Title: | Tools for Microclimate and Biophysical Ecology |
Description: | Tools for translating environmental change into organismal response. Microclimate models to vertically scale weather station data to organismal heights. The biophysical modeling tools include both general models for heat flows and specific models to predict body temperatures for a variety of ectothermic taxa. Additional functions model and temporally partition air and soil temperatures and solar radiation. Utility functions estimate the organismal and environmental parameters needed for biophysical ecology. 'TrenchR' focuses on relatively simple and modular functions so users can create transparent and flexible biophysical models. Many functions are derived from Gates (1980) <doi:10.1007/978-1-4612-6024-0> and Campbell and Norman (1988) <isbn:9780387949376>. |
Version: | 1.1.1 |
Maintainer: | Lauren Buckley <lbuckley@uw.edu> |
License: | MIT + file LICENSE |
Date: | 2023-08-24 |
URL: | https://trenchproject.github.io/TrenchR/, https://github.com/trenchproject/TrenchR |
BugReports: | https://github.com/trenchproject/TrenchR/issues |
VignetteBuilder: | knitr |
Depends: | R (≥ 3.3.1) |
Imports: | deSolve, msm, Rdpack (≥ 0.7), stats, zoo |
Suggests: | covr, knitr, rmarkdown, testthat |
RdMacros: | Rdpack |
Encoding: | UTF-8 |
RoxygenNote: | 7.2.3 |
NeedsCompilation: | no |
Packaged: | 2023-09-13 23:04:53 UTC; laurenbuckley |
Author: | Lauren Buckley |
Repository: | CRAN |
Date/Publication: | 2023-09-13 23:50:06 UTC |
TrenchR: Tools for Microclimate and Biophysical Ecology
Description
Tools for translating environmental change into organismal response. Microclimate models to vertically scale weather station data to organismal heights. The biophysical modeling tools include both general models for heat flows and specific models to predict body temperatures for a variety of ectothermic taxa. Additional functions model and temporally partition air and soil temperatures and solar radiation. Utility functions estimate the organismal and environmental parameters needed for biophysical ecology. 'TrenchR' focuses on relatively simple and modular functions so users can create transparent and flexible biophysical models. Many functions are derived from Gates (1980) doi: 10.1007/978-1-4612-6024-0 and Campbell and Norman (1988) <isbn:9780387949376>.
Author(s)
Maintainer: Lauren Buckley lbuckley@uw.edu (ORCID)
Authors:
Bryan Briones Ortiz
Isaac Caruso
Aji John (ORCID)
Ofir Levy (ORCID)
Abigail Meyer
Eric Riddell (ORCID)
Yutaro Sakairi
Juniper Simonis (ORCID)
Other contributors:
Brian Helmuth (ORCID) [contributor]
See Also
Useful links:
Report bugs at https://github.com/trenchproject/TrenchR/issues
Properties of Dry Air
Description
The function calculates several properties of dry air and related characteristics shown as output variables below. The program is based on equations from List (1971) and code implementation from NicheMapR (Kearney and Porter 2017; Kearney and Porter 2020).
The user must supply values for the input variables db
, bp
, and alt
. If alt
is known (-1000 < alt < 20000) but not BP, then set bp = 0
.
Usage
DRYAIR(db, bp = 0, alt = 0)
Arguments
db |
|
bp |
|
alt |
|
Value
Named list
with elements
patmos
:numeric
standard atmospheric pressure (Pa)density
:numeric
density (kg m-3)visdyn
:numeric
dynamic viscosity (kg m-1 s-1)viskin
:numeric
kinematic viscosity (m2 s-1)difvpr
:numeric
diffusivity of water vapor in air (m2 s-1)thcond
:numeric
thermal conductivity (W K-1 m-1)htovpr
:numeric
latent heat of vaporization of water (J kg-1)tcoeff
:numeric
temperature coefficient of volume expansion (K-1)ggroup
:numeric
group of variables in Grashof number (m-3 K-1)bbemit
:numeric
black body emittance (W m-2)emtmax
:numeric
wave length of maximum emittance (m)
References
Kearney MR, Porter WP (2017).
“NicheMapR - an R package for biophysical modelling: the microclimate model.”
Ecography, 40, 664-674.
doi: 10.1111/ecog.02360.
Kearney MR, Porter WP (2020).
“NicheMapR - an R package for biophysical modelling: the ectotherm and Dynamic Energy Budget models.”
Ecography, 43(1), 85-96.
doi: 10.1111/ecog.04680.
List RJ (1971).
“Smithsonian Meteorological Tables.”
Smithsonian Miscellaneous Collections, 114(1), 1-527.
https://repository.si.edu/handle/10088/23746.
Examples
DRYAIR(db = 30,
bp = 100*1000,
alt = 0)
Grashof Number
Description
The function estimates the Grashof Number, which describes the ability of a parcel of fluid warmer or colder than the surrounding fluid to rise against or fall with the attractive force of gravity. The Grashof Number is estimated as the ratio of a buoyant force times an inertial force to the square of a viscous force (Campbell and Norman 1998).
Usage
Grashof_number(T_a, T_g, D, nu)
Arguments
T_a |
|
T_g |
|
D |
|
nu |
|
Value
numeric
Grashof number.
References
Campbell GS, Norman JM (1998). Introduction to environmental biophysics, 2nd ed. edition. Springer, New York. ISBN 0387949372.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Nusselt_from_Grashof()
,
Nusselt_from_Reynolds()
,
Nusselt_number()
,
Prandtl_number()
,
Qconduction_animal()
,
Qconduction_substrate()
,
Qconvection()
,
Qemitted_thermal_radiation()
,
Qevaporation()
,
Qmetabolism_from_mass_temp()
,
Qmetabolism_from_mass()
,
Qnet_Gates()
,
Qradiation_absorbed()
,
Qthermal_radiation_absorbed()
,
Reynolds_number()
,
T_sky()
,
Tb_CampbellNorman()
,
Tb_Gates2()
,
Tb_Gates()
,
Tb_butterfly()
,
Tb_grasshopper()
,
Tb_limpetBH()
,
Tb_limpet()
,
Tb_lizard_Fei()
,
Tb_lizard()
,
Tb_mussel()
,
Tb_salamander_humid()
,
Tb_snail()
,
Tbed_mussel()
,
Tsoil()
,
actual_vapor_pressure()
,
boundary_layer_resistance()
,
external_resistance_to_water_vapor_transfer()
,
free_or_forced_convection()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient_simple()
,
heat_transfer_coefficient()
,
saturation_vapor_pressure()
,
saturation_water_vapor_pressure()
Examples
Grashof_number(T_a = 30,
T_g = 35,
D = 0.001,
nu = 1.2)
Grashof Number as in Gates (1980)
Description
The function estimates the Grashof Number, which describes the ability of a parcel of fluid warmer or colder than the surrounding fluid to rise against or fall with the attractive force of gravity (Gates 1980). The Grashof Number is estimated as the ratio of a buoyant force times an inertial force to the square of a viscous force.
Usage
Grashof_number_Gates(T_a, T_g, beta, D, nu)
Arguments
T_a |
|
T_g |
|
beta |
|
D |
|
nu |
|
Value
numeric
Grashof number.
References
Gates DM (1980). Biophysical Ecology. Springer-Verlag, New York, NY, USA.
See Also
Other biophysical models:
Grashof_number()
,
Nusselt_from_Grashof()
,
Nusselt_from_Reynolds()
,
Nusselt_number()
,
Prandtl_number()
,
Qconduction_animal()
,
Qconduction_substrate()
,
Qconvection()
,
Qemitted_thermal_radiation()
,
Qevaporation()
,
Qmetabolism_from_mass_temp()
,
Qmetabolism_from_mass()
,
Qnet_Gates()
,
Qradiation_absorbed()
,
Qthermal_radiation_absorbed()
,
Reynolds_number()
,
T_sky()
,
Tb_CampbellNorman()
,
Tb_Gates2()
,
Tb_Gates()
,
Tb_butterfly()
,
Tb_grasshopper()
,
Tb_limpetBH()
,
Tb_limpet()
,
Tb_lizard_Fei()
,
Tb_lizard()
,
Tb_mussel()
,
Tb_salamander_humid()
,
Tb_snail()
,
Tbed_mussel()
,
Tsoil()
,
actual_vapor_pressure()
,
boundary_layer_resistance()
,
external_resistance_to_water_vapor_transfer()
,
free_or_forced_convection()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient_simple()
,
heat_transfer_coefficient()
,
saturation_vapor_pressure()
,
saturation_water_vapor_pressure()
Examples
Grashof_number_Gates(T_a = 30,
T_g = 35,
beta = 0.00367,
D = 0.001,
nu = 1.2)
Nusselt Number from the Grashof Number
Description
The function estimates the Nusselt number from the Grashof Number (Gates 1980).
