trans_behav: Thermoregulatory model using a transient heat budget

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

Thermoregulatory model using a transient heat budget

Description

This model uses the transient heat budget models (i.e. accounting for heat storage and hence lag-effects of body mass) to simulate thermoregulatory behaviour of a diurnally active ectotherm. It uses a set of events to break out of the ordinary differential equation solver of the transient heat budget (onelump_var or twolump functions) to simulate thermoregulation around setpoints, specifically the transition from sitting in the shade overnight to basking in the sun perpendicular to the sun's rays (T_B_min), from basking to foraging in the open in an 'average' posture (T_F_min), from foraging in the open to moving into the shade (T_F_max), and then transitioning to basking in the afternoon and finally retreating to the shade for the evening. It also computes the operative temperature (Te) of a non-thermoregulating animal in the open, i.e. the steady state body temperature the animal would come to if it had zero heat capacity, and the body temperature of a non thermoregulating animal in the open accounting for the effect of thermal mass. The function computes a series of summary statistics about the length of basking and foraging bouts, activity time, time spent above high temperature thresholds (T_F_max and CT_max), and the extremes of body temperature.

Usage

trans_behav(
  Tc_init = rep(20, 60),
  Ts_init = Tc_init + 0.1,
  To_init = Tc_init + 0.2,
  Ww_g = 500,
  T_F_min = 33,
  T_F_max = 38,
  T_B_min = 25,
  CT_max = 43,
  rho_body = 932,
  x_shell = 0.001,
  lump = 1,
  q = 0,
  c_body = 3073,
  c_body_inner = c_body,
  c_body_outer = c_body,
  k_flesh = 0.5,
  k_inner = k_flesh,
  k_outer = k_flesh,
  emis = 0.95,
  alpha = 0.85,
  geom = 2,
  shape_b = 1/5,
  shape_c = 1/5,
  shape_coefs = c(10.4713, 0.688, 0.425, 0.85, 3.798, 0.683, 0.694, 0.743),
  posture = "n",
  orient = 1,
  fatosk = 0.4,
  fatosb = 0.4,
  dyn_q = 0,
  fluid = 0,
  alpha_sub = 0.2,
  pdif = 0.1,
  shade = 90,
  metout = metout,
  shadmet = shadmet,
  soil = soil,
  shadsoil = shadsoil,
  press = 101325
)

