### this seleted list of functions are used to generate recommendation: shared with Ezui for ### documentaion and parmater checking. ############################################################################################################################################# ############################################################################################################################################# ############################################################################################################################################# #######################################################//#################################################################################### # provides dry matter in kg/ha runLINTUL2 <- function(inputData_soil=inputData_soil,inputData_Weather=inputData_Weather, STTIME=STTIME, FINTIM=FINTIM, DELT=1){ long <- inputData_Weather$long lat <- inputData_Weather$lat YR <- unique(inputData_Weather$Year)[1] YR2 <- YR+1 param_noIrrigation <- LINTUL2_CASSAVA_parameters(irri=FALSE, soiltype="test") param_noIrrigation[["ROOTDM"]] <- unique(inputData_soil$ROOTDM) param_noIrrigation[["WCFC"]] <- inputData_soil$WCFC param_noIrrigation[["WCWP"]] <- inputData_soil$WCWP param_noIrrigation[["WCST"]] <- inputData_soil$WCST param_noIrrigation[["WCWET"]] <- inputData_soil$WCWET param_noIrrigation[["WCAD"]] <- inputData_soil$WCAD param_noIrrigation[["DRATE"]] <- 50 param_noIrrigation[["STTIME"]] <- STTIME require(deSolve) #state_wlim1 <- ode(LINTUL2_CASSAVA_iniSTATES_MTC(param_noIrrigation), seq(STTIME, FINTIM, by = DELT), LINTUL2_CASSAVA, param_noIrrigation, WDATA = inputData_Weather, method = "euler") state_wlim1 <- ode(LINTUL2_CASSAVA_iniSTATES_MTC(param_noIrrigation), seq(STTIME, FINTIM, by = DELT), LINTUL2_CASSAVA_MC, param_noIrrigation, WDATA = inputData_Weather, method = "euler") var_wlim1 <- get_results(state_wlim1, YR, inputData_Weather, STTIME, FINTIM) locData <- unique(data.frame(lat = lat, long = long, plantingDate=STTIME)) ## get weekly WLY for harvest time from 8 to 12 months WLY_estimates <- var_wlim1$WSO #WLY_time <- as.data.frame(matrix(nrow=1, ncol=22, data=WLY_estimates[seq(214, 365, 7)])) WLY_time <- as.data.frame(matrix(nrow=1, ncol=32, data=WLY_estimates[seq(235, 455, 7)])) WLY_time <- WLY_time * 10 colnames(WLY_time) <- paste("WLY", seq(235, 455, 7), sep="_") tsumDD <- data.frame(lat=unique(locData$lat), long=unique(locData$long), Tsumcrop = var_wlim1$TSUMCROP, TSUM = var_wlim1$TSUM, SproutDate = c(1:455)) tsumDD <- tsumDD[order(tsumDD$Tsumcrop), ] tsumDD <- tsumDD[tsumDD$Tsumcrop > 0, ][1,] QWW <- cbind(locData, WLY_time) QWW$TSUM <- tsumDD$TSUM QWW$TSUMCROP <- tsumDD$Tsumcrop QWW$SproutDate <- tsumDD$SproutDate return(QWW) } ############################################################################################################################################# ############################################################################################################################################# ############################################################################################################################################# #######################################################//#################################################################################### LINTUL2_CASSAVA_iniSTATES_MTC <-function(param_noIrrigation){ parvalues <- param_noIrrigation return( c(ROOTD = parvalues[['ROOTDI']], # m : initial rooting depth (at crop emergence) WA = 1000 * parvalues[['ROOTDI']] * parvalues[['WCI']], # mm : initial soil water amount TSUM = 0, # deg. C: temperature sum