Usage
Nusselt_from_Grashof(Gr)
Arguments
Gr |
|
Value
numeric
Nusselt number (dimensionless).
References
Gates DM (1980). Biophysical Ecology. Springer-Verlag, New York, NY, USA.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Grashof_number()
,
Nusselt_from_Reynolds()
,
Nusselt_number()
,
Prandtl_number()
,
Qconduction_animal()
,
Qconduction_substrate()
,
Qconvection()
,
Qemitted_thermal_radiation()
,
Qevaporation()
,
Qmetabolism_from_mass_temp()
,
Qmetabolism_from_mass()
,
Qnet_Gates()
,
Qradiation_absorbed()
,
Qthermal_radiation_absorbed()
,
Reynolds_number()
,
T_sky()
,
Tb_CampbellNorman()
,
Tb_Gates2()
,
Tb_Gates()
,
Tb_butterfly()
,
Tb_grasshopper()
,
Tb_limpetBH()
,
Tb_limpet()
,
Tb_lizard_Fei()
,
Tb_lizard()
,
Tb_mussel()
,
Tb_salamander_humid()
,
Tb_snail()
,
Tbed_mussel()
,
Tsoil()
,
actual_vapor_pressure()
,
boundary_layer_resistance()
,
external_resistance_to_water_vapor_transfer()
,
free_or_forced_convection()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient_simple()
,
heat_transfer_coefficient()
,
saturation_vapor_pressure()
,
saturation_water_vapor_pressure()
Examples
Nusselt_from_Grashof(Gr = 5)
Nusselt Number from the Reynolds Number
Description
The function estimates the Nusselt number from the Reynolds number for various taxa using Mitchell (1976) (Table 1: Convective Heat Transfer Relations for Animal Shapes).
Usage
Nusselt_from_Reynolds(Re, taxon = "cylinder")
Arguments
Re |
|
taxon |
|
Value
numeric
Nusselt number (dimensionless).
References
Mitchell JW (1976). “Heat transfer from spheres and other animal forms.” Biophysical Journal, 16(6), 561-569. ISSN 0006-3495, doi: 10.1016/S0006-3495(76)85711-6.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Grashof_number()
,
Nusselt_from_Grashof()
,
Nusselt_number()
,
Prandtl_number()
,
Qconduction_animal()
,
Qconduction_substrate()
,
Qconvection()
,
Qemitted_thermal_radiation()
,
Qevaporation()
,
Qmetabolism_from_mass_temp()
,
Qmetabolism_from_mass()
,
Qnet_Gates()
,
Qradiation_absorbed()
,
Qthermal_radiation_absorbed()
,
Reynolds_number()
,
T_sky()
,
Tb_CampbellNorman()
,
Tb_Gates2()
,
Tb_Gates()
,
Tb_butterfly()
,
Tb_grasshopper()
,
Tb_limpetBH()
,
Tb_limpet()
,
Tb_lizard_Fei()
,
Tb_lizard()
,
Tb_mussel()
,
Tb_salamander_humid()
,
Tb_snail()
,
Tbed_mussel()
,
Tsoil()
,
actual_vapor_pressure()
,
boundary_layer_resistance()
,
external_resistance_to_water_vapor_transfer()
,
free_or_forced_convection()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient_simple()
,
heat_transfer_coefficient()
,
saturation_vapor_pressure()
,
saturation_water_vapor_pressure()
Examples
Nusselt_from_Reynolds(Re = 5,
taxon = "cylinder")
Nusselt Number
Description
The function estimates the Nusselt Number, which describes dimensionless conductance (Gates 1980).
Usage
Nusselt_number(H_L, D, K)
Arguments
H_L |
|
D |
|
K |
|
Value
numeric
Nusselt number.
References
Gates DM (1980). Biophysical Ecology. Springer-Verlag, New York, NY, USA.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Grashof_number()
,
Nusselt_from_Grashof()
,
Nusselt_from_Reynolds()
,
Prandtl_number()
,
Qconduction_animal()
,
Qconduction_substrate()
,
Qconvection()
,
Qemitted_thermal_radiation()
,
Qevaporation()
,
Qmetabolism_from_mass_temp()
,
Qmetabolism_from_mass()
,
Qnet_Gates()
,
Qradiation_absorbed()
,
Qthermal_radiation_absorbed()
,
Reynolds_number()
,
T_sky()
,
Tb_CampbellNorman()
,
Tb_Gates2()
,
Tb_Gates()
,
Tb_butterfly()
,
Tb_grasshopper()
,
Tb_limpetBH()
,
Tb_limpet()
,
Tb_lizard_Fei()
,
Tb_lizard()
,
Tb_mussel()
,
Tb_salamander_humid()
,
Tb_snail()
,
Tbed_mussel()
,
Tsoil()
,
actual_vapor_pressure()
,
boundary_layer_resistance()
,
external_resistance_to_water_vapor_transfer()
,
free_or_forced_convection()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient_simple()
,
heat_transfer_coefficient()
,
saturation_vapor_pressure()
,
saturation_water_vapor_pressure()
Examples
Nusselt_number(H_L = 20,
D = 0.01,
K = 0.5)
Prandtl Number
Description
The function estimates the Prandtl Number, which describes the ratio of kinematic viscosity to thermal diffusivity (Gates 1980).
Usage
Prandtl_number(c_p, mu, K)
Arguments
c_p |
|
mu |
|
K |
|
Value
numeric
Prandtl number.
References
Gates DM (1980). Biophysical Ecology. Springer-Verlag, New York, NY, USA.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Grashof_number()
,
Nusselt_from_Grashof()
,
Nusselt_from_Reynolds()
,
Nusselt_number()
,
Qconduction_animal()
,
Qconduction_substrate()
,
Qconvection()
,
Qemitted_thermal_radiation()
,
Qevaporation()
,
Qmetabolism_from_mass_temp()
,
Qmetabolism_from_mass()
,
Qnet_Gates()
,
Qradiation_absorbed()
,
Qthermal_radiation_absorbed()
,
Reynolds_number()
,
T_sky()
,
Tb_CampbellNorman()
,
Tb_Gates2()
,
Tb_Gates()
,
Tb_butterfly()
,
Tb_grasshopper()
,
Tb_limpetBH()
,
Tb_limpet()
,
Tb_lizard_Fei()
,
Tb_lizard()
,
Tb_mussel()
,
Tb_salamander_humid()
,
Tb_snail()
,
Tbed_mussel()
,
Tsoil()
,
actual_vapor_pressure()
,
boundary_layer_resistance()
,
external_resistance_to_water_vapor_transfer()
,
free_or_forced_convection()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient_simple()
,
heat_transfer_coefficient()
,
saturation_vapor_pressure()
,
saturation_water_vapor_pressure()
Examples
Prandtl_number(c_p = 29.3,
mu = 0.00001,
K = 0.5)
Conductance Assuming Animal Thermal Conductivity is Rate Limiting
Description
The function calculates conductance (W) of an ectothermic animal to its substrate. Method assumes the major resistance to conduction is within surface layers of the animal and that the interior of the animal is equal in temperature to its surface (thermally well mixed) (Spotila et al. 1992).
Usage
Qconduction_animal(T_g, T_b, d, K = 0.5, A, proportion)
Arguments
T_g |
|
T_b |
|
d |
|
K |
|
A |
|
proportion |
|
Value
numeric
conductance (W).
References
Galushko D, Ermakov N, Karpovski M, Palevski A, Ishay JS, Bergman DJ (2005).
“Electrical, thermoelectric and thermophysical properties of hornet cuticle.”
Semiconductor Science and Technology, 20(3), 286–289.
doi: 10.1088/0268-1242/20/3/005.
Spotila JR, Feder ME, Burggren WW (1992).
“Biophysics of Heat and Mass Transfer.”
