ellipsoid: Ellipsoid endotherm model

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

Ellipsoid endotherm model

Description

An implementation of the model described in Porter, W. P., and M. Kearney. 2009. Size, shape, and the thermal niche of endotherms. Proceedings of the National Academy of Sciences 106:19666-19672. with additional rough calculations for water loss. Note this model is only relevant for conditions where there is no solar radiation and air/ground/sky temperatures are equal. Originally coded into R from Excel by John Baumgartner. Requires the NicheMapR functions WETAIR.rh, DRYAIR and VAPPRS Modified to allow use with rasters 2 Aug 2018 Modified to allow user-specified basal metabolic rates and Q10 effects 2 Aug 2018

Usage

ellipsoid(
  posture = 4.5,
  mass = 0.5,
  density = 1000,
  coreT = 37,
  furdepth = 5,
  furcond = 0.04,
  O2eff = 0.2,
  stress = 0.6,
  airT = 20,
  windspd = 1,
  rh = 50,
  Q10 = 3,
  basal = NA,
  basmult = 1
)

Arguments

posture	= 4.5, Shape, ratio of long to short axis of a prolate ellipsoid
mass	= 0.5, Body mass (kg)
density	= 1000, Body density (kg/m3)
coreT	= 37, Core temperature (deg C)
furdepth	= 5, Fur depth (mm)
furcond	= 0.04, Conductivity of fur (W/Cm)
O2eff	= 0.2, Oxygen extraction efficiency (decimal %)
stress	= 0.6, Fraction of basal metabolic rate at which evaporative water loss is required (decimal %)
airT	= 20, Air temperature (deg C)
windspd	= 1, Wind speed (m/s)
rh	= 50, Relative humidity (%)
basal	= NA, user specified basal metabolic rate (W)
basmult	= 1, multiplier to adjust mouse-elephant predicted basal metabolic rate

Details

Note that the parameter 'stress' is a fudge factor that accounts for physiological thermoregulatory adjustments during heat stress (e.g. core temperature increases, changes in flesh conductivity, changes in posture) that are not captured dynamically in this function (but some of these could be modelled dynamically on the basis of this function).

Value

• 1 AirTemp - Air temperature for calculation (deg C)

• 2 Windspeed - Wind speed for calculation (m/s)

• 3 RelHum - Relative humidity for calculation (%)

• 4 Tcore - Core temperature for calculation (deg C)

• 5 UCT - Upper Critical Temperature (deg C)

• 6 LCT - Lower Critical Temperature (deg C)

• 7 Qresp_gph - Respiration rate (W)

• 8 Qresp_W - Respiration rate (W)

• 9 Qresp_kjph - Respiration rate (kJ/h)

• 10 Tskin - Skin temperature (deg C)

• 11 Qgen - required heat generation (W)

• 12 QgenFinal - Required heat generation capped at basal (W)

• 13 mlO2ph - Oxygen consumption rate (ml/h)

• 14 PctBasal - Metabolic rate (% of basal)

• 15 status - 1=cold, 2=happy, 3=hot

• 16 H2Oloss_W - Watts of heat to be dumped

• 17 H2O_gph - Water loss rate required to dump heat based on latent heat of vaporization

• 18 massph_percent - Percent of body mass lost as water per hour

• 19 timetodeath - Time to death (hours) from desiccation (15% desiccated) if no water to drink

Examples

# compute metabolic and water loss rate as a function of air temperature
endo<-ellipsoid(airT=seq(5,45), windspd = 0.1)
endo<-as.data.frame(endo)
plot(endo$AirTemp,endo$QgenFinal,type='l', xlab = "Air Temperature (deg C)", ylab = "Metabolic Rate (W)", main="Metabolic Rate vs. Air Temperaure")
plot(endo$AirTemp,endo$H2O_gph,type='l', xlab = "Air Temperature (deg C)", ylab = "Water Loss Rate (g/h)", main="Water Loss Rate vs. Air Temperaure")

# compute thermoneutral zone as a function of body mass
masses<-10^seq(-3,2,0.5) # log sequence of masses
endo<-ellipsoid(mass = masses)
endo<-as.data.frame(endo)
ylims<-c(min(endo$UCT,endo$LCT),max(endo$UCT,endo$LCT))
plot(masses,endo$UCT, col='red',type='l', ylim=ylims, xlab="body mass (kg)",ylab="temperature (deg C)", main = "Upper and Lower Critical Temperatures vs Mass")
points(masses,endo$LCT, type='l', col='blue')

micro<-micro_global(loc = c(139.5, -25.9)) # run the microclimate model at Birdsville with default settings

metout<-as.data.frame(micro$metout) # above ground microclimatic conditions, min shade
shadmet<-as.data.frame(micro$shadmet) # above ground microclimatic conditions, max shade
soil<-as.data.frame(micro$soil) # soil temperatures, minimum shade
shadsoil<-as.data.frame(micro$shadsoil) # soil temperatures, maximum shade

# append dates
days<-rep(seq(1,12),24)
days<-days[order(days)]
dates<-days+metout$TIME/60/24-1 # dates for hourly output
dates2<-seq(1,12,1) # dates for daily output
metout<-cbind(dates,metout)
soil<-cbind(dates,soil)
shadmet<-cbind(dates,shadmet)
shadsoil<-cbind(dates,shadsoil)

endo<-cbind(metout[,1:3],ellipsoid(airT = shadmet$TALOC, windspd = shadmet$VLOC, rh = shadmet$RHLOC))

with(endo,{plot(H2O_gph ~ dates,xlab = "Date and Time", ylab = "Water Loss Rate (g/h)"
, type = "l",main=paste("Evaporative Water Loss",sep=""))})
with(endo,{plot(QgenFinal ~ dates,xlab = "Date and Time", ylab = "Metabolic Rate (W)"
, type = "l",main=paste("Metabolic Heat Generation",sep=""))})
with(endo,{plot(PctBasal ~ dates,xlab = "Date and Time", ylab = "Metabolic Rate (% of basal)"
, type = "l",main=paste("Metabolic Heat Generation",sep=""))})
with(endo,{plot(Tskin ~ dates,xlab = "Date and Time", ylab = "Skin and Core Temperature (deg C)"
, type = "l",main=paste("Skin and Core Temperature",sep=""),ylim=c(min(cbind(endo$Tcore,endo$Tskin)),
 max(cbind(endo$Tcore,endo$Tskin))))})
with(endo,{points(Tcore ~ dates,xlab = "Date and Time",lty=2, type = "l")})
with(endo,{plot(timetodeath ~ dates,xlab = "Date and Time", ylab = "Time to Death (h)"
, type = "l",main=paste("Time to Death by Desiccation",sep=""), ylim=c(0,24))})

mrke/NicheMapR documentation built on June 9, 2024, 12:38 p.m.