TSUMCROP =0, TSUMCROPLEAFAGE =0, DORMTSUM = 0, PUSHDORMRECTSUM = 0, PUSHREDISTENDTSUM = 0, DORMTIME = 0, WCUTTING = parvalues[['WCUTTINGUNIT']] * parvalues[['NCUTTINGS']], TRAIN = 0, # mm : rain sum PAR = 0, # MJ m-2: PAR sum LAI = 0, # m2 m-2: leaf area index WLVD = 0, # g m-2 : dry weight of dead leaves WLV = 0, WST = 0, # g m-2 : dry weight of stems WSO = 0, # g m-2 : dry weight of storage organs WRT = 0, # g m-2 : dry weight of roots WLVG = 0, TRAN = 0, # mm : actual transpiration EVAP = 0, # mm : actual evaporation PTRAN = 0, # mm : potential transpiration PEVAP = 0, # mm : potential evaporation REDISTLVG = 0, REDISTSO = 0, PUSHREDISTSUM = 0, WSOFASTRANSLSO =0 )) } ############################################################################################################################################# ############################################################################################################################################# ############################################################################################################################################# #######################################################//#################################################################################### get_results <- function(state_out, year, wdata, STTIME,FINTIM){ #get only relevant weather data WDATA <- wdata[STTIME:FINTIM,] parv <- LINTUL2_CASSAVA_parameters() state_out = data.frame(state_out) #Determine rate variables from change in states. dt= state_out[2:nrow(state_out),1] - state_out[1:nrow(state_out)-1,1] dstate = (state_out[2: nrow(state_out), 2:ncol(state_out)] - state_out[1:(nrow(state_out)-1),2:ncol(state_out)]) #Add 0s to first day and determine rates of change rate_out = rbind(0,dstate/dt) colnames(rate_out)<-c("RROOTD","RWA","RTSUM", "RTSUMCROP", "RTSUMCROPLEAFAGE", "RDORMSUM", "RPUSHDORMRECTSUM", "RPUSHREDISTENDTSUM", "RDORMTIME", "RWCUTTING", "RTRAIN","RPAR","RLAI", "RWLVD", "RWLV", "RWST","RWSO","RWRT", "RLVG","RTRAN","REVAP","RPTRAN","RPEVAP" ,"RREDISTLVG","RREDISTSO","RPUSHREDISTSUM","RWSOFASTRANSLSO") # Determine water content of rooted soil WC <- 0.001 * state_out$WA/state_out$ROOTD RNINTC <- pmin(WDATA$RAIN,0.25 * state_out$LAI) # interception of rain by the canopy (mm d-1) # Potential evaporation (mm d-1) and transpiration (mm d-1) are calculated according to Penman-Monteith PENM <- penman(WDATA$DAVTMP,WDATA$VP,WDATA$DTR,state_out$LAI,WDATA$WN,RNINTC) # Actual evaporation (mm d-1) and transpiration (mm d-1) EVA <- evaptr(PENM$PEVAP,PENM$PTRAN,state_out$ROOTD,state_out$WA, parv[["WCAD"]],parv[["WCWP"]],parv[["WCFC"]],parv[["WCWET"]],parv[["WCST"]],parv[["TRANCO"]],1) # The transpiration reduction factor is defined as the ratio between actual and potential transpiration PENM$PTRAN[PENM$PTRAN== 0] <- 1 TRANRF <- rate_out[["RTRAN"]]/rate_out[["RPTRAN"]] #Determine harvest index HI <- state_out[["WSO"]] / (state_out[["WSO"]]+state_out[["WLVG"]]+state_out[["WRT"]]+state_out[["WST"]]) #convert from g m-2 to t ha-1 with factor 10E-2: t/g=10E-6 * factor m2/ha=10E4 = 0.01 WSOTHA <- state_out[["WSO"]] * 0.01 result <- data.frame(cbind(year, state_out, rate_out,TRANRF,HI,WSOTHA)) return(result) } ############################################################################################################################################# ############################################################################################################################################# ############################################################################################################################################# #######################################################//#################################################################################### LINTUL2_CASSAVA_MC <-function(Time, State, Pars, WDATA){ Pars <- as.data.frame(as.list(Pars)) State <- as.data.frame(as.list(State)) parsSatate <- cbind(Pars, State) #intergration with delay for RROOTD #with(as.list(c(State, Pars)), { RTRAIN <- WDATA$RAIN[Time] # rain rate, mm d-1 DTEFF <- max(0, WDATA$DAVTMP[Time] - parsSatate$TBASE) # effective daily temperature (for crop development a treshold temperature (TBASE) needs to be exceeded) RPAR <- parsSatate$FPAR * WDATA$DTR[Time] # PAR MJ m-2 d-1 #determine rates when crop is still growing if(parsSatate$TSUM < parsSatate$FINTSUM){ # Determine water content of rooted soil WC <- 0.001 * parsSatate$WA/parsSatate$ROOTD # TAP <- ifelse((Time-parsSatate$DOYPL) >= 0, 1, 0) RTSUM <- DTEFF * ifelse((Time-parsSatate$DOYPL) >= 0, 1, 0) #RTSUM <- DTEFF*ifelse((Time-parsSatate$DOYPL) >= 0, 1, 0) # TSUM after planting #RTSUM <- DTEFF*ifelse((Time-STTIME) >= 0, 1, 0) # TSUM after planting # Once the emergence date is reached and enough water is available the crop emerges (1), once the crop is established is does not disappear again (2) if((WC-parsSatate$WCWP) >= 0 && (parsSatate$TSUM-parsSatate$OPTEMERGTSUM) >= 0) { # (1) emerg1 <- 1} else { emerg1 <- 0 } if(parsSatate$TSUMCROP > 0) { # (2) emerg2 <- 1 } else { emerg2 <- 0} # Emergence of the crop is used to calculate the accumulated temperature sum. EMERG <- max(emerg1,emerg2) RTSUMCROP <- DTEFF*EMERG # Root depth # If soil water content drops to, or below, wilting point fibrous root growth stops. # As long as the crop has not reached its maximum rooting depth and has not started flowering yet, fibrous root growth continues. if((parsSatate$ROOTD-parsSatate$ROOTDM) < 0 && (WC-parsSatate$WCWP) >= 0) { # The rooting depth (m) is calculated from a maximum rate of change in rooting depth, the emergence of the crop and the constraints mentioned above. RROOTD <- parsSatate$RRDMAX * EMERG }else{ RROOTD = 0 } EXPLOR <- 1000 * RROOTD * parsSatate$WCFC # exploration rate of new soil water layers by root depth growth (mm d-1) RNINTC <- min(RTRAIN, (parsSatate$FRACRNINTC * parsSatate$LAI)) # interception of rain by the canopy (mm d-1) # Potential evaporation (mm d-1) and transpiration (mm d-1) are calculated according to Penman-Monteith PENM <- penman(WDATA$DAVTMP[Time],WDATA$VP[Time],WDATA$DTR[Time],parsSatate$LAI,WDATA$WN[Time],RNINTC) RPTRAN <- PENM$PTRAN RPEVAP <- PENM$PEVAP WCSD <- parsSatate$WCWP * parsSatate$TWCSD WCCR <- parsSatate$WCWP + pmax(WCSD-parsSatate$WCWP, (parsSatate$PTRAN/(parsSatate$PTRAN+parsSatate$TRANCO) * (parsSatate$WCFC-parsSatate$WCWP))/1000) # Actual evaporation (mm d-1) and transpiration (mm d-1) EVA <- evaptr(RPEVAP,RPTRAN,parsSatate$ROOTD,parsSatate$WA,parsSatate$WCAD,parsSatate$WCWP,parsSatate$TWCSD,parsSatate$WCFC,parsSatate$WCWET,parsSatate$WCST,parsSatate$TRANCO, parsSatate$DELT) RTRAN <- EVA$TRAN REVAP <- EVA$EVAP # The transpiration reduction factor is defined as the ratio between actual and potential transpiration TRANRF = ifelse(RPTRAN <= 0, 1, RTRAN/RPTRAN) # Drainage (below the root zone; mm d-1), surface water runoff (mm d-1) and irrigation rate (mm d-1) DRUNIR <- drunir(RTRAIN,RNINTC,REVAP,RTRAN,parsSatate$IRRIGF,parsSatate$DRATE,parsSatate$DELT,parsSatate$WA,parsSatate$ROOTD,parsSatate$WCFC,parsSatate$WCST) # Rate of change of soil water amount (mm d-1) RWA <- (RTRAIN + EXPLOR + DRUNIR$IRRIG) - (RNINTC + DRUNIR$RUNOFF + RTRAN + REVAP + DRUNIR$DRAIN) WC <- 0.001 * parsSatate$WA/parsSatate$ROOTD # Light interception (MJ m-2 d-1) and total crop growth rate (g m-2 d-1) PARINT <- RPAR * (1 - exp(-parsSatate$K_EXT * parsSatate$LAI)) LUE <- parsSatate$LUE_OPT * approx(TTB[,1], TTB[,2], WDATA$DAVTMP[Time])$y # Dormancy and recovery from dormancy if ((WC-WCSD) <= 0 && (parsSatate$LAI - parsSatate$LAI_MIN) <= 0){ dormancy = 1 } else { dormancy = 0 } if ((WC - parsSatate$RECOV * WCCR) >= 0 && (WC - parsSatate$WCWP) >= 0){ pushdor = 1 } else { pushdor = 0 } if (parsSatate$WSO == 0) { WSOREDISTFRAC = 1 } else { WSOREDISTFRAC = parsSatate$REDISTSO/parsSatate$WSO } PUSHREDISTEND = max(ifelse((WSOREDISTFRAC-parsSatate$WSOREDISTFRACMAX) >= 0, 1, 0), ifelse((parsSatate$REDISTLVG - parsSatate$WLVGNEWN)>= 0, 1, 0), ifelse((parsSatate$PUSHREDISTSUM - parsSatate$TSUMREDISTMAX) >= 0, 1, 0)) *ifelse(-parsSatate$PUSHREDISTSUM >= 0, 0, 1) PUSHREDIST = ifelse((parsSatate$PUSHDORMRECTSUM - parsSatate$DELREDIST) >= 0, 1, 0)* (1 - PUSHREDISTEND) PUSHDORMREC = pushdor*ifelse(-parsSatate$DORMTSUM >= 0, 0, 1) * (1 - PUSHREDIST) * ifelse((parsSatate$TSUMCROP - parsSatate$TSUMSBR) >= 0, 1, 0) DORMANCY = max(dormancy, PUSHDORMREC) * (1 - PUSHREDIST) * ifelse((parsSatate$TSUMCROP - parsSatate$TSUMSBR) >= 0, 1, 0) RDORMTSUM = DTEFF *DORMANCY - (parsSatate$DORMTSUM/parsSatate$DELT) * PUSHREDIST RPUSHDORMRECTSUM = DTEFF * PUSHDORMREC - (parsSatate$PUSHDORMRECTSUM/parsSatate$DELT) * (1 - PUSHDORMREC) * (1 - PUSHREDIST) RPUSHREDISTSUM = DTEFF * PUSHREDIST - (parsSatate$PUSHREDISTSUM/parsSatate$DELT) * PUSHREDISTEND RPUSHREDISTENDTSUM = DTEFF * PUSHREDIST - (parsSatate$PUSHREDISTENDTSUM/parsSatate$DELT) * (1 - PUSHREDISTEND) RDORMTIME = DORMANCY # Dry matter redistribution after dormancy RREDISTSO = parsSatate$RRREDISTSO * parsSatate$WSO * PUSHREDIST - (parsSatate$REDISTSO/parsSatate$DELT) *ifelse(-parsSatate$DORMTSUM >= 0, 0, 1) RREDISTLVG = parsSatate$SO2LV * RREDISTSO * (1- DORMANCY) RREDISTMAINTLOSS = (1 - parsSatate$SO2LV) * RREDISTSO GTOTAL <- LUE * PARINT * TRANRF * (1 - DORMANCY) # Relative death rate (d-1) due to aging RDRDV = ifelse(parsSatate$TSUMCROPLEAFAGE - parsSatate$TSUMLLIFE >= 0, approx(RDRT[,1], RDRT[,2], WDATA$DAVTMP[Time])$y, 0) # Relative death rate (d-1) due to self shading RDRSH <- parsSatate$RDRSHM * (parsSatate$LAI - parsSatate$LAICR) / parsSatate$LAICR if(RDRSH < 0) { RDRSH <- 0 } else if(RDRSH >= parsSatate$RDRSHM) { RDRSH <- parsSatate$RDRSHM } RTSUMCROPLEAFAGE <- DTEFF * EMERG - (parsSatate$TSUMCROPLEAFAGE/parsSatate$DELT) * PUSHREDIST ENHSHED <- max(ifelse((WC-WCSD) >= 0, 0, 1), ifelse((WC-parsSatate$WCWET) >= 0, 1, 0))*ifelse((parsSatate$TSUMCROPLEAFAGE-parsSatate$FRACTLLFENHSH*parsSatate$TSUMLLIFE) >= 0, 1, 0) # Relative death rate (d-1) due to severe drought RDRSD <- parsSatate$RDRB *ENHSHED # Effective relative death rate (1; d-1) and the resulting decrease in LAI (2; m2 m-2 d-1) and leaf weight (3; g m-2 d-1) RDR <- max(RDRDV, RDRSH, RDRSD) * ifelse((parsSatate$TSUMCROPLEAFAGE - parsSatate$TSUMLLIFE) >= 0, 1, 0) # (1) DLAI <- parsSatate$LAI * RDR * (1 - parsSatate$FASTRANSLSO) * (1 - DORMANCY) # (2) # Allocation to roots (2), leaves (4), stems (5) and storage organs (6) # fractions allocated are modified for water availability (1 and 3) FRTMOD <- max(1, 1/(TRANRF+0.5)) # (1) FRT <- approx(FRTTB[,1],FRTTB[,2],parsSatate$TSUMCROP)$y * FRTMOD # (2) FSHMOD <- (1 - FRT) / (1 - FRT / FRTMOD) # (3) FLV <- approx(FLVTB[,1],FLVTB[,2],parsSatate$TSUMCROP)$y * FSHMOD # (4) FST <- approx(FSTTB[,1],FSTTB[,2],parsSatate$TSUMCROP)$y * FSHMOD # (5) # Error in approx(FSTTB[, 1], FSTTB[, 2], TSUMCROP) : # object 'TSUMCROP' not