Environmental Physiology of the Amphibians.
https://press.uchicago.edu/ucp/books/book/chicago/E/bo3636401.html.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Grashof_number()
,
Nusselt_from_Grashof()
,
Nusselt_from_Reynolds()
,
Nusselt_number()
,
Prandtl_number()
,
Qconduction_substrate()
,
Qconvection()
,
Qemitted_thermal_radiation()
,
Qevaporation()
,
Qmetabolism_from_mass_temp()
,
Qmetabolism_from_mass()
,
Qnet_Gates()
,
Qradiation_absorbed()
,
Qthermal_radiation_absorbed()
,
Reynolds_number()
,
T_sky()
,
Tb_CampbellNorman()
,
Tb_Gates2()
,
Tb_Gates()
,
Tb_butterfly()
,
Tb_grasshopper()
,
Tb_limpetBH()
,
Tb_limpet()
,
Tb_lizard_Fei()
,
Tb_lizard()
,
Tb_mussel()
,
Tb_salamander_humid()
,
Tb_snail()
,
Tbed_mussel()
,
Tsoil()
,
actual_vapor_pressure()
,
boundary_layer_resistance()
,
external_resistance_to_water_vapor_transfer()
,
free_or_forced_convection()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient_simple()
,
heat_transfer_coefficient()
,
saturation_vapor_pressure()
,
saturation_water_vapor_pressure()
Examples
Qconduction_animal(T_g = 293,
T_b = 303,
d = 10^-6,
K = 0.5,
A = 10^-3,
proportion = 0.2)
Conductance Assuming Substrate Thermal Conductivity is Rate Limiting
Description
The function calculates conductance (W) of an ectothermic animal to its substrate. The method assumes the major resistance to conduction is the substrate and that the interior of the animal is equal in temperature to its surface (thermally well mixed) (Spotila et al. 1992).
Usage
Qconduction_substrate(T_g, T_b, D, K_g = 0.5, A, proportion)
Arguments
T_g |
|
T_b |
|
D |
|
K_g |
|
A |
|
proportion |
|
Value
numeric
conductance (W).
References
Spotila JR, Feder ME, Burggren WW (1992). “Biophysics of Heat and Mass Transfer.” Environmental Physiology of the Amphibians. https://press.uchicago.edu/ucp/books/book/chicago/E/bo3636401.html.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Grashof_number()
,
Nusselt_from_Grashof()
,
Nusselt_from_Reynolds()
,
Nusselt_number()
,
Prandtl_number()
,
Qconduction_animal()
,
Qconvection()
,
Qemitted_thermal_radiation()
,
Qevaporation()
,
Qmetabolism_from_mass_temp()
,
Qmetabolism_from_mass()
,
Qnet_Gates()
,
Qradiation_absorbed()
,
Qthermal_radiation_absorbed()
,
Reynolds_number()
,
T_sky()
,
Tb_CampbellNorman()
,
Tb_Gates2()
,
Tb_Gates()
,
Tb_butterfly()
,
Tb_grasshopper()
,
Tb_limpetBH()
,
Tb_limpet()
,
Tb_lizard_Fei()
,
Tb_lizard()
,
Tb_mussel()
,
Tb_salamander_humid()
,
Tb_snail()
,
Tbed_mussel()
,
Tsoil()
,
actual_vapor_pressure()
,
boundary_layer_resistance()
,
external_resistance_to_water_vapor_transfer()
,
free_or_forced_convection()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient_simple()
,
heat_transfer_coefficient()
,
saturation_vapor_pressure()
,
saturation_water_vapor_pressure()
Examples
Qconduction_substrate(T_g = 293,
T_b = 303,
D = 0.01,
K_g = 0.3,
A = 10^-2,
proportion = 0.2)
Organismal Convection
Description
The function calculates convection from an organism to its environment as in Mitchell (1976). It includes an enhancement factor associated with outdoor environments.
Usage
Qconvection(T_a, T_b, A, proportion, H_L = 10.45, ef = 1.23)
Arguments
T_a |
|
T_b |
|
A |
|
proportion |
|
H_L |
|
ef |
|
Value
numeric
convection (W).
References
Mitchell JW (1976). “Heat transfer from spheres and other animal forms.” Biophysical Journal, 16(6), 561-569. ISSN 0006-3495, doi: 10.1016/S0006-3495(76)85711-6.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Grashof_number()
,
Nusselt_from_Grashof()
,
Nusselt_from_Reynolds()
,
Nusselt_number()
,
Prandtl_number()
,
Qconduction_animal()
,
Qconduction_substrate()
,
Qemitted_thermal_radiation()
,
Qevaporation()
,
Qmetabolism_from_mass_temp()
,
Qmetabolism_from_mass()
,
Qnet_Gates()
,
Qradiation_absorbed()
,
Qthermal_radiation_absorbed()
,
Reynolds_number()
,
T_sky()
,
Tb_CampbellNorman()
,
Tb_Gates2()
,
Tb_Gates()
,
Tb_butterfly()
,
Tb_grasshopper()
,
Tb_limpetBH()
,
Tb_limpet()
,
Tb_lizard_Fei()
,
Tb_lizard()
,
Tb_mussel()
,
Tb_salamander_humid()
,
Tb_snail()
,
Tbed_mussel()
,
Tsoil()
,
actual_vapor_pressure()
,
boundary_layer_resistance()
,
external_resistance_to_water_vapor_transfer()
,
free_or_forced_convection()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient_simple()
,
heat_transfer_coefficient()
,
saturation_vapor_pressure()
,
saturation_water_vapor_pressure()
Examples
Qconvection(T_a = 293,
T_b = 303,
H_L = 10.45,
A = 0.0025,
proportion = 0.85)
Emitted Thermal Radiation
Description
The function estimates the net thermal radiation (W) emitted by the surface of an animal (Gates 1980; Spotila et al. 1992).
Usage
Qemitted_thermal_radiation(
epsilon = 0.96,
A,
psa_dir,
psa_ref,
T_b,
T_g,
T_sky = NA,
T_a,
enclosed = FALSE
)
Arguments
epsilon |
|
A |
|
psa_dir |
|
psa_ref |
|
T_b |
|
T_g |
|
T_sky |
|
T_a |
|
enclosed |
|
Value
numeric
emitted thermal radiation, Qemit
(W).
References
Gates DM (1980).
Biophysical Ecology.
Springer-Verlag, New York, NY, USA.
Spotila JR, Feder ME, Burggren WW (1992).
“Biophysics of Heat and Mass Transfer.”
Environmental Physiology of the Amphibians.
https://press.uchicago.edu/ucp/books/book/chicago/E/bo3636401.html.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Grashof_number()
,
Nusselt_from_Grashof()
,
Nusselt_from_Reynolds()
,
Nusselt_number()
,
Prandtl_number()
,
Qconduction_animal()
,
Qconduction_substrate()
,
Qconvection()
,
Qevaporation()
,
Qmetabolism_from_mass_temp()
,
Qmetabolism_from_mass()
,
Qnet_Gates()
,
Qradiation_absorbed()
,
Qthermal_radiation_absorbed()
,
Reynolds_number()
,
T_sky()
,
Tb_CampbellNorman()
,
Tb_Gates2()
,
Tb_Gates()
,
Tb_butterfly()
,
Tb_grasshopper()
,
Tb_limpetBH()
,
Tb_limpet()
,
Tb_lizard_Fei()
,
Tb_lizard()
,
Tb_mussel()
,
Tb_salamander_humid()
,
Tb_snail()
,
Tbed_mussel()
,
Tsoil()
,
actual_vapor_pressure()
,
boundary_layer_resistance()
,
external_resistance_to_water_vapor_transfer()
,
free_or_forced_convection()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient_simple()
,
heat_transfer_coefficient()
,
saturation_vapor_pressure()
,
saturation_water_vapor_pressure()
Examples
Qemitted_thermal_radiation(epsilon = 0.96,
A = 1,
psa_dir = 0.4,
psa_ref = 0.5,
T_b = 303,
T_g = 293,
T_a = 298,
enclosed = FALSE)
Heat Loss Associated with Evaporative Water Loss
Description
The function estimates heat loss associated with evaporative water loss for an amphibian (Spotila et al. 1992) or lizard. The lizard estimation is based on empirical measurements in Porter et al. (1973)).
Usage
Qevaporation(A, T_b, taxon, e_s = NA, e_a = NA, hp = NA, H = NA, r_i = NA)
Arguments
A |
|
T_b |
|
taxon |
|
e_s |
|
e_a |
|
hp |
|
H |
|
r_i |
|
Value
numeric
evaporative heat loss (W).
References
Porter WP, Mitchell JW, Bekman A, DeWitt CB (1973).
“Behavioral implications of mechanistic ecology: thermal and behavioral modeling of desert ectotherms and their microenvironments.”
