R/soilGoTxt.R

In dirt: soil science related functions

# Author: Robert J. Hijmans
# May 2011
# Version 1.0
# Licence GPL v3



.getChon <- function(version) {
c('hzname', 'desgndisc', 'desgnmaster', 'desgnmasterprime', 'desgnvert', 'hzdept_l', 'hzdept_r', 'hzdept_h', 'hzdepb_l', 'hzdepb_r', 'hzdepb_h', 'hzthk_l', 'hzthk_r', 'hzthk_h', 'fraggt10_l', 'fraggt10_r', 'fraggt10_h', 'frag3to10_l', 'frag3to10_r', 'frag3to10_h', 'sieveno4_l', 'sieveno4_r', 'sieveno4_h', 'sieveno10_l', 'sieveno10_r', 'sieveno10_h', 'sieveno40_l', 'sieveno40_r', 'sieveno40_h', 'sieveno200_l', 'sieveno200_r', 'sieveno200_h', 'sandtotal_l', 'sandtotal_r', 'sandtotal_h', 'sandvc_l', 'sandvc_r', 'sandvc_h', 'sandco_l', 'sandco_r', 'sandco_h', 'sandmed_l', 'sandmed_r', 'sandmed_h', 'sandfine_l', 'sandfine_r', 'sandfine_h', 'sandvf_l', 'sandvf_r', 'sandvf_h', 'silttotal_l', 'silttotal_r', 'silttotal_h', 'siltco_l', 'siltco_r', 'siltco_h', 'siltfine_l', 'siltfine_r', 'siltfine_h', 'claytotal_l', 'claytotal_r', 'claytotal_h', 'claysizedcarb_l', 'claysizedcarb_r', 'claysizedcarb_h', 'om_l', 'om_r', 'om_h', 'dbtenthbar_l', 'dbtenthbar_r', 'dbtenthbar_h', 'dbthirdbar_l', 'dbthirdbar_r', 'dbthirdbar_h', 'dbfifteenbar_l', 'dbfifteenbar_r', 'dbfifteenbar_h', 'dbovendry_l', 'dbovendry_r', 'dbovendry_h', 'partdensity', 'ksat_l', 'ksat_r', 'ksat_h', 'awc_l', 'awc_r', 'awc_h', 'wtenthbar_l', 'wtenthbar_r', 'wtenthbar_h', 'wthirdbar_l', 'wthirdbar_r', 'wthirdbar_h', 'wfifteenbar_l', 'wfifteenbar_r', 'wfifteenbar_h', 'wsatiated_l', 'wsatiated_r', 'wsatiated_h', 'lep_l', 'lep_r', 'lep_h', 'll_l', 'll_r', 'll_h', 'pi_l', 'pi_r', 'pi_h', 'aashind_l', 'aashind_r', 'aashind_h', 'kwfact', 'kffact', 'caco3_l', 'caco3_r', 'caco3_h', 'gypsum_l', 'gypsum_r', 'gypsum_h', 'sar_l', 'sar_r', 'sar_h', 'ec_l', 'ec_r', 'ec_h', 'cec7_l', 'cec7_r', 'cec7_h', 'ecec_l', 'ecec_r', 'ecec_h', 'sumbases_l', 'sumbases_r', 'sumbases_h', 'ph1to1h2o_l', 'ph1to1h2o_r', 'ph1to1h2o_h', 'ph01mcacl2_l', 'ph01mcacl2_r', 'ph01mcacl2_h', 'freeiron_l', 'freeiron_r', 'freeiron_h', 'feoxalate_l', 'feoxalate_r', 'feoxalate_h', 'extracid_l', 'extracid_r', 'extracid_h', 'extral_l', 'extral_r', 'extral_h', 'aloxalate_l', 'aloxalate_r', 'aloxalate_h', 'pbray1_l', 'pbray1_r', 'pbray1_h', 'poxalate_l', 'poxalate_r', 'poxalate_h', 'ph2osoluble_l', 'ph2osoluble_r', 'ph2osoluble_h', 'ptotal_l', 'ptotal_r', 'ptotal_h', 'excavdifcl', 'excavdifms', 'cokey', 'chkey')
}