found FSO <- approx(FSOTB[,1],FSOTB[,2],parsSatate$TSUMCROP)$y * FSHMOD # (6) # stem cutting growth WCUTTINGMIN <- parsSatate$WCUTTINGMINPRO * parsSatate$WCUTTINGIP # Leaf growth and senescence FRACSLACROPAGE <- approx(FRACSLATB[,1], FRACSLATB[,2], parsSatate$TSUMCROP)$y SLA <- parsSatate$SLA_MAX *FRACSLACROPAGE RWSOFASTRANSLSO = parsSatate$WLVG * RDR * parsSatate$FASTRANSLSO * (1 - DORMANCY) DLV <- (parsSatate$WLVG * RDR - RWSOFASTRANSLSO) * (1 - DORMANCY) RWLVD <- DLV # Change in biomass (g m-2 d-1) for green leaves (1), stems (2), storage organs (3) and roots (4) if (parsSatate$TSUM > parsSatate$OPTEMERGTSUM && parsSatate$WST == 0){ RWCUTTING <- parsSatate$WCUTTING *(-parsSatate$FST_CUTT - parsSatate$FRT_CUTT - parsSatate$FLV_CUTT - parsSatate$FSO_CUTT) RWST <- parsSatate$WCUTTINGIP * parsSatate$FST_CUTT RWRT <- parsSatate$WCUTTINGIP * parsSatate$FRT_CUTT RWLVG <- parsSatate$WCUTTINGIP * parsSatate$FLV_CUTT RWSO <- parsSatate$WCUTTINGIP * parsSatate$FSO_CUTT } else if (parsSatate$TSUMCROP > 16.8) { # A little bit of cheating RWCUTTING <- -parsSatate$RDRWCUTTING * parsSatate$WCUTTING * ifelse((parsSatate$WCUTTING-WCUTTINGMIN) >= 0, 1, 0) * TRANRF * EMERG * (1 - DORMANCY) RWLVG <- (abs(GTOTAL)+abs(RWCUTTING)) * FLV - DLV + RREDISTLVG * PUSHREDIST # (1) RWST <- (abs(GTOTAL)+abs(RWCUTTING)) * FST # (2) RWSO <- (abs(GTOTAL)+abs(RWCUTTING)) * FSO + RWSOFASTRANSLSO - RREDISTSO # (3) RWRT <- (abs(GTOTAL)+abs(RWCUTTING)) * FRT # (4) } else{ RWCUTTING <- 0 RWLVG <- 0 RWST <- 0 RWSO <- 0 RWRT <- 0 } RWLV = RWLVG+RWLVD WGTOTAL = parsSatate$WLV+parsSatate$WST+parsSatate$WCUTTING+parsSatate$WSO+parsSatate$WRT GLV <- FLV * (GTOTAL + abs(RWCUTTING)) + RREDISTLVG * PUSHREDIST GLAI <- gla(DTEFF, parsSatate$TSUMCROP, parsSatate$LAII, parsSatate$RGRL, parsSatate$DELT, SLA, parsSatate$LAI, GLV, parsSatate$TSUMLA_MIN, TRANRF, WC, parsSatate$WCWP, RWCUTTING, FLV, parsSatate$LAIEXPOEND,DORMANCY) # Error in gla(DTEFF, parsSatate$TSUMCROP, LAII, RGRL, DELT, SLA, parsSatate$LAI, : # object 'RGRL' not found # Change in LAI (m2 m-2 d-1) due to new growth of leaves RLAI <- GLAI - DLAI }else{ #all plant related rates are set to 0 RROOTD <- 0 RWLVG <- 0 RWA <- 0 RTSUMCROP <- 0 RLAI <- 0 RWLVG <- 0 RWLVD <- 0 RWLV <- 0 RWST <- 0 RWSO <- 0 RWRT <- 0 RTRAN <- 0 REVAP <- 0 RPTRAN <- 0 RPEVAP <- 0 RGTOTAL <- 0 RDORMTSUM <- 0 RTSUM <- 0 RTSUMCROPLEAFAGE <- 0 RPUSHREDISTENDTSUM <- 0 RPUSHDORMRECTSUM <- 0 RDORMTIME <- 0 RWCUTTING <- 0 RREDISTLVG <- 0 RREDISTSO <- 0 RPUSHREDISTSUM <- 0 RWSOFASTRANSLSO <- 0 } return(list(c(RROOTD,RWA,RTSUM, RTSUMCROP, RTSUMCROPLEAFAGE,RDORMTSUM,RPUSHDORMRECTSUM,RPUSHREDISTENDTSUM, RDORMTIME, RWCUTTING, RTRAIN,RPAR,RLAI,RWLVD, RWLV,RWST,RWSO,RWRT, RWLVG,RTRAN,REVAP,RPTRAN,RPEVAP,RREDISTLVG,RREDISTSO,RPUSHREDISTSUM,RWSOFASTRANSLSO))) #}) } ############################################################################################################################################# ############################################################################################################################################# ############################################################################################################################################# #######################################################//#################################################################################### #---------------------------------------------------------------------# # FUNCTION adapted parameters # # Purpose: Listing the input parameters for Lintul2 # #---------------------------------------------------------------------# LINTUL2_CASSAVA_parameters <-function(irri=FALSE,soiltype="clay") { #get the true defaults PARAM <- LINTUL2_CASSAVA_DEFAUL_PARAMETERS() #change what is desired PARAM[["DOYEM"]] <- 32 # day nr of emergence if(irri==TRUE){ PARAM[["IRRIGF"]] <- 1 } if(soiltype=="clay"){ PARAM[["ROOTDM"]] <- 1.2 # m : maximum rooting depth PARAM[["WCAD"]] <- 0.08 # m3 m-3 : soil water content at air dryness PARAM[["WCWP"]] <- 0.20 # m3 m-3 : soil water content at wilting point PARAM[["WCFC"]] <- 0.46 # m3 m-3 : soil water content at field capacity PARAM[["WCWET"]] <- 0.49 # m3 m-3 : critical soil water content for transpiration reduction due to waterlogging PARAM[["WCST"]] <- 0.52 # m3 m-3 : soil water content at full saturation PARAM[["DRATE"]] <- 50 # mm d-1 : max drainage rate }else if( soiltype=="sand"){ PARAM[["ROOTDM"]] <- 0.6 # m : maximum rooting depth PARAM[["WCAD"]] <- 0.05 # m3 m-3 : soil water content at air dryness PARAM[["WCWP"]] <- 0.08 # m3 m-3 : soil water content at wilting point PARAM[["WCFC"]] <- 0.16 # m3 m-3 : soil water content at field capacity PARAM[["WCWET"]] <- 0.40 # m3 m-3 : critical soil water content for transpiration reduction due to waterlogging PARAM[["WCST"]] <- 0.42 # m3 m-3 : soil water content at full saturation PARAM[["DRATE"]] <- 50 # mm d-1 : max drainage rate }else if( soiltype=="sandPRAC"){ PARAM[["ROOTDM"]] <- 0.3 # m : maximum rooting depth PARAM[["WCAD"]] <- 0.04 # m3 m-3 : soil water content at air dryness PARAM[["WCWP"]] <- 0.09 # m3 m-3 : soil water content at wilting point PARAM[["WCFC"]] <- 0.28 # m3 m-3 : soil water content at field capacity PARAM[["WCWET"]] <- 0.32 # m3 m-3 : critical soil water content for transpiration reduction due to waterlogging PARAM[["WCST"]] <- 0.38 # m3 m-3 : soil water content at full saturation PARAM[["DRATE"]] <- 50 # mm d-1 : max drainage rate }else if( soiltype=="Nitisol"){ PARAM[["ROOTDM"]] <- 0.9 # m : maximum rooting depth PARAM[["WCAD"]] <- 0.01 # m3 m-3 : soil water content at air dryness PARAM[["WCWP"]] <- 0.20 # m3 m-3 : soil water content at wilting point PARAM[["WCFC"]] <- 0.36 # m3 m-3 : soil water content at field capacity PARAM[["WCWET"]] <- 0.37 # m3 m-3 : critical soil water content for transpiration reduction due to waterlogging PARAM[["WCST"]] <- 0.48 # m3 m-3 : soil water content at full saturation PARAM[["DRATE"]] <- 50 # mm d-1 : max drainage rate }else if( soiltype=="Gleysol"){ PARAM[["ROOTDM"]] <- 0.9 # m : maximum rooting depth PARAM[["WCAD"]] <- 0.01 # m3 m-3 : soil water content at air dryness PARAM[["WCWP"]] <- 0.15 # m3 m-3 : soil water content at wilting point PARAM[["WCFC"]] <- 0.28 # m3 m-3 : soil water content at field capacity PARAM[["WCWET"]] <- 0.30 # m3 m-3 : critical soil water content for transpiration reduction due to waterlogging PARAM[["WCST"]] <- 0.39 # m3 m-3 : soil water content at full saturation PARAM[["DRATE"]] <- 50 # mm d-1 : max drainage rate }else if( soiltype=="Ferralsol"){ PARAM[["ROOTDM"]] <- 0.9 # m : maximum rooting depth PARAM[["WCAD"]] <- 0.01 # m3 m-3 : soil water content at air dryness PARAM[["WCWP"]] <- 0.18 # m3 m-3 : soil water content at wilting point PARAM[["WCFC"]] <- 0.34 # m3 m-3 : soil water content at field capacity PARAM[["WCWET"]] <- 0.39 # m3 m-3 : critical soil water content for transpiration reduction due to waterlogging PARAM[["WCST"]] <- 0.53 # m3 m-3 : soil water content at full saturation PARAM[["DRATE"]] <- 50 # mm d-1 : max drainage rate }else if( soiltype=="Arenosol"){ PARAM[["ROOTDM"]] <- 0.9 # m : maximum rooting depth PARAM[["WCAD"]] <- 0.01 # m3 m-3 : soil water content at air dryness PARAM[["WCWP"]] <- 