Oecologia, 13, 1-54.
Spotila JR, Feder ME, Burggren WW (1992).
“Biophysics of Heat and Mass Transfer.”
Environmental Physiology of the Amphibians.
https://press.uchicago.edu/ucp/books/book/chicago/E/bo3636401.html.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Grashof_number()
,
Nusselt_from_Grashof()
,
Nusselt_from_Reynolds()
,
Nusselt_number()
,
Prandtl_number()
,
Qconduction_animal()
,
Qconduction_substrate()
,
Qconvection()
,
Qemitted_thermal_radiation()
,
Qmetabolism_from_mass_temp()
,
Qmetabolism_from_mass()
,
Qnet_Gates()
,
Qradiation_absorbed()
,
Qthermal_radiation_absorbed()
,
Reynolds_number()
,
T_sky()
,
Tb_CampbellNorman()
,
Tb_Gates2()
,
Tb_Gates()
,
Tb_butterfly()
,
Tb_grasshopper()
,
Tb_limpetBH()
,
Tb_limpet()
,
Tb_lizard_Fei()
,
Tb_lizard()
,
Tb_mussel()
,
Tb_salamander_humid()
,
Tb_snail()
,
Tbed_mussel()
,
Tsoil()
,
actual_vapor_pressure()
,
boundary_layer_resistance()
,
external_resistance_to_water_vapor_transfer()
,
free_or_forced_convection()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient_simple()
,
heat_transfer_coefficient()
,
saturation_vapor_pressure()
,
saturation_water_vapor_pressure()
Examples
Qevaporation(A = 0.1,
T_b = 293,
taxon = "amphibian",
e_s = 0.003,
e_a = 0.002,
hp = 0.5,
H = 20,
r_i = 50)
Qevaporation(A = 0.1,
T_b = 293,
taxon = "lizard")
Metabolism as a Function of Mass
Description
The function estimates the field metabolic rate (W) of various taxa as a function of mass (g). The function does not account for temperature and is based on empirical relationships from Nagy (2005).
Usage
Qmetabolism_from_mass(m, taxon = "reptile")
Arguments
m |
|
taxon |
|
Value
numeric
metabolism (W).
References
Nagy KA (2005). “Field metabolic rate and body size.” Journal of Experimental Biology, 208, 1621-1625. doi: 10.1242/jeb.01553, https://journals.biologists.com/jeb/article/208/9/1621/9364/Field-metabolic-rate-and-body-size.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Grashof_number()
,
Nusselt_from_Grashof()
,
Nusselt_from_Reynolds()
,
Nusselt_number()
,
Prandtl_number()
,
Qconduction_animal()
,
Qconduction_substrate()
,
Qconvection()
,
Qemitted_thermal_radiation()
,
Qevaporation()
,
Qmetabolism_from_mass_temp()
,
Qnet_Gates()
,
Qradiation_absorbed()
,
Qthermal_radiation_absorbed()
,
Reynolds_number()
,
T_sky()
,
Tb_CampbellNorman()
,
Tb_Gates2()
,
Tb_Gates()
,
Tb_butterfly()
,
Tb_grasshopper()
,
Tb_limpetBH()
,
Tb_limpet()
,
Tb_lizard_Fei()
,
Tb_lizard()
,
Tb_mussel()
,
Tb_salamander_humid()
,
Tb_snail()
,
Tbed_mussel()
,
Tsoil()
,
actual_vapor_pressure()
,
boundary_layer_resistance()
,
external_resistance_to_water_vapor_transfer()
,
free_or_forced_convection()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient_simple()
,
heat_transfer_coefficient()
,
saturation_vapor_pressure()
,
saturation_water_vapor_pressure()
Examples
Qmetabolism_from_mass(m = 12,
taxon = "reptile")
Metabolism as a Function of Mass and Body Temperature
Description
The function estimates basal (or resting) metabolic rate (W) as a function of mass (g) and temperature (C). The function is based on empirical data and the metabolic theory of ecology (assumes a 3/4 scaling exponent) (Gillooly et al. 2001).
Usage
Qmetabolism_from_mass_temp(m, T_b, taxon)
Arguments
m |
|
T_b |
|
taxon |
|
Value
numeric
basal metabolism (W).
References
Gillooly JF, Brown JH, West GB, Savage VM, Charnov EL (2001). “Effects of size and temperature on metabolic rate.” Science, 293, 2248-2251. doi: 10.1126/science.1061967.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Grashof_number()
,
Nusselt_from_Grashof()
,
Nusselt_from_Reynolds()
,
Nusselt_number()
,
Prandtl_number()
,
Qconduction_animal()
,
Qconduction_substrate()
,
Qconvection()
,
Qemitted_thermal_radiation()
,
Qevaporation()
,
Qmetabolism_from_mass()
,
Qnet_Gates()
,
Qradiation_absorbed()
,
Qthermal_radiation_absorbed()
,
Reynolds_number()
,
T_sky()
,
Tb_CampbellNorman()
,
Tb_Gates2()
,
Tb_Gates()
,
Tb_butterfly()
,
Tb_grasshopper()
,
Tb_limpetBH()
,
Tb_limpet()
,
Tb_lizard_Fei()
,
Tb_lizard()
,
Tb_mussel()
,
Tb_salamander_humid()
,
Tb_snail()
,
Tbed_mussel()
,
Tsoil()
,
actual_vapor_pressure()
,
boundary_layer_resistance()
,
external_resistance_to_water_vapor_transfer()
,
free_or_forced_convection()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient_simple()
,
heat_transfer_coefficient()
,
saturation_vapor_pressure()
,
saturation_water_vapor_pressure()
Examples
Qmetabolism_from_mass_temp(m = 100,
T_b = 30,
taxon = "reptile")
Net Energy Exchange Between an Animal and the Environment
Description
The function estimates the net energy exchange (W) between an animal and the environment. The function follows Gates (1980) and others.
Usage
Qnet_Gates(Qabs, Qemit, Qconv, Qcond, Qmet, Qevap)
Arguments
Qabs |
|
Qemit |
|
Qconv |
|
Qcond |
|
Qmet |
|
Qevap |
|
Value
numeric
net energy exchange (W).
References
Gates DM (1980). Biophysical Ecology. Springer-Verlag, New York, NY, USA.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Grashof_number()
,
Nusselt_from_Grashof()
,
Nusselt_from_Reynolds()
,
Nusselt_number()
,
Prandtl_number()
,
Qconduction_animal()
,
Qconduction_substrate()
,
Qconvection()
,
Qemitted_thermal_radiation()
,
Qevaporation()
,
Qmetabolism_from_mass_temp()
,
Qmetabolism_from_mass()
,
Qradiation_absorbed()
,
Qthermal_radiation_absorbed()
,
Reynolds_number()
,
T_sky()
,
Tb_CampbellNorman()
,
Tb_Gates2()
,
Tb_Gates()
,
Tb_butterfly()
,
Tb_grasshopper()
,
Tb_limpetBH()
,
Tb_limpet()
,
Tb_lizard_Fei()
,
Tb_lizard()
,
Tb_mussel()
,
Tb_salamander_humid()
,
Tb_snail()
,
Tbed_mussel()
,
Tsoil()
,
actual_vapor_pressure()
,
boundary_layer_resistance()
,
external_resistance_to_water_vapor_transfer()
,
free_or_forced_convection()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient_simple()
,
heat_transfer_coefficient()
,
saturation_vapor_pressure()
,
saturation_water_vapor_pressure()
Examples
Qnet_Gates(Qabs = 500,
Qemit = 10,
Qconv = 100,
Qcond = 100,
Qmet = 10,
Qevap = 5)
Absorbed Solar and Thermal Radiation
Description
The function estimates solar and thermal radiation (W) absorbed by the surface of an animal following (Gates 1980) and (Spotila et al. 1992).
Usage
Qradiation_absorbed(
a = 0.9,
A,
psa_dir,
psa_dif,
psa_ref,
S_dir,
S_dif,
S_ref = NA,
rho = NA
)
Arguments
a |
|
A |
|
psa_dir |
|
psa_dif |
|
psa_ref |
|
S_dir |
|
S_dif |
|
S_ref |
|
rho |
|
Value
numeric
solar radiation absorbed (W)
References
Gates DM (1980).
Biophysical Ecology.
Springer-Verlag, New York, NY, USA.
Spotila JR, Feder ME, Burggren WW (1992).
“Biophysics of Heat and Mass Transfer.”