Arguments

Tc_init	= Tairf(1), initial temperature (°C) Organism shape, 0-5, Determines whether standard or custom shapes/surface area/volume relationships are used: 0=plate, 1=cyl, 2=ellips, 3=lizard (desert iguana), 4=frog (leopard frog), 5=custom (see details)
Ts_init	= Tc_init + 0.1, initial shell temperature (°C)
To_init	= Tc_init + 0.2, initial surface temperature (°C)
Ww_g	= 500, weight (g)
T_F_min	= 33, # minimum foraging body temperature threshold (°C)
T_F_max	= 38, # maximum foraging body temperature threshold (°C)
T_B_min	= 25, # basking body temperature threshold (°C)
CT_max	= 43, # critical thermal maximum (°C)
rho_body	= 932, animal density (kg/m3)
x_shell	= 0.001, shell thickness, m
lump	= 1, one lump (1) or two lump (2) model?
q	= 0, metabolic rate (W/m3)
c_body	= 3073, specific heat of flesh (J/kg-°C)
c_body_inner	= c_body, Specific heat of flesh J/(kg-°C)
c_body_outer	= c_body, Specific heat of outer shell J/(kg-°C)
k_flesh	= 0.5, conductivity of flesh (W/m-K)
k_inner	= k_flesh, Thermal conductivity of inner shell (W/m-K, range: 0.412-2.8)
k_outer	= k_flesh, Thermal conductivity of outer shell (W/m-K, range: 0.412-2.8)
emis	= 0.95, emissivity of skin (-)
alpha	= 0.85, animal solar absorptivity (-)
geom	= 2, Organism shape, 0-5, Determines whether standard or custom shapes/surface area/volume relationships are used: 0=plate, 1=cyl, 2=ellips, 3=lizard (desert iguana), 4=frog (leopard frog), 5=custom (see parameter 'shape_coeffs')
shape_b	= 1/5, Proportionality factor (-) for going from volume to area, represents ratio of width:height for a plate, length:diameter for cylinder, b axis:a axis for ellipsoid
shape_c	= 1/5, Proportionality factor (-) for going from volume to area, represents ratio of length:height for a plate, c axis:a axis for ellipsoid
shape_coefs	= c(10.4713,.688,0.425,0.85,3.798,.683,0.694,.743), Custom surface area coefficients. Operates if posture = 5, and consists of 4 pairs of values representing the parameters a and b of a relationship AREA=a*Ww_g^b, where AREA is in cm2 and Ww_g is in g. The first pair are a and b for total surface area, then a and b for ventral area, then for sillhouette area normal to the sun, then sillhouette area perpendicular to the sun
posture	= 'n', pointing normal 'n' or parallel 'p' to the sun's rays, or average 'a'?
orient	= 1, does the object orient toward the sun? (0,1)
fatosk	= 0.4, solar configuration factor to sky (-)
fatosb	= 0.4, solar configuration factor to substrate (-)
dyn_q	= 0, dynamic metabolic heat generation as a function of temperature, based on approxfun called qf (1) or constant based on parameter q (0)
fluid	= 0, fluid type, air (0) or water (1)
alpha_sub	= 0.2, substrate solar reflectivity, decimal percent
pdif	= 0.1, proportion of solar energy that is diffuse (rather than direct beam)
shade	= 90, maximum shade level (%)
metout	= metout, aboveground minimum shade microclimate output table from NicheMapR's microclimate model
shadmet	= shadmet, metout, aboveground maximum shademicroclimate output table from NicheMapR's microclimate model
soil	= soil, minimum shade soil temperature output table from NicheMapR's microclimate model
shadsoil	= shadsoil, maximum shade soil temperature output table from NicheMapR's microclimate model
press	= 101325, air pressure (Pa) Outputs: day_results variables: 1 time - time (hours) 2 hour - hour of day (rounded to nearest hour) 3 T_air_shd - shaded air temperature at animal height (°C) 4 Tb - body temperature of thermoregulating animal (°C) 5 Tb_final - steady state temperature in current environment (°C) 6 Tb_open - body temperature of animal staying in the open (°C) 7 Te_open - operative temperature (zero heat capacity) of animal in open (°C) 8 time_constant - time constant of animal (minutes) 9 dTb_dt - rate of change of body temperature (°C / minute) 10 posture - posture of animal ('n' = normal to sun's rays, 'p' = parallel to sun's rays , 'f' = foraging posture) 11 active - is the animal inactive (0) or active (1)? 12 state - activity state (0 = sleeping, 1 = basking, 2 = foraging in open, 3 = cooling in shade) 13 mrate - total metabolic rate for time step (J) act_window variables: 1 time - time (hours) 2 forage_sun - total foraging time in sun for this hour (minutes) 3 max_bout_shd - maximum foraging bout in sun for this hour (minutes) 4 forage_shd - total foraging time in shade for this hour (minutes) 5 max_bout_shd - maximum foraging bout in shade for this hour (minutes) sum_stats variables: 1 Ww_g - wet weight of animal (g) 2 T_F_min - minimum foraging temperature (°C) 3 T_F_max - maximum foraging temperature (°C) 4 max_bout_sun - longest foraging bout in sun (minutes) 5 max_bout_shd - longest foraging bout in shade (minutes) 6 sum_activity_sun - total activity in sun (minutes) 7 sum_activity_shd - total activity in shade (minutes) 8 bouts_sun - total number of foraging bouts in sun (#) 9 bouts_shd - total number of foraging bouts in shade (#) 10 morning_bask - morning basking time (minutes) 11 morning_forage_sun - first foraging bout length in sun (minutes) 12 morning_forage_shd - first foraging bout length in shade (minutes) 13 first_midday_bout_sun - second foraging bout length in sun (minutes) 14 first_midday_bout_shd - second foraging bout length in shade (minutes) 15 mean_midday_bout_shd - average length of foraging bouts between the first and last foraging bouts in sun (mins) 16 mean_midday_bout_sun - average length of foraging bouts between the first and last foraging bouts in shade (mins) 17 afternoon_forage_sun - last foraging bout length in sun (minutes) 18 afternoon_forage_shd - last foraging bout length in shade (minutes) 19 mrate_sum - cumulative metabolic rate (kJ) 20 mrate_sum_inactive_sun - cumulative metabolic rate while inactive, sun forager (kJ) 21 mrate_sum_inactive_shd - cumulative metabolic rate while inactive, shade forager (kJ) 22 mrate_sum_active_sun - cumulative metabolic rate while active in sun (kJ) 23 mrate_sum_active_shd - cumulative metabolic rate while active in shade (kJ) 24 T_F_max_time_Te - time operative temperature in open spent above maximum foraging temperature (minutes) 25 CT_max_time_Te - time operative temperature in open spent above critical thermal maximum (minutes) 26 T_F_max_time_Tb_open - time body temperature in open spent above maximum foraging temperature (minutes) 27 CT_max_time_Tb_open - time body temperature in open spent above critical thermal maximum (minutes) 28 T_F_maxtime - time body temperature of thermoregulating animal spent above maximum foraging temperature (minutes) 29 CT_max_time - time body temperature of thermoregulating animal spent above critical thermal maximum (minutes) 30 max_Tb_open - maximum body temperature in open (°C) 31 min_Tb_open - minimum body temperature in open (°C) 32 max_Te - maximum operative temperature in open (°C) 33 min_Te - minimum operative temperature in open (°C) 34 max_Tb - maximum body temperature of thermoregulating animal (°C) 35 min_Tb - minimum body temperature of thermoregulating animal (°C)

