R/ectorun.R

In mrke/NicheMapR: R implementation of Niche Mapper software for biophysical modelling

#' ectorun
#'
#' R wrapper for Fortran binary of Niche Mapper microclimate model
#' @param ecto A vector of input variables for the microclimate model
#' @param metout The above ground micrometeorological conditions under the minimum specified shade
#' @param shadmet The above ground micrometeorological conditions under the maximum specified shade
#' @param soil Hourly predictions of the soil temperatures under the minimum specified shade
#' @param shadsoil Hourly predictions of the soil temperatures under the maximum specified shade
#' @param soilmoist Hourly predictions of the soil moisture under the minimum specified shade
#' @param shadmoist Hourly predictions of the soil moisture under the maximum specified shade
#' @param soilpot Hourly predictions of the soil water potential under the minimum specified shade
#' @param shadpot Hourly predictions of the soil water potential under the maximum specified shade
#' @param humid Hourly predictions of the soil humidity under the minimum specified shade
#' @param shadhumid Hourly predictions of the soil humidity under the maximum specified shade
#' @param tcond Hourly predictions of the soil thermal conductivity under the minimum specified shade
#' @param shadtcond Hourly predictions of the soil humidity under the maximum specified shade
#' @param DEP Depths used for the microclimate model
#' @param rainfall Daily rainfall
#' @param rainhr Hourly rainfall (overwrites rainfall if non-negative
#' @param debmod Dynamic Energy Budget (DEB) model parameters
#' @param deblast Initial DEB state
#' @param foodwaters Food water content (add units)
#' @param foodlevels Food levels (add units)
#' @param SKINW Hourly skin wetness, \%
#' @param g_vs_ab leaf vapour conductance, abaxial (bottom of leaf), mol m-2 s-1
#' @param g_vs_ad leaf vapour conductance, adaxial (top of leaf), mol m-2 s-1
#' @param PDIF Hourly diffuse fraction of solar radiation, -
#' @param wetlandTemps Temperature of water body, deg C
#' @param wetlandDepths Depth of water body
#' @param GLMtemps General Lake Model water temperatures
#' @param GLMO2s General Lake Model water O2 partial pressures
#' @param GLMsalts General Lake Model water salinities
#' @param GLMpHs General Lake Model water pHs
#' @param GLMfoods General Lake Model water food densities
#' @param arrhenius Arrhenius thermal response
#' @param arrhenius2 Arrhenius thermal response for temperature size rule
#' @param thermal_stages Stage-specific thermal physiology
#' @param behav_stages Stage-specific behaviour
#' @param water_stages Stage-specific water related parameters
#' @param nutri_stages Stage-specific nutrition related parameters
#' @param MINSHADES Minimum shade levels
#' @param MAXSHADES Maximum shade levels
#' @param S_instar For the Insect DEB model
#' @useDynLib "NicheMapR"
#' @export
ectorun <- function(ecto) {
  ndays<-ecto$ndays
  a <- .Fortran("ectotherm",
                as.integer(ecto$ndays),
                as.integer(ecto$nstages),
                as.double(ecto$ectoinput),
                as.double(ecto$metout),
                as.double(ecto$shadmet),
                as.double(ecto$soil),
                as.double(ecto$shadsoil),
                as.double(ecto$soilmoist),
                as.double(ecto$shadmoist),
                as.double(ecto$soilpot),
                as.double(ecto$shadpot),
                as.double(ecto$humid),
                as.double(ecto$shadhumid),
                as.double(ecto$tcond),
                as.double(ecto$shadtcond),
                as.double(ecto$DEP),
                as.double(ecto$rainfall),
                as.double(ecto$rainhr),
                as.double(ecto$preshr),
                as.double(ecto$debmod),
                as.double(ecto$deblast),
                as.double(ecto$foodwaters),
                as.double(ecto$foodlevels),
                as.double(ecto$wetlandTemps),
                as.double(ecto$wetlandDepths),
                as.double(ecto$GLMtemps),
                as.double(ecto$GLMO2s),
                as.double(ecto$GLMsalts),
                as.double(ecto$GLMpHs),
                as.double(ecto$GLMfoods),
                as.double(ecto$arrhenius),
                as.double(ecto$arrhenius2),
                as.double(ecto$thermal_stages),
                as.double(ecto$behav_stages),
                as.double(ecto$water_stages),
                as.double(ecto$nutri_stages),
                as.double(ecto$minshades),
                as.double(ecto$maxshades),
                as.double(ecto$SKINW),
                as.double(ecto$g_vs_ab),
                as.double(ecto$g_vs_ad),
                as.double(ecto$PDIF),
                as.double(ecto$S_instar),
                environ=matrix(data = 0, nrow = ndays * 24, ncol = 29),
                enbal=matrix(data = 0, nrow = ndays * 24, ncol = 13),
                masbal=matrix(data = 0, nrow = ndays * 24, ncol = 21),
                debout=matrix(data = 0, nrow = ndays * 24, ncol = 31),
                yearout=matrix(data = 0, nrow = 1, ncol = 20),
                yearsout=matrix(data = 0, nrow = ceiling(ndays / 365), ncol = 43),
                PACKAGE = "NicheMapR"
  )