Environmental Physiology of the Amphibians.
https://press.uchicago.edu/ucp/books/book/chicago/E/bo3636401.html.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Grashof_number()
,
Nusselt_from_Grashof()
,
Nusselt_from_Reynolds()
,
Nusselt_number()
,
Prandtl_number()
,
Qconduction_animal()
,
Qconduction_substrate()
,
Qconvection()
,
Qemitted_thermal_radiation()
,
Qevaporation()
,
Qmetabolism_from_mass_temp()
,
Qmetabolism_from_mass()
,
Qnet_Gates()
,
Qthermal_radiation_absorbed()
,
Reynolds_number()
,
T_sky()
,
Tb_CampbellNorman()
,
Tb_Gates2()
,
Tb_Gates()
,
Tb_butterfly()
,
Tb_grasshopper()
,
Tb_limpetBH()
,
Tb_limpet()
,
Tb_lizard_Fei()
,
Tb_lizard()
,
Tb_mussel()
,
Tb_salamander_humid()
,
Tb_snail()
,
Tbed_mussel()
,
Tsoil()
,
actual_vapor_pressure()
,
boundary_layer_resistance()
,
external_resistance_to_water_vapor_transfer()
,
free_or_forced_convection()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient_simple()
,
heat_transfer_coefficient()
,
saturation_vapor_pressure()
,
saturation_water_vapor_pressure()
Examples
Qradiation_absorbed(a = 0.9,
A = 1,
psa_dir = 0.5,
psa_dif = 0.5,
psa_ref = 0.5,
S_dir = 1000,
S_dif = 200,
rho = 0.5)
Absorbed Thermal Radiation
Description
The function estimates longwave (thermal) radiation (W) absorbed from the sky and the ground (Campbell and Norman 1998; Riddell et al. 2018).
Usage
Qthermal_radiation_absorbed(
T_a,
T_g,
epsilon_ground = 0.97,
a_longwave = 0.965
)
Arguments
T_a |
|
T_g |
|
epsilon_ground |
|
a_longwave |
|
Value
numeric
thermal radiation absorbed (W).
Author(s)
Eric Riddell
References
Bartlett PN, Gates DM (1967).
“The energy budget of a lizard on a tree trunk.”
Ecology, 48, 316-322.
Buckley LB (2008).
“Linking traits to energetics and population dynamics to predict lizard ranges in changing environments.”
American Naturalist, 171(1), E1 - E19.
doi: 10.1086/523949, https://pubmed.ncbi.nlm.nih.gov/18171140/.
Campbell GS, Norman JM (1998).
Introduction to environmental biophysics, 2nd ed. edition.
Springer, New York.
ISBN 0387949372.
Riddell EA, Odom JP, Damm JD, Sears MW (2018).
“Plasticity reveals hidden resistance to extinction under climate change in the global hotspot of salamander diversity.”
Science Advances, 4(4).
doi: 10.1126/sciadv.aar5471.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Grashof_number()
,
Nusselt_from_Grashof()
,
Nusselt_from_Reynolds()
,
Nusselt_number()
,
Prandtl_number()
,
Qconduction_animal()
,
Qconduction_substrate()
,
Qconvection()
,
Qemitted_thermal_radiation()
,
Qevaporation()
,
Qmetabolism_from_mass_temp()
,
Qmetabolism_from_mass()
,
Qnet_Gates()
,
Qradiation_absorbed()
,
Reynolds_number()
,
T_sky()
,
Tb_CampbellNorman()
,
Tb_Gates2()
,
Tb_Gates()
,
Tb_butterfly()
,
Tb_grasshopper()
,
Tb_limpetBH()
,
Tb_limpet()
,
Tb_lizard_Fei()
,
Tb_lizard()
,
Tb_mussel()
,
Tb_salamander_humid()
,
Tb_snail()
,
Tbed_mussel()
,
Tsoil()
,
actual_vapor_pressure()
,
boundary_layer_resistance()
,
external_resistance_to_water_vapor_transfer()
,
free_or_forced_convection()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient_simple()
,
heat_transfer_coefficient()
,
saturation_vapor_pressure()
,
saturation_water_vapor_pressure()
Examples
Qthermal_radiation_absorbed(T_a = 20,
T_g = 25,
epsilon_ground = 0.97,
a_longwave = 0.965)
Reynolds Number
Description
The function estimates the Reynolds Number, which describes the dynamic properties of the fluid surrounding the animal as the ratio of internal viscous forces (Gates 1980).
Usage
Reynolds_number(u, D, nu)
Arguments
u |
|
D |
|
nu |
|
Value
numeric
Reynolds number.
References
Gates DM (1980). Biophysical Ecology. Springer-Verlag, New York, NY, USA.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Grashof_number()
,
Nusselt_from_Grashof()
,
Nusselt_from_Reynolds()
,
Nusselt_number()
,
Prandtl_number()
,
Qconduction_animal()
,
Qconduction_substrate()
,
Qconvection()
,
Qemitted_thermal_radiation()
,
Qevaporation()
,
Qmetabolism_from_mass_temp()
,
Qmetabolism_from_mass()
,
Qnet_Gates()
,
Qradiation_absorbed()
,
Qthermal_radiation_absorbed()
,
T_sky()
,
Tb_CampbellNorman()
,
Tb_Gates2()
,
Tb_Gates()
,
Tb_butterfly()
,
Tb_grasshopper()
,
Tb_limpetBH()
,
Tb_limpet()
,
Tb_lizard_Fei()
,
Tb_lizard()
,
Tb_mussel()
,
Tb_salamander_humid()
,
Tb_snail()
,
Tbed_mussel()
,
Tsoil()
,
actual_vapor_pressure()
,
boundary_layer_resistance()
,
external_resistance_to_water_vapor_transfer()
,
free_or_forced_convection()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient_simple()
,
heat_transfer_coefficient()
,
saturation_vapor_pressure()
,
saturation_water_vapor_pressure()
Examples
Reynolds_number(u = 1,
D = 0.001,
nu = 1.2)
Gaussian-Quadratic Function Thermal Performance Curve
Description
The function constructs a thermal performance curve by combining as a Gaussian function to describe the rise in performance up to the optimal temperature and a quadratic decline to zero performance at critical thermal maxima and higher temperatures (Deutsch et al. 2008).
Usage
TPC(T_b, T_opt, CT_min, CT_max)
Arguments
T_b |
|
T_opt |
|
CT_min , CT_max |
|
Value
performance
References
Deutsch CA, Tewksbury JJ, Huey RB, Sheldon KS, Ghalambor CK, Haak DC, Martin PR (2008). “Impacts of climate warming on terrestrial ectotherms across latitude.” Proceedings of the National Academy of Science of the United States of America, 105, 6668-6672. doi: 10.1073/pnas.0709472105.
Examples
TPC(T_b = 0:60,
T_opt = 30,
CT_min = 10,
CT_max = 40)
Beta Function Thermal Performance Curve
Description
The function constructs a thermal performance curve based on a beta function (Asbury and Angilletta 2010).
Usage
TPC_beta(T_b, shift = -1, breadth = 0.1, aran = 0, tolerance = 43, skew = 0.7)
Arguments
T_b |
|
shift |
|
breadth |
|
aran |
|
tolerance |
|
skew |
|
Value
numeric
performance.
References
Asbury DA, Angilletta MJ (2010). “Thermodynamic effects on the evolution of performance curves.” American Naturalist, 176(2), E40-E49. doi: 10.1086/653659.
Examples
TPC_beta(T_b = 0:60,
shift = -1,
breadth = 0.1,
aran = 0,
tolerance = 43,
skew = 0.7)
Effective radiant temperature of sky (K)
Description
This function estimates the effective radiant temperature of the sky (K) using either the Brunt or Swinbank formulations (Gates 1980).
Usage
T_sky(T_a, formula)
Arguments
T_a |
|
formula |
|
Value
numeric
T_sky (K).