.getMapn <- function(version) {
c('musym', 'muname', 'mukind', 'mustatus', 'muacres', 'mapunitlfw_l', 'mapunitlfw_r', 'mapunitlfw_h', 'mapunitpfa_l', 'mapunitpfa_r', 'mapunitpfa_h', 'farmlndcl', 'muhelcl', 'muwathelcl', 'muwndhelcl', 'interpfocus', 'invesintens', 'iacornsr', 'nhiforsoigrp', 'nhspiagr', 'vtsepticsyscl', 'mucertstat', 'lkey', 'mukey')
}

.getComn <- function(version) {
c('comppct_l', 'comppct_r', 'comppct_h', 'compname', 'compkind', 'majcompflag', 'otherph', 'localphase', 'slope_l', 'slope_r', 'slope_h', 'slopelenusle_l', 'slopelenusle_r', 'slopelenusle_h', 'runoff', 'tfact', 'wei', 'weg', 'erocl', 'earthcovkind1', 'earthcovkind2', 'hydricon', 'hydricrating', 'drainagecl', 'elev_l', 'elev_r', 'elev_h', 'aspectccwise', 'aspectrep', 'aspectcwise', 'geomdesc', 'albedodry_l', 'albedodry_r', 'albedodry_h', 'airtempa_l', 'airtempa_r', 'airtempa_h', 'map_l', 'map_r', 'map_h', 'reannualprecip_l', 'reannualprecip_r', 'reannualprecip_h', 'ffd_l', 'ffd_r', 'ffd_h', 'nirrcapcl', 'nirrcapscl', 'nirrcapunit', 'irrcapcl', 'irrcapscl', 'irrcapunit', 'cropprodindex', 'constreeshrubgrp', 'wndbrksuitgrp', 'rsprod_l', 'rsprod_r', 'rsprod_h', 'foragesuitgrpid', 'wlgrain', 'wlgrass', 'wlherbaceous', 'wlshrub', 'wlconiferous', 'wlhardwood', 'wlwetplant', 'wlshallowwat', 'wlrangeland', 'wlopenland', 'wlwoodland', 'wlwetland', 'soilslippot', 'frostact', 'initsub_l', 'initsub_r', 'initsub_h', 'totalsub_l', 'totalsub_r', 'totalsub_h', 'hydgrp', 'corcon', 'corsteel', 'taxclname', 'taxorder', 'taxsuborder', 'taxgrtgroup', 'taxsubgrp', 'taxpartsize', 'taxpartsizemod', 'taxceactcl', 'taxreaction', 'taxtempcl', 'taxmoistscl', 'taxtempregime', 'soiltaxedition', 'castorieindex', 'flecolcomnum', 'flhe', 'flphe', 'flsoilleachpot', 'flsoirunoffpot', 'fltemik2use', 'fltriumph2use', 'indraingrp', 'innitrateleachi', 'misoimgmtgrp', 'vasoimgtgrp', 'mukey', 'cokey')
}



.getSoilGoTxt <- function(tab, props, ignoreVersion=FALSE, ...) {

	verf <- paste(tab, '/version.txt', sep="")
	cmpf <- paste(tab, '/comp.txt', sep="")
	chof <- paste(tab, '/chorizon.txt', sep="")

	vers <- readLines(verf)
	
	if (vers[1] == "SSURGOV2.1") {
		vers <- vers[1]
	} else {
		if (!ignoreVersion) {
			stop('unknown version: ', vers[1], '\n Please report this.\n You can try to use this file anyway, at your own risk, using argument "ignoreVersion=TRUE"')
		}
	}
	
	horiz <- try(read.table(chof, sep='|'), silent=TRUE)
	if (class(horiz) == 'try-error') {
		warning('table chorizon has no records. Assuming there are no soils in this area')
		cn <- unique(c('cokey', props, "hzdept_r", "hzdepb_r", 'cokey', 'mukey', 'comppct_r'))
		d <- data.frame(matrix(nrow=0, ncol=length(cn)))
		colnames(d) <- cn
		return(d)
	}
	
	colnames(horiz) <- .getChon(vers)

#	mapf <- paste(tab, '/mapunit.txt', sep="")
#	map <- read.table(mapf, sep='|')
#	colnames(map) <- .getMapn(vers)
#	map <- map[, c('mukey', 'cokey')]

	comp <- read.table(cmpf, sep='|')
	colnames(comp) <- .getComn(vers)
	comp <- comp[,c('cokey', 'mukey', 'comppct_r')]

    props <- unique(c('cokey', props, c("hzdept_r", "hzdepb_r")))
	horiz <- horiz[, props]	
	
	merge(horiz, comp, by='cokey')
}