  environ <- matrix(data = 0, nrow = 24 * ndays, ncol = 29)
  enbal <- matrix(data = 0, nrow = 24 * ndays, ncol = 13)
  masbal <- matrix(data = 0, nrow = 24 * ndays, ncol = 21)
  debout <- matrix(data = 0, nrow = 24 * ndays, ncol = 31)
  yearout <- matrix(data = 0, nrow = 1, ncol = 20)
  yearsout <- matrix(data = 0, nrow = ceiling(ndays / 365), ncol = 43)

  storage.mode(environ)<-"double"
  storage.mode(enbal)<-"double"
  storage.mode(masbal)<-"double"
  storage.mode(debout)<-"double"
  storage.mode(yearout)<-"double"
  storage.mode(yearsout)<-"double"
  environ<-a$environ
  enbal<-a$enbal
  masbal<-a$masbal
  debout<-a$debout
  environ[,4] <- environ[,4] - 1 # make first hour midnight
  enbal[,4] <- enbal[,4] - 1 # make first hour midnight
  masbal[,4] <- masbal[,4] - 1 # make first hour midnight
  debout[,4] <- debout[,4] - 1 # make first hour midnight
  yearout<-a$yearout
  yearsout<-a$yearsout
  environ.names<-c("DOY", "YEAR", "DAY", "TIME", "TC", "SHADE", "SOLAR", "DEP", "ACT", "TA", "TSUB", "TSKY", "VEL", "RELHUM", "ZEN", "CONDEP", "WATERTEMP", "DAYLENGTH", "WINGANGLE", "WINGTEMP", "FLYING", "FLYTIME", "PO2WATER", "SALWATER", "ABSAN", "PTCOND", "POSTURE", "PANT","PCTWET")
  enbal.names<-c("DOY", "YEAR", "DAY", "TIME", "QSOL", "QIRIN", "QMET", "QEVAP", "QIROUT", "QCONV", "QCOND", "ENB", "NTRY")
  masbal.names<-c("DOY", "YEAR", "DAY", "TIME", "O2_ml", "CO2_ml", "NWASTE_g", "H2OFree_g", "H2OMet_g", "DryFood_g", "WetFood_g", "DryFaeces_g", "WetFaeces_G", "Urine_g", "H2OResp_g", "H2OCut_g", "H2OEye_g", "H2OBal_g", "H2OCumBal_g", "H2OLiq_g", "PSI_kPa")
  debout.names<-c("DOY", "YEAR", "DAY", "TIME", "STAGE", "V", "E", "E_H", "L_W", "WETMASS", "WETGONAD", "WETGUT", "PCT_DESIC", "E_S", "E_R", "E_B", "BREEDING", "PREGNANT", "V_BABY", "E_BABY", "H_S", "Q", "P_SURV", "p_A", "p_C", "p_M", "p_G", "p_D", "p_J", "p_R", "p_B")
  yearout.names<-c("DEVTIME", "BIRTHDAY", "BIRTHMASS", "MONMATURE", "MONREPRO", "LENREPRO", "FECUNDITY", "CLUTCHES", "ANNUALACT", "MINRESERVE", "LASTFOOD", "TOTFOOD", "MINTB", "MAXTB", "Pct_Des", "LifeSpan", "GenTime", "R0", "rmax", "Length")
  yearsout.names<-c("YEAR", "MaxStg", "MaxWgt", "MaxLen", "Tmax", "Tmin", "MinRes", "MaxDes", "MinShade", "MaxShade", "MinDep", "MaxDep", "Bsk", "Forage", "Dist", "Food", "Drink", "NWaste", "Faeces", "O2", "Clutch", "Fec", "CauseDeath", "tLay", "tEgg", "tStg1", "tStg2", "tStg3", "tStg4", "tStg5", "tStg6", "tStg7", "tStg8", "mStg1", "mStg2", "mStg3", "mStg4", "mStg5", "mStg6", "mStg7", "mStg8", "surviv", "deathstage")

  colnames(environ)<-environ.names
  colnames(enbal)<-enbal.names
  colnames(masbal)<-masbal.names
  colnames(debout)<-debout.names
  colnames(yearout)<-yearout.names
  colnames(yearsout)<-yearsout.names
  return (list(environ=environ, enbal=enbal, masbal=masbal, debout=debout, yearout=yearout, yearsout=yearsout))
}