References
Gates DM (1980). Biophysical Ecology. Springer-Verlag, New York, NY, USA.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Grashof_number()
,
Nusselt_from_Grashof()
,
Nusselt_from_Reynolds()
,
Nusselt_number()
,
Prandtl_number()
,
Qconduction_animal()
,
Qconduction_substrate()
,
Qconvection()
,
Qemitted_thermal_radiation()
,
Qevaporation()
,
Qmetabolism_from_mass_temp()
,
Qmetabolism_from_mass()
,
Qnet_Gates()
,
Qradiation_absorbed()
,
Qthermal_radiation_absorbed()
,
Reynolds_number()
,
Tb_CampbellNorman()
,
Tb_Gates2()
,
Tb_Gates()
,
Tb_butterfly()
,
Tb_grasshopper()
,
Tb_limpetBH()
,
Tb_limpet()
,
Tb_lizard_Fei()
,
Tb_lizard()
,
Tb_mussel()
,
Tb_salamander_humid()
,
Tb_snail()
,
Tbed_mussel()
,
Tsoil()
,
actual_vapor_pressure()
,
boundary_layer_resistance()
,
external_resistance_to_water_vapor_transfer()
,
free_or_forced_convection()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient_simple()
,
heat_transfer_coefficient()
,
saturation_vapor_pressure()
,
saturation_water_vapor_pressure()
Examples
T_sky(T_a=293, formula="Swinbank")
Operative Environmental Temperature of an Ectotherm based on Campbell and Norman (1988)
Description
The function estimates body temperatures (C, operative environmental temperature) of an ectotherm using an approximation based on Campbell and Norman (1998) and Mitchell (1976).
Usage
Tb_CampbellNorman(
T_a,
T_g,
S,
a_s = 0.7,
a_l = 0.96,
epsilon = 0.96,
c_p = 29.3,
D,
u
)
Arguments
T_a |
|
T_g |
|
S |
|
a_s |
|
a_l |
|
epsilon |
|
c_p |
|
D |
|
u |
|
Details
Boundary conductance uses a factor of 1.4 to account for increased convection (Mitchell 1976). The function assumes forced conduction.
Value
numeric
operative environmental temperature, T_e
(C).
References
Bartlett PN, Gates DM (1967).
“The energy budget of a lizard on a tree trunk.”
Ecology, 48, 316-322.
Campbell GS, Norman JM (1998).
Introduction to environmental biophysics, 2nd ed. edition.
Springer, New York.
ISBN 0387949372.
Gates DM (1980).
Biophysical Ecology.
Springer-Verlag, New York, NY, USA.
Mitchell JW (1976).
“Heat transfer from spheres and other animal forms.”
Biophysical Journal, 16(6), 561-569.
ISSN 0006-3495, doi: 10.1016/S0006-3495(76)85711-6.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Grashof_number()
,
Nusselt_from_Grashof()
,
Nusselt_from_Reynolds()
,
Nusselt_number()
,
Prandtl_number()
,
Qconduction_animal()
,
Qconduction_substrate()
,
Qconvection()
,
Qemitted_thermal_radiation()
,
Qevaporation()
,
Qmetabolism_from_mass_temp()
,
Qmetabolism_from_mass()
,
Qnet_Gates()
,
Qradiation_absorbed()
,
Qthermal_radiation_absorbed()
,
Reynolds_number()
,
T_sky()
,
Tb_Gates2()
,
Tb_Gates()
,
Tb_butterfly()
,
Tb_grasshopper()
,
Tb_limpetBH()
,
Tb_limpet()
,
Tb_lizard_Fei()
,
Tb_lizard()
,
Tb_mussel()
,
Tb_salamander_humid()
,
Tb_snail()
,
Tbed_mussel()
,
Tsoil()
,
actual_vapor_pressure()
,
boundary_layer_resistance()
,
external_resistance_to_water_vapor_transfer()
,
free_or_forced_convection()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient_simple()
,
heat_transfer_coefficient()
,
saturation_vapor_pressure()
,
saturation_water_vapor_pressure()
Examples
Tb_CampbellNorman (T_a = 30,
T_g = 30,
S = 823,
a_s = 0.7,
a_l = 0.96,
epsilon = 0.96,
c_p = 29.3,
D = 0.17,
u = 1)
Operative Environmental Temperature of an Ectotherm Based on Gates (1980)
Description
The function predicts body temperatures (C, operative environmental temperature) of an ectotherm using the approximation in Gates (1980). The functions omits evaporative and metabolic heat loss (Mitchell 1976; Kingsolver 1983).
Usage
Tb_Gates(
A,
D,
psa_dir,
psa_ref,
psa_air,
psa_g,
T_g,
T_a,
Qabs,
epsilon,
H_L,
ef = 1.3,
K
)
Arguments
A |
|
D |
|
psa_dir |
|
psa_ref |
|
psa_air |
|
psa_g |
|
T_g |
|
T_a |
|
Qabs |
|
epsilon |
|
H_L |
|
ef |
|
K |
|
Value
numeric
operative environmental temperature, T_e
(C).
References
Galushko D, Ermakov N, Karpovski M, Palevski A, Ishay JS, Bergman DJ (2005).
“Electrical, thermoelectric and thermophysical properties of hornet cuticle.”
Semiconductor Science and Technology, 20(3), 286–289.
doi: 10.1088/0268-1242/20/3/005.
Gates DM (1980).
Biophysical Ecology.
Springer-Verlag, New York, NY, USA.
Kingsolver JG (1983).
“Thermoregulation and Flight in Colias Butterflies: Elevational Patterns and Mechanistic Limitations.”
Ecology, 64(3), 534-545.
doi: 10.2307/1939973.
Mitchell JW (1976).
“Heat transfer from spheres and other animal forms.”
Biophysical Journal, 16(6), 561-569.
ISSN 0006-3495, doi: 10.1016/S0006-3495(76)85711-6.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Grashof_number()
,
Nusselt_from_Grashof()
,
Nusselt_from_Reynolds()
,
Nusselt_number()
,
Prandtl_number()
,
Qconduction_animal()
,
Qconduction_substrate()
,
Qconvection()
,
Qemitted_thermal_radiation()
,
Qevaporation()
,
Qmetabolism_from_mass_temp()
,
Qmetabolism_from_mass()
,
Qnet_Gates()
,
Qradiation_absorbed()
,
Qthermal_radiation_absorbed()
,
Reynolds_number()
,
T_sky()
,
Tb_CampbellNorman()
,
Tb_Gates2()
,
Tb_butterfly()
,
Tb_grasshopper()
,
Tb_limpetBH()
,
Tb_limpet()
,
Tb_lizard_Fei()
,
Tb_lizard()
,
Tb_mussel()
,
Tb_salamander_humid()
,
Tb_snail()
,
Tbed_mussel()
,
Tsoil()
,
actual_vapor_pressure()
,
boundary_layer_resistance()
,
external_resistance_to_water_vapor_transfer()
,
free_or_forced_convection()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient_simple()
,
heat_transfer_coefficient()
,
saturation_vapor_pressure()
,
saturation_water_vapor_pressure()
Examples
Tb_Gates (A = 0.1,
D = 0.025,
psa_dir = 0.6,
psa_ref = 0.4,
psa_air = 0.5,
psa_g = 0.1,
T_g = 30,
T_a = 37,
Qabs = 2,
epsilon = 0.95,
H_L = 10,
ef = 1.23,
K = 0.5)
Operative Environmental Temperature of an Ectotherm Based on a Variant of Gates (1980)
Description
The function predicts body temperatures (C, operative environmental temperature) of an ectotherm using the approximation in Gates (1980). The function omits evaporative and metabolic heat loss.
Usage
Tb_Gates2(A, D, T_g, T_a, Qabs, u, epsilon)
Arguments
A |
|
D |
|
T_g |
|
T_a |
|
Qabs |
|
u |
|
epsilon |
|
Value
numeric
operative environmental temperature (C).
References
Gates DM (1980). Biophysical Ecology. Springer-Verlag, New York, NY, USA.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Grashof_number()
,
Nusselt_from_Grashof()
,
Nusselt_from_Reynolds()
,
Nusselt_number()
,
Prandtl_number()
,
Qconduction_animal()
,
Qconduction_substrate()
,
Qconvection()
,
Qemitted_thermal_radiation()
,
Qevaporation()
,
Qmetabolism_from_mass_temp()
,
Qmetabolism_from_mass()
,
Qnet_Gates()
,
Qradiation_absorbed()
,
Qthermal_radiation_absorbed()
,
Reynolds_number()
,
T_sky()
,
Tb_CampbellNorman()
,
Tb_Gates()
,
Tb_butterfly()
,
Tb_grasshopper()
,
Tb_limpetBH()
,
Tb_limpet()
,
Tb_lizard_Fei()
,
Tb_lizard()
,
Tb_mussel()
,
Tb_salamander_humid()
,
Tb_snail()
,
Tbed_mussel()
,
Tsoil()
,
actual_vapor_pressure()
,
boundary_layer_resistance()
,
external_resistance_to_water_vapor_transfer()
,
free_or_forced_convection()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient_simple()
,
heat_transfer_coefficient()
,
saturation_vapor_pressure()
,
saturation_water_vapor_pressure()
Examples
Tb_Gates2(A = 1,
D = 0.001,
T_g = 27,
T_a = 37,
Qabs = 2,
u = 0.1,
epsilon = 1)
Operative Environmental Temperature of a Butterfly
Description
The function estimates body temperatures (C, operative environmental temperatures) of a butterfly based on Kingsolver (1983) and Buckley and Kingsolver (2012). The function is designed for butterflies that bask with closed wings such as Colias.