0.04 # m3 m-3 : soil water content at wilting point PARAM[["WCFC"]] <- 0.07 # m3 m-3 : soil water content at field capacity PARAM[["WCWET"]] <- 0.08 # m3 m-3 : critical soil water content for transpiration reduction due to waterlogging PARAM[["WCST"]] <- 0.11 # m3 m-3 : soil water content at full saturation PARAM[["DRATE"]] <- 50 # mm d-1 : max drainage rate } else if (soiltype=="test"){ PARAM[["ROOTDM"]] <- 0.9 # m : maximum rooting depth PARAM[["WCAD"]] <- 0.01 # m3 m-3 : soil water content at air dryness PARAM[["WCWP"]] <- 0.12 # m3 m-3 : soil water content at wilting point PARAM[["WCFC"]] <- 0.41 # m3 m-3 : soil water content at field capacity PARAM[["WCWET"]] <- 0.46 # m3 m-3 : critical soil water content for transpiration reduction due to waterlogging PARAM[["WCST"]] <- 0.52 # m3 m-3 : soil water content at full saturation PARAM[["DRATE"]] <- 50 # mm d-1 : max drainage rate } return(PARAM) } ############################################################################################################################################# ############################################################################################################################################# ############################################################################################################################################# #######################################################//#################################################################################### #---------------------------------------------------------------------# # FUNCTION LINTUL2_DEFAUL_PARAMETERS # # Purpose: Listing the default input parameters for Lintul2 # #---------------------------------------------------------------------# LINTUL2_CASSAVA_DEFAUL_PARAMETERS <-function() { #All defaults return(c( # LINTUL 2 ROOTDI = 0.1, # M : initial rooting depth (at crop emergence) WCI = 0.41, # m3 m-3 : initial soil water content SLAI = 0.017, # m2 g-1 : specific leaf area LAII = 0.02603125,# m2 m-2 ROOTDM = 0.35, # m : maximum rooting depth RRDMAX = 0.012, # m d-1 : max rate increase of rooting depth SLAI = 0.017, WCAD = 0.01, # m3 m-3 : soil water content at air dryness WCWP = 0.12, # m3 m-3 : soil water content at wilting point WCFC = 0.41, # m3 m-3 : soil water content at field capacity WCWET = 0.46, # m3 m-3 : critical soil water content for transpiration reduction due to waterlogging WCST = 0.52, # m3 m-3 : soil water content at full saturation FRACRNINTC = 0.25, # (-) : fraction of rain intercepted TRANCO = 8, # mm d-1 : transpiration constant (indicating level of drought tolerance) DRATE = 50, # mm d-1 : max drainage rate IRRIGF = 0, # (-) : irrigation rate relative to the rate required to keep soil water status at field capacity TBASE = 15, # deg. C : base temperature #TBASE = 12, # deg. C : base temperature LUE = 3.0, # g MJ-1 : light use efficiency K_EXT = 0.67, # (-) : extinction coefficient for PAR RGRL = 0.003, # 1/(deg. C d): relative growth rate of LAI during exponential growth TSUMAN = 1110, # deg. C : temperature sum at anthesis FINTSUM = 5460, #4320, # deg. C : temperature sum at which simulation stops, 5400 is used to simulate until 15 MAP LAICR = 3.5, # m2 m-2 : critical LAI beyond which leaf shedding is stimulated RDRSHM = 0.09, # d-1 : max relative death rate of leaves due to shading FPAR = 0.5, # (-) : Fraction PAR, MJ PAR/MJ DTR # LINTUL CASSAVA DOYPL = 113, # d : daynumber at crop planting. TWCSD = 1.05, # (-) : Proportion of WCWP at which water content at severe drought (WCSD) is assumed to be reached (5% above WCWP) SLA_MAX = 0.03, # m2 g-1 : maximum