Examples

library(NicheMapR)

# define animal biophysical functional traits
Ww_g <- 500 # wet weight (g)
Usrhyt <- 0.05 # height of animal (mid-point) above ground (m)
alpha <- 0.85 # solar absorptivity (-)
T_F_min <- 33 # minimum foraging Tb (deg C)
T_F_max <- 43 # maximum foraging Tb (deg C)
T_B_min <- 18 # basking Tb, moving from shade to sun (deg C)
CT_max <- 48 # critical thermal maximum (deg C)
shape_b <- 1/5 # shape coefficient a, -
shape_c <- 1/5 # shape coefficient b, -
rho_body <- 1000 # animal density, kg/m3
c_body <- 3073 # heat capacity (J/kg-C)
q <- 0 # metabolic rate, W/m3
k_flesh <- 0.5 # thermal conductivity of flesh, W/mK
geom <- 2 # shape, -

# get microclimate data
loc <- c(130, -25)
maxshade <- 90
micro <- micro_global(loc = loc, maxshade = maxshade, Usrhyt = Usrhyt) # run the model with default location and settings
metout <- as.data.frame(micro$metout) # above ground microclimatic conditions, min shade
soil <- as.data.frame(micro$soil) # soil temperatures, minimum shade
shadmet <- as.data.frame(micro$shadmet) # above ground microclimatic conditions, min shade
shadsoil <- as.data.frame(micro$shadsoil) # soil temperatures, minimum shade
# get air pressure
elevation <- micro$elev
press <- 101325 * ((1 - (0.0065 * elevation / 288)) ^ (1 / 0.190284))

mons <- c("January", "February", "March", "April", "May", "June", "July", "August", "September", "October", "November", "December")
DOYs <- unique(metout$DOY)

