egg_water: Tracy et al. 1978 egg water budget model (requires the...

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

Tracy et al. 1978 egg water budget model (requires the deSolve package)

Description

Function for computing the exchange of gaseous and liquid water between an egg and soil under environmental conditions that vary with time, using interpolation functions to estimate environmental conditions at particular time intervals. Michael Kearney developed this R function based on Tracy, C. R., Packard, G. C., and Packard, M. J. (1978). Water relations of chelonian eggs. Physiological Zoology 51, 378–387. Parameter examples come from this paper.

Usage

ode(y = c(m_init, psi_e_init), times = t, func = egg_water, parms = indata)

Arguments

t	time intervals (s) at which output is required
m_init	= 5.8 / 1000, mass of freshly laid egg (kg)
psi_e_init	= -707, water potential of freshly laid egg (J/kg)
shape	= 0.6, ratio of minor axes major axis of ellipsoid (-)
f_air	= 0.5, fraction of egg surface exposed to air
K_e	= 1.12 * 60 * 24 / 1e6 / (3600 * 24 * 10), hydraulic conductance of egg (kg m-2 s-1 (J/kg)-1), converted from original μg cm-2 min-1 bar-1
spec_hyd	= 0.5, water potential-specific hydration (m3 m-3 (J/kg)-1)
pct_wet	= 0.24, percent of surface area acting as a free-water surface for evaporation (%)
P_e	= -0.5052209, soil air entry potential (J/kg), derived from soil texture data via the function 'pedotransfer' and used to get soil hydraulic conductivity
b	= 1.41005, Campbell's b parameter (-), derived from soil texture data via the function 'pedotransfer' and used to get soil hydraulic conductivity
K_sat	= 0.003733307, soil saturated hydraulic conductivity (kg m-1 s-1 (J/kg)-1) derived from soil texture data via the function 'pedotransfer' and used to get soil hydraulic conductivity
elev	= 0, elevation (m), needed for properties of air
vel	= 0.001, wind speed (m/s)
Tsoilf	soil temperature function with time, generated by 'approxfun' (°C)
Tbf	body temperature function with time, generated by 'approxfun'(°C)
RHsoilf	relative humidity function with time, generated by 'approxfun' (fractional)
PSIsoilf	soil water potential with time, generated by 'approxfun' (J/kg)

Value

m Egg mass (kg)

psi_e Egg water potential (J/kg)

Examples

library(NicheMapR)

# egg functional traits
m_init <- 5.8 / 1000 # kg, mass of freshly laid egg
psi_e_init <- -707 # J/kg, water potential of freshly laid egg
shape <- 0.6 # -, ratio of minor axes major axis of ellipsoid (-)
f_air <- 0.5 # -, fraction of egg surface exposed to air
K_e <- 1.12 * 60 * 24 / 1e6 / (3600 * 24 * 10) # kg m-2 s-1 (J/kg)-1, hydraulic conductance of egg
spec_hyd <- 0.0304 / 100 # m3 m-3 (J/kg)-1, water potential-specific hydration, empirically determined from linear model
pct_wet <- 0.25 # %, percent of surface area acting as a free-water surface for evaporation

# get soil properties based on texture
pct_sand <- 99 # %
pct_silt <- 0 # %
pct_clay <- 100 - pct_sand # %
bulkdens <- 1.3 # Mg/m3
soilpro <- matrix(data = c(0, bulkdens, pct_clay, pct_silt, pct_sand), nrow = 1, ncol = 5)
colnames(soilpro) <- c('depth', 'blkdens', 'clay', 'silt', 'sand')

#Now get hydraulic properties for this soil using Cosby et al. 1984 pedotransfer functions.
soil.hydro <- pedotransfer(soilpro = as.data.frame(soilpro), DEP = 0, model = 2)
P_e <- soil.hydro$PE # J/kg
b <- soil.hydro$BB # -
K_sat <- soil.hydro$KS # kg s/m3

t <- seq(0, 24 * 3600 * 150, 24 * 3600) # seconds

elev <- 0 # m, need elevation for air properties
vel <- 0.001 # m/s, wind speed
T_soil <- 29 # deg C, soil temperature
T_egg <- T_soil + 0.15 # deg C, egg temperature
RH_soil <- 0.99 # fractional, relative humidity
PSI_soil <- -100 # J/kg, soil water potential

# use approxfun to create interpolations for the required environmental variables
Tsoilf <- approxfun(t, rep(T_soil, length(t)), rule = 2) # deg C, soil temperature
Tbf <- approxfun(t, rep(T_egg, length(t)), rule = 2) # deg C, body temperature in soil
RHsoilf <- approxfun(t, rep(RH_soil, length(t)), rule = 2) # fractional, relative humidity
PSIsoilf <- approxfun(t, rep(PSI_soil, length(t)), rule = 2) # J/kg, soil water potential

# input parameters
indata <- list(shape = shape, K_e = K_e, spec_hyd = spec_hyd, f_air = f_air, pct_wet = pct_wet, elev = elev, vel = vel, K_sat = K_sat, P_e = P_e, b = b)

# solve
egg_ode <- as.data.frame(deSolve::ode(y = c(m_init, psi_e_init), times = t, func = egg_water, parms = indata))
colnames(egg_ode) = c("time", "m", "psi_e")

# plot results
par(mfrow = c(2, 1))
with(egg_ode, plot(t / (24 * 3600), m * 1000, type = 'l', ylab = 'egg mass, g', xlab = 'time, days', col = 'black'))
with(egg_ode, plot(t / (24 * 3600), psi_e, type = 'l', ylab = 'egg water potential, J / kg', xlab = 'time, days', col = 'black', ylim = c(psi_e_init, PSI_soil)))
abline(h = PSI_soil, lty = 2, col = 'blue')

mrke/NicheMapR documentation built on April 3, 2024, 10:05 a.m.