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Commit1b7526c

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Added MUSLE and APLE linkages.
1 parentf479455 commit1b7526c

29 files changed

+795
-194
lines changed

‎DESCRIPTION‎

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Package: VFS
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Title: Vegetated Filter Strip and Erosion Model
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Version: 0.9.3
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Version: 0.9.3-1
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Date: 2018-09-06
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Authors@R: c(person("Sarah", "Goslee", role = c("aut", "cre"),
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email = "Sarah.Goslee@ars.usda.gov"),

‎R/APLE.R‎

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# APLE short form
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APLE<-function(soilP,clay,OM,precip,runoff,erosion,manureP=25,manureSolids=25,manureWEP=50,manureIn=40,fertP=10,fertIn=40) {
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## Inputs
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# soilP: soil test Mehlich 3 (mg / kg)
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# clay: soil clay (%)
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# OM: soil organic matter (%)
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# precip: annual precipitation (in)
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# runoff: annual runoff (in)
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# erosion: annual erosion (ton / ac)
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# manureP: manure P applied (kg / ha): default 25
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# manureSolids: manure solids (%): default 50
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# manureWEP: manure WEP / TP (%): default 50
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# manureIn: manure incorporated (%): default 40
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# fertP: fertilizer P applied (kg / ha): default 10
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# fertIn: fertilizer incorporated (%): default 40
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## Conversions and coefficients
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# runoff (L / ha)
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runoffL<- (runoff*25.4)/10*100^4/1000
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# erosion (kg / ha)
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erosion<-erosion*2000/2.205*2.471
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# erosion enrichment ratio
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eer<- ifelse(erosion==0,0, max(exp(2.2-0.25* log(erosion)),1))
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# soil dissolved P extraction coefficient: default 0.005
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Pcoef<-0.005
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# soil organic carbon (%)
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SOC<-OM*0.58
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# soil PSP
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soilPSP<- min(0.9, max(0.05, (-0.053* log(clay)+0.001* (soilP/2)-0.029*SOC+0.42)))
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# soil labile P (mg / kg)
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soilPlabile<-soilP/2
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# soil active P (mg / kg)
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soilPactive<-soilPlabile* (1-soilPSP)/soilPSP
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# soil stable P (mg / kg)
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soilPstable<-soilPactive*4
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# soil organic P (mg / kg)
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soilPorganic<-SOC*10000/8/14
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# soil total P (mg / kg)
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soilPtotal<-soilPlabile+soilPactive+soilPstable+soilPorganic
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# AB manure WEP mineralized (kg / ha)
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manureWEPmineral<- (ifelse(manureSolids<15, (manureP* (1- (manureWEP/100))* ((100-manureIn)/100)*0.4), (manureP* (1- (manureWEP/100))* ((100-manureIn)/100))))*0.15
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# AC manure WEP available (kg / ha)
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manureWEPavail<- ifelse(manureSolids<15, (manureP* (manureWEP/100)* ((100-manureIn)/100)*0.4), (manureP* (manureWEP/100)* ((100-manureIn)/100)))+manureWEPmineral
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# AD manure PD factor
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manurePD<- (runoff/precip)^0.225
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# AE fertilizer P available (kg / ha)
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fertPavail<- (fertP* ((100-fertIn)/100))
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# AF fertilizer PD factor
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fertPD<-0.034* exp((runoff/precip)*3.4)
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# AH soil erosion P loss (kg / ha)
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lossErosion<-erosion*soilPtotal*eer/1000000
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# AI soil dissolved P loss (kg / ha)
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lossDissolvedSoil<-soilP*0.5*Pcoef*runoffL/1000000
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# AJ manure dissolved P loss (kg / ha)
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lossDissolvedManure<-manureWEPavail*runoff/precip*manurePD
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# AK fertilizer dissolved P loss (kg / ha)
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lossDissolvedFert<-fertPavail*runoff/precip*fertPD
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# AL total P loss (kg / ha)
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lossTotal<-lossErosion+lossDissolvedSoil+lossDissolvedManure+lossDissolvedFert
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list(lossErosion=lossErosion,lossDissolvedSoil=lossDissolvedSoil,lossDissolvedManure=lossDissolvedManure,lossDissolvedFert=lossDissolvedFert,lossTotal=lossTotal)
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}
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‎R/MUSLE.R‎