Usage
Tb_butterfly(
T_a,
T_g,
T_sh,
u,
S_sdir,
S_sdif,
z,
D,
delta,
alpha,
r_g = 0.3,
shade = FALSE
)
Arguments
T_a |
|
T_g |
|
T_sh |
|
u |
|
S_sdir |
|
S_sdif |
|
z |
|
D |
|
delta |
|
alpha |
|
r_g |
|
shade |
|
Details
Thermal radiative flux is calculated following Gates (1980) based on Swinbank (1960). Kingsolver (1983) estimates using the Brunt equation with black body sky temperature from Swinbank (1963).
Value
numeric
predicted body (operative environmental) temperature (C).
References
Buckley LB, Kingsolver JG (2012).
“The demographic impacts of shifts in climate means and extremes on alpine butterflies.”
Functional Ecology, 26(4), 969-977.
doi: 10.1111/j.1365-2435.2012.01969.x.
Gates DM (1980).
Biophysical Ecology.
Springer-Verlag, New York, NY, USA.
Kingsolver JG (1983).
“Thermoregulation and Flight in Colias Butterflies: Elevational Patterns and Mechanistic Limitations.”
Ecology, 64(3), 534-545.
doi: 10.2307/1939973.
Swinbank WC (1960).
“Wind profile in thermally stratified flow.”
Nature, 186, 463-464.
Swinbank WC (1963).
“Long-wave radiation from clear skies.”
Quarterly Journal of the Royal Meteorological Society, 89, 339-348.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Grashof_number()
,
Nusselt_from_Grashof()
,
Nusselt_from_Reynolds()
,
Nusselt_number()
,
Prandtl_number()
,
Qconduction_animal()
,
Qconduction_substrate()
,
Qconvection()
,
Qemitted_thermal_radiation()
,
Qevaporation()
,
Qmetabolism_from_mass_temp()
,
Qmetabolism_from_mass()
,
Qnet_Gates()
,
Qradiation_absorbed()
,
Qthermal_radiation_absorbed()
,
Reynolds_number()
,
T_sky()
,
Tb_CampbellNorman()
,
Tb_Gates2()
,
Tb_Gates()
,
Tb_grasshopper()
,
Tb_limpetBH()
,
Tb_limpet()
,
Tb_lizard_Fei()
,
Tb_lizard()
,
Tb_mussel()
,
Tb_salamander_humid()
,
Tb_snail()
,
Tbed_mussel()
,
Tsoil()
,
actual_vapor_pressure()
,
boundary_layer_resistance()
,
external_resistance_to_water_vapor_transfer()
,
free_or_forced_convection()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient_simple()
,
heat_transfer_coefficient()
,
saturation_vapor_pressure()
,
saturation_water_vapor_pressure()
Examples
Tb_butterfly(T_a = 25,
T_g = 25,
T_sh = 20,
u = 0.4,
S_sdir = 300,
S_sdif = 100,
z = 30,
D = 0.36,
delta = 1.46,
alpha = 0.6,
r_g = 0.3)
Operative Environmental Temperature of a Grasshopper
Description
The function estimates body temperatures (C, operative environmental temperatures) of a grasshopper based on Lactin and Johnson (1998). Part of the model is based on Swinbank (1963), following Gates (1962) in Kingsolver (1983).
Usage
Tb_grasshopper(
T_a,
T_g,
u,
S,
K_t,
psi,
l,
Acondfact = 0.25,
z = 0.001,
abs = 0.7,
r_g = 0.3
)
Arguments
T_a |
|
T_g |
|
u |
|
S |
|
K_t |
|
psi |
|
l |
|
Acondfact |
|
z |
|
abs |
|
r_g |
|
Details
Total radiative flux is calculated as thermal radiative heat flux plus convective heat flux, following Kingsolver (1983), with the Erbs et al. (1982) model from Wong and Chow (2001).
Energy balance is based on Kingsolver (1983).
Radiation is calculated without area dependence (Anderson et al. 1979).
The body of a grasshopper female is approximated by a rotational ellipsoid with half the body length as the semi-major axis (Samietz et al. 2005).
The diffuse fraction is corrected following Olyphant (1984).
Value
numeric
predicted body (operative environmental) temperature (C).
References
Anderson RV, Tracy CR, Abramsky Z (1979).
“Habitat Selection in Two Species of Short-Horned Grasshoppers. The Role of Thermal and Hydric Stresses.”
Oecologia, 38(3), 359–374.
doi: 10.1007/BF00345194.
Erbs D, Klein S, Duffie J (1982).
“Estimation of the diffuse radiation fraction for hourly, daily and monthly-average global radiation.”
Solar Energy, 28, 293-302.
Gates DM (1962).
“Leaf temperature and energy exchange.”
Archiv fur Meteorologie, Geophysik und Bioklimatologie, Serie B volume, 12, 321-336.
Kingsolver JG (1983).
“Thermoregulation and Flight in Colias Butterflies: Elevational Patterns and Mechanistic Limitations.”
Ecology, 64(3), 534-545.
doi: 10.2307/1939973.
Lactin DJ, Johnson DL (1998).
“Convective heat loss and change in body temperature of grasshopper and locust nymphs: Relative importance of wind speed, insect size and insect orientation.”
Journal of Thermal Biology, 23(1), 5-13.
ISSN 0306-4565, doi: 10.1016/S0306-4565(97)00037-5, https://www.sciencedirect.com/science/article/pii/S0306456597000375.
Olyphant G (1984).
“Insolation Topoclimates and Potential Ablation in Alpine Snow Accumulation Basins: Front Range, Colorado.”
Water Resources Research, 20(4), 491-498.
Samietz J, Salser MA, Dingle H (2005).
“Altitudinal variation in behavioural thermoregulation: local adaptation vs. plasticity in California grasshoppers.”
Journal of Evolutionary Biology, 18(4), 1087-1096.
doi: 10.1111/j.1420-9101.2005.00893.x.
Swinbank WC (1963).
“Long-wave radiation from clear skies.”
Quarterly Journal of the Royal Meteorological Society, 89, 339-348.
Wong LT, Chow WK (2001).
“Solar radiation model.”
Applied Energy, 69(3), 191-224.
ISSN 0306-2619, doi: 10.1016/S0306-2619(01)00012-5, https://www.sciencedirect.com/science/article/pii/S0306261901000125.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Grashof_number()
,
Nusselt_from_Grashof()
,
Nusselt_from_Reynolds()
,
Nusselt_number()
,
Prandtl_number()
,
Qconduction_animal()
,
Qconduction_substrate()
,
Qconvection()
,
Qemitted_thermal_radiation()
,
Qevaporation()
,
Qmetabolism_from_mass_temp()
,
Qmetabolism_from_mass()
,
Qnet_Gates()
,
Qradiation_absorbed()
,
Qthermal_radiation_absorbed()
,
Reynolds_number()
,
T_sky()
,
Tb_CampbellNorman()
,
Tb_Gates2()
,
Tb_Gates()
,
Tb_butterfly()
,
Tb_limpetBH()
,
Tb_limpet()
,
Tb_lizard_Fei()
,
Tb_lizard()
,
Tb_mussel()
,
Tb_salamander_humid()
,
Tb_snail()
,
Tbed_mussel()
,
Tsoil()
,
actual_vapor_pressure()
,
boundary_layer_resistance()
,
external_resistance_to_water_vapor_transfer()
,
free_or_forced_convection()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient_simple()
,
heat_transfer_coefficient()
,
saturation_vapor_pressure()
,
saturation_water_vapor_pressure()
Examples
Tb_grasshopper(T_a = 25,
T_g = 25,
u = 0.4,
S = 400,
K_t = 0.7,
psi = 30,
l = 0.02,
Acondfact = 0.25,
z = 0.001,
abs = 0.7,
r_g = 0.3)
Operative Environmental Temperature of a Limpet
Description
The function estimates body temperatures (C, operative environmental temperatures) of a limpet based on Denny and Harley (2006).
