to.split.on=axis.name,climdex.vars.subset=indices,thresholds.files=thresholds.files,fclimdex.compatible=fclimdex.compatible,
	cluster.type="SOCK",ehfdef=EHF_DEF,max.vals.millions=maxvals,
	thresholds.name.map=c(tx05thresh="tx05thresh",tx10thresh="tx10thresh", tx50thresh="tx50thresh", tx90thresh="tx90thresh",tx95thresh="tx95thresh", 
			tn05thresh="tn05thresh",tn10thresh="tn10thresh",tn50thresh="tn50thresh",tn90thresh="tn90thresh",tn95thresh="tn95thresh",
			tx90thresh_15days="tx90thresh_15days",tn90thresh_15days="tn90thresh_15days",tavg90thresh_15days="tavg90thresh_15days",
			tavg05thresh="tavg05thresh",tavg95thresh="tavg95thresh",
			txraw="txraw",tnraw="tnraw",precraw="precraw", 
			r95thresh="r95thresh", r99thresh="r99thresh"))