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# Daily MUSLE sediment loss
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MUSLE<-function(Q,qp,A,C=0.085,P=0.40,K,LS) {
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# Q: runoff volume - m3/day
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# qp: runoff peak discharge m3/s
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# A: field area (ha)
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# returns S: Sediment yield - t/day
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11.8* (Q*qp*A)^0.56* (C*P*K*LS)
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}
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‎R/MUSLEfactors.R‎

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MUSLE.K<-function(fc,fm,ff) {
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# PTF from Goslee, unpublished data (manuscript in review)
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Sa<-fc*100
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Si<-fm*100
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Cl<-ff*100
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Sa2<-Sa^2
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SaI<-1/Sa
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SaL<- log(Sa)
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Si<-Si
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SiI<-1/Si
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SiL<- log(Si)
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Cl<-Cl
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Cl2<-Cl^2
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ClL<- log(Cl)
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Kf<-0.93721+-0.00007*Sa2+-0.06562*SaI+-0.04880*SaL+-0.00239*Si+0.01337*SiI+0.00534*SiL+-0.01202*Cl+0.00004*Cl2+0.00762*ClL
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if(Kf<0.30)Kf<-0.03
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if(Kf>0.69)Kf<-0.69
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Kf
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}
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####
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MUSLE.LS<-function(FieldLength,FieldSlope) {
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slopelength<-FieldLength# ft
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slopeanglep<-100*FieldSlope# percent
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slopeangled<- atan(FieldSlope)* (360/ (2*pi))# degrees
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m<-NA
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if(slopeanglep>5)m<-0.5
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if(slopeanglep>3&slopeanglep<=5)m<-0.4
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if(slopeanglep>1&slopeanglep<=3)m<-0.3
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if(slopeanglep<=1)m<-0.2
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LS<- (slopelength/72.6)^m* (65.41* sin(slopeangled* (2*pi)/360)^2+4.56* sin(slopeangled* (2*pi)/360)+0.065)
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LS
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}
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###
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peak<-function(intensity,area,c=0.25) {
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# intensity: mm/hr
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# area: ha
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intensity<-intensity/25.4# convert intensity to inch/hour
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area<-area*2.47105# convert drainage area to acres
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peakd<-c*intensity*area# cfs
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peakd*0.0283168# return m3/second
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}
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R/VFSsim.R renamed to R/VFS.R

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VFSsim<-
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VFS<-
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function(nyears=1000,thissoil,thisbuffer,rain,temperature,Duration=2,FieldArea=4000,VFSwidth=10.7,VFSslope=0.02,FieldSlope,z=1000,a=1,b= c(.5,1,1.5,2.5),carrysoilwater=TRUE,runoffcalc=TRUE) {
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# nyears: number of years to simulate
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VFSwidth<-3.28084*VFSwidth
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## Assume a square field
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FieldLength<- sqrt(FieldArea)
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FieldLength<-3.28084*FieldLength
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FieldLength<- sqrt(FieldArea)#m2
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FieldLength<-3.28084*FieldLength# ft
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## If field slope isn't specified, use VFS slope
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if(missing(FieldSlope))FieldSlope<-VFSslope

‎R/VFSAPLE.R‎

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VFSAPLE<-function(x,soilP,OM,manureP=25,manureSolids=25,manureWEP=50,manureIn=40,fertP=10,fertIn=40) {
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if(!inherits(x,"VFS")) {
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stop("VFSAPLE requires the output of VFS\n")
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}
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# mean annual rainfall in mm
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precip<-x$AnnualRainfall[,1]
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precip<-precip/25.4# inches
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# mean annual runoff in mm
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runoff<-x$AnnualRunoff[,1]
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runoff<-runoff/25.4# inches
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# field characteristics
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clay<-100*x$field[["clay"]]# percent
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# mean annual erosion BEFORE vegetated filter strip t/ha
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erosionPre<-x$AnnualLoadInMUSLE[,1]
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erosionPre<-erosionPre*0.44609
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# mean annual erosion AFTER vegetated filter strip t/ha
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erosionPost<-x$AnnualLoadOutMUSLE[,1]
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erosionPost<-erosionPost*0.44609
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preVFS<- APLE(soilP,clay,OM,precip,runoff,erosionPre,manureP=25,manureSolids=25,manureWEP=50,manureIn=40,fertP=10,fertIn=40)
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postVFS<- APLE(soilP,clay,OM,precip,runoff,erosionPost,manureP=25,manureSolids=25,manureWEP=50,manureIn=40,fertP=10,fertIn=40)
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# percent change in erosion P and in total P losses
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pErosion<-100* (preVFS$lossErosion-postVFS$lossErosion)/postVFS$lossErosion
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pTotal<-100* (preVFS$lossTotal-postVFS$lossTotal)/postVFS$lossTotal
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list(preVFS=preVFS,postVFS=postVFS,pErosion=pErosion,pTotal=pTotal)
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}
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‎data/weather.rda‎