# loop through each month and run transient model with behaviour
for(i in 1:12){

  # subset current month
  metout_in <- subset(metout, DOY == DOYs[i])
  shadmet_in <- subset(shadmet, DOY == DOYs[i])
  soil_in <- subset(soil, DOY == DOYs[i])
  shadsoil_in <- subset(shadmet, DOY == DOYs[i])

  # run transient behavioural simulation
  trans <- trans_behav(Ww_g = Ww_g, alpha = alpha, T_F_min = T_F_min, T_F_max = T_F_max,
                       CT_max = CT_max, T_B_min = T_B_min, geom = geom, shape_b = shape_b, shape_c = shape_c,
                       rho_body = rho_body, k_flesh = k_flesh, q = q, lump = 1,
                       metout = metout_in, shadmet = shadmet_in, soil = soil_in, shadsoil = shadsoil_in,
                       press = press, alpha_sub = 1 - micro$REFL, shade = micro$maxshade)

  results <- as.data.frame(trans$day_results)
  sum_stats <- as.data.frame(trans$sum_stats)
  act_window <- as.data.frame(trans$act_window)

  # collate
  if(i == 1){
    all_act_window <- act_window
  }else{
    all_act_window <- rbind(all_act_window, act_window)
  }

  results$hours <- results$time / 3600

  # plot hourly results for the current day
  plot(results$Tb_open ~ results$hours, type = 'l', ylim = c(-10, 80), col = 'grey', xaxs = 'i', ylab = "temperature, deg C", xlab = "time",
       main = paste0(if(length(loc) == 2){paste("lon", loc[1], "lat", loc[2])}else{loc}, ", ", mons[i], ", ", Ww_g," g"), xlim = c(0, 23))
  grid(nx = 23, ny = 0, col = "lightgray", lty = "dotted", lwd = par("lwd"), equilogs = TRUE)
  abline(T_F_max, 0, col = 'red', lty = 2)
  abline(T_F_min, 0, col = 'light blue', lty = 2)
  abline(CT_max, 0, col = 'red')
  points(results$T_air_shd ~ results$hours, type = 'l', col = 'blue')
  points(results$Tb ~ results$hours, type = 'l', col = 'orange', lty = 1, lwd = 2)
  text(3, 60, paste0("bouts ", round(sum_stats$bouts_sun, 0)), cex = 1)
  text(3, 65, paste0("maximum bout ", round(sum_stats$max_foraging_bout_sun / 60, 1), " hrs"), cex = 1)
  text(3, 70, paste0("total activity ", round(sum_stats$sum_activity_sun / 60, 1), " hrs"), cex = 1)
}

# make seasonal activity plot
all_act_window$ZEN <- metout$ZEN
all_act_window$DOY <- metout$DOY
foraging<-subset(all_act_window, forage_sun > 0)
night<-subset(all_act_window, ZEN==90)
with(night, plot(time ~ DOY, pch=15, cex = 2, xlim = c(1, 365), col = 'dark blue', xlab = 'day of year', ylab = 'hour of day', main = "Seasonal Activity Plot, Sun"))
with(foraging, points(time ~ DOY, pch = 15, cex = forage_sun / 30, col = 'orange'))
foraging<-subset(all_act_window, forage_shd > 0)
with(night, plot(time ~ DOY, pch=15, cex = 2, xlim = c(1, 365), col = 'dark blue', xlab = 'day of year', ylab = 'hour of day', main = "Seasonal Activity Plot, Shade"))
with(foraging, points(time ~ DOY, pch = 15, cex = forage_shd / 30, col = 'orange'))

mtext(text =  paste0('Seasonal Activity Plot, ', if(length(loc) == 2){paste("lon", loc[1], "lat", loc[2])}else{loc}, " ", Ww_g," g"), outer = TRUE, side = 3, line = 0)

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