specific leaf area LAIEXPOEND = 0.75, # m2 m-2 : maximum leaf area index for exponential growth phase TSUMLA_MIN = 180, # deg. C d : Temperature sum accumulation for minimum leaf area FRACTLLFENHSH= 0.85, # (-) : Fraction of leaf life at which enhanced shedding can be induced DELREDIST = 12, # deg. C d : Delay for redistribution of dry matter TSUMRROOTEND = 720, # deg. C : development time from leaf appearance to leaf senescence RECOV = 0.7, # (-) : Proportion of critical soil water content above which the crop recovers from drought # a. emergence OPTEMERGTSUM = 180, # deg. c : Optimal amount of Tsum accumulated from planting to emergence # b. simulation of first branching TSUMSBR = 780, # deg. C : Temperature sum accumulation to first branching # c. simulation of maturity and harvest # d. stem cutting growth FST_CUTT = 0.03, # gstem gcuttings-1 : Fraction of initial cutting allocated to stem FRT_CUTT = 0.03, # groots gcuttings-1 : Fraction of initial cutting allocated to adventitious roots FLV_CUTT = 0.07, # gleaves gcuttings-1 : Fraction of initial cutting allocated to leaves FSO_CUTT = 0, # gstorage gcuttings-1 : Fraction of initial cutting allocated to storage roots RDRWCUTTING = 0.017, # d-1 : Relative decrease rate of cutting weight WCUTTINGUNIT = 14, # g : Average weight per cutting WCUTTINGMINPRO= 0.15, # g m-2 : Minimum proportion of the stem cutting weight that remains unchanged # NCUTTINGS = 1.5625, # m-2 : Number of cuttings planted per m2 # NCUTTINGS = 1, # m-2 : Number of cuttings planted per m2; for TZ NCUTTINGS = 1.25, # m-2 : Number of cuttings planted per m2; for NG MC WCUTTINGIP = 17.5, #21.875, # e. leaf area index growth # f. total biomass growth #LUE_OPT = 1.5, # g MJ PAR-1 : Light use effeciency at optimum growing conditions LUE_OPT = 1.7, # g MJ PAR-1 : Light use effeciency at optimum growing conditions # g. leaf, stem, fibrous roots and storage roots growth RRREDISTSO = 0.01, # d-1 : Relative rate of redistribution of dry matter from storage roots to leaves # h. senescence FASTRANSLSO = 0.45, # (-) : Proportion of senesced leaf weight translocated to storage roots before shedding of the leaf RDRB = 0.09, # d-1 : basic relative death rate of the leaves TSUMLLIFE = 1200, # deg. C d : Temperature sum accumulation to leaf life # i. dry matter partitioning TSUMSOBULKINIT = 540, # deg. C : Temperature sum accumulation for start of storage roots bulking # j. dormancy and recovery from dormancy LAI_MIN = 0.09, # m2 m-2 : minimum leaf area index WSOREDISTFRACMAX = 0.05, # (-) : Maximum proportion of dry matter redistribution from storage roots for the formation of new leaves WLVGNEWN = 10, # g DM m-2 : Minimum amount of new leaves weight produced in the redistribution phase TSUMREDISTMAX= 144, # deg. C : Maximum temperature sum accumulation to indicate the duration of dry matter redistribution # k. biomass production upon the recovery from dormancy SO2LV = 0.8, # g leaves DM g-1 storage : Converstion rate of storage organs dry matter to leaf dry matter DELT = 1 )) } ############################################################################################################################################# ############################################################################################################################################# ############################################################################################################################################# #######################################################//####################################################################################