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Binary file not shown.

‎man/APLE.Rd‎

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\name{APLE}
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\alias{APLE}
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\title{
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AgriculturalPhosphorusLossEstimator
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}
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\description{
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AgriculturallossofphosphorusbasedonsoilP,additionsoffertilizerandmanure,anderosion..
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}
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\usage{
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APLE(soilP,clay,OM,precip,runoff,erosion,manureP=25,manureSolids=25,
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manureWEP=50,manureIn=40,fertP=10,fertIn=40)
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}
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\arguments{
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\item{soilP}{
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%%~~Describe \code{soilP}here~~
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}
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\item{clay}{
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%%~~Describe \code{clay}here~~
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}
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\item{OM}{
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%%~~Describe \code{OM}here~~
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}
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\item{precip}{
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%%~~Describe \code{precip}here~~
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}
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\item{runoff}{
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%%~~Describe \code{runoff}here~~
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}
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\item{erosion}{
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%%~~Describe \code{erosion}here~~
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}
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\item{manureP}{
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%%~~Describe \code{manureP}here~~
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}
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\item{manureSolids}{
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%%~~Describe \code{manureSolids}here~~
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}
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\item{manureWEP}{
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%%~~Describe \code{manureWEP}here~~
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}
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\item{manureIn}{
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%%~~Describe \code{manureIn}here~~
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}
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\item{fertP}{
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%%~~Describe \code{fertP}here~~
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}
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\item{fertIn}{
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%%~~Describe \code{fertIn}here~~
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}
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}
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\details{
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%%~~Ifnecessary,moredetailsthanthedescriptionabove~~
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}
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\value{
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%%~Describethevaluereturned
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%%IfitisaLIST,use
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%% \item{comp1 }{Descriptionof'comp1'}
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%% \item{comp2 }{Descriptionof'comp2'}
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%%...
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}
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\references{
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%%~putreferencestotheliterature/websitehere~
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}
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\author{
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SarahGoslee
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}
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\seealso{
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\code{\link{VFSAPLE}}
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}
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\examples{
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}
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‎man/MUSLE.K.Rd‎

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\name{MUSLE.K}
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\alias{MUSLE.K}
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\title{
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EstimatesoilerodibilityfactorK.
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}
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\description{
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EstimatesMUSLEsoilerodibilityfromamultipleregressionmodelofsoiltexture.
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}
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\usage{
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MUSLE.K(fc,fm,ff)
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}
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\arguments{
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\item{fc}{
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Fractionofcoarse material (sand)inthe soil (0-1).
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}
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\item{fm}{
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Fractionofmedium material (silt)inthe soil (0-1).
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}
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\item{ff}{
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Fractionoffine material (clay)inthe soil (0-1).
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}
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}
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\details{
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IfKisnotavailablefromothersources,itcanbeestimatedfromsoil texture (Goslee,inreview).
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}
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\value{
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ReturnsthesoilerodibilityfactorK.
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}
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\references{
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Wischmeier,W.H.,andSmith,D.D.1978.Predictingrainfallerosionlosses-aguidetoconservationplanning.U.S.DepartmentofAgriculture,AgricultureHandbookNo.537.
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}
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\author{
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SarahGoslee
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}
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\seealso{
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\code{\link{MUSLE}}
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}
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\examples{
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Kf<- MUSLE.K(.3,.5,.2)
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}
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