Usage
Tb_limpet(T_a, T_r, l, h, S, u, psi, c, position = "anterior")
Arguments
T_a |
|
T_r |
|
l |
|
h |
|
S |
|
u |
|
psi |
|
c |
|
position |
|
Details
The original equation uses a finite-difference approach where they divide the rock into series of chunks, and calculate the temperature at each node to derive the conductive heat. For simplification, here it takes the rock temperature as a parameter, and conductive heat is calculated as a product of the area, thermal conductivity of rock and the temperature difference between the rock and the body.
Limpets are simulated as cones following and using solar emissivity values from Campbell and Norman (1998).
The area of the limpet's shell (m2) is projected according to the direction at which sunlight strikes the organism (Pennell and Deignan 1989).
Air conductivity values (W m-1 K-1) are calculated following Denny and Harley (2006).
Value
numeric
predicted body (operative environmental) temperature (C).
References
Campbell GS, Norman JM (1998).
Introduction to environmental biophysics, 2nd ed. edition.
Springer, New York.
ISBN 0387949372.
Denny MW, Harley CDG (2006).
“Hot limpets: predicting body temperature in a conductance-mediated thermal system.”
Journal of Experimental Biology, 209(13), 2409-2419.
ISSN 0022-0949, doi: 10.1242/jeb.02356.
Pennell S, Deignan J (1989).
“Computing the Projected Area of a Cone.”
SIAM Review, 31, 299-302.
doi: 10.1137/1031052.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Grashof_number()
,
Nusselt_from_Grashof()
,
Nusselt_from_Reynolds()
,
Nusselt_number()
,
Prandtl_number()
,
Qconduction_animal()
,
Qconduction_substrate()
,
Qconvection()
,
Qemitted_thermal_radiation()
,
Qevaporation()
,
Qmetabolism_from_mass_temp()
,
Qmetabolism_from_mass()
,
Qnet_Gates()
,
Qradiation_absorbed()
,
Qthermal_radiation_absorbed()
,
Reynolds_number()
,
T_sky()
,
Tb_CampbellNorman()
,
Tb_Gates2()
,
Tb_Gates()
,
Tb_butterfly()
,
Tb_grasshopper()
,
Tb_limpetBH()
,
Tb_lizard_Fei()
,
Tb_lizard()
,
Tb_mussel()
,
Tb_salamander_humid()
,
Tb_snail()
,
Tbed_mussel()
,
Tsoil()
,
actual_vapor_pressure()
,
boundary_layer_resistance()
,
external_resistance_to_water_vapor_transfer()
,
free_or_forced_convection()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient_simple()
,
heat_transfer_coefficient()
,
saturation_vapor_pressure()
,
saturation_water_vapor_pressure()
Examples
Tb_limpet(T_a = 25,
T_r = 30,
l = 0.0176,
h = 0.0122,
S = 1300,
u = 1,
psi = 30,
c = 1,
position = "anterior")
Operative Environmental Temperature of a Limpet Based on a Model by Helmuth
Description
The function predicts body temperatures (C, operative environmental temperatures) of a limpet. The function was provided by Brian Helmuth – although radiation and convection are altered from his original model – and based on Denny and Harley (2006).
Usage
Tb_limpetBH(T_a, T_r, l, h, S, u, s_aspect, s_slope, c)
Arguments
T_a |
|
T_r |
|
l |
|
h |
|
S |
|
u |
|
s_aspect |
|
s_slope |
|
c |
|
Details
The original equation uses a finite-difference approach where they divide the rock into series of chunks, and calculate the temperature at each node to derive the conductive heat. For simplification, here it takes the rock temperature as a parameter, and conductive heat is calculated by the product of the area, thermal conductivity of rock and the difference in temperatures of the rock and the body.
Limpets are simulated as cones following and using solar emissivity values from Campbell and Norman (1998).
The area of the limpet's shell (m2) is projected in the direction at which sunlight strikes the organism Pennell and Deignan (1989).
Air conductivity values (W m-1 K-1) are calculated following Denny and Harley (2006).
Value
numeric
predicted body (operative environmental) temperature (C).
Author(s)
Brian Helmuth et al.
References
Campbell GS, Norman JM (1998).
Introduction to environmental biophysics, 2nd ed. edition.
Springer, New York.
ISBN 0387949372.
Denny MW, Harley CDG (2006).
“Hot limpets: predicting body temperature in a conductance-mediated thermal system.”
Journal of Experimental Biology, 209(13), 2409-2419.
ISSN 0022-0949, doi: 10.1242/jeb.02356.
Pennell S, Deignan J (1989).
“Computing the Projected Area of a Cone.”
SIAM Review, 31, 299-302.
doi: 10.1137/1031052.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Grashof_number()
,
Nusselt_from_Grashof()
,
Nusselt_from_Reynolds()
,
Nusselt_number()
,
Prandtl_number()
,
Qconduction_animal()
,
Qconduction_substrate()
,
Qconvection()
,
Qemitted_thermal_radiation()
,
Qevaporation()
,
Qmetabolism_from_mass_temp()
,
Qmetabolism_from_mass()
,
Qnet_Gates()
,
Qradiation_absorbed()
,
Qthermal_radiation_absorbed()
,
Reynolds_number()
,
T_sky()
,
Tb_CampbellNorman()
,
Tb_Gates2()
,
Tb_Gates()
,
Tb_butterfly()
,
Tb_grasshopper()
,
Tb_limpet()
,
Tb_lizard_Fei()
,
Tb_lizard()
,
Tb_mussel()
,
Tb_salamander_humid()
,
Tb_snail()
,
Tbed_mussel()
,
Tsoil()
,
actual_vapor_pressure()
,
boundary_layer_resistance()
,
external_resistance_to_water_vapor_transfer()
,
free_or_forced_convection()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient_simple()
,
heat_transfer_coefficient()
,
saturation_vapor_pressure()
,
saturation_water_vapor_pressure()
Examples
Tb_limpetBH(T_a = 25,
T_r = 30,
l = 0.0176,
h = 0.0122,
S = 1300,
u = 1,
s_aspect = 90,
s_slope = 60,
c = 1)
Operative Environmental Temperature of a Lizard
Description
The function estimates body temperature (C, operative environmental temperature) of a lizard based on Campbell and Norman (1998). The function was designed for Sceloporus lizards and described in Buckley (2008).
Usage
Tb_lizard(
T_a,
T_g,
u,
svl,
m,
psi,
rho_s,
elev,
doy,
sun = TRUE,
surface = TRUE,
a_s = 0.9,
a_l = 0.965,
epsilon_s = 0.965,
F_d = 0.8,
F_r = 0.5,
F_a = 0.5,
F_g = 0.5
)
Arguments
T_a |
|
T_g |
|
u |
|
svl |
|
m |
|
psi |
|
rho_s |
|
elev |
|
doy |
|
sun |
|
surface |
|
a_s |
|
a_l |
|
epsilon_s |
|
F_d |
|
F_r |
|
F_a |
|
F_g |
|
Details
The proportion of radiation that is direct is determined following Sears et al. (2011).
Boundary conductance uses a factor of 1.4 to account for increased convection (Mitchell 1976).
Value
T_e numeric
predicted body (operative environmental) temperature (C).
References
Bartlett PN, Gates DM (1967).
“The energy budget of a lizard on a tree trunk.”
Ecology, 48, 316-322.
Buckley LB (2008).
“Linking traits to energetics and population dynamics to predict lizard ranges in changing environments.”
American Naturalist, 171(1), E1 - E19.
doi: 10.1086/523949, https://pubmed.ncbi.nlm.nih.gov/18171140/.
Campbell GS, Norman JM (1998).
Introduction to environmental biophysics, 2nd ed. edition.
Springer, New York.
ISBN 0387949372.
Gates DM (1980).
Biophysical Ecology.
Springer-Verlag, New York, NY, USA.
Mitchell JW (1976).
“Heat transfer from spheres and other animal forms.”
Biophysical Journal, 16(6), 561-569.
ISSN 0006-3495, doi: 10.1016/S0006-3495(76)85711-6.
Sears MW, Raskin E, Angilletta Jr. MJ (2011).
“The World Is not Flat: Defining Relevant Thermal Landscapes in the Context of Climate Change.”
Integrative and Comparative Biology, 51(5), 666-675.
ISSN 1540-7063, doi: 10.1093/icb/icr111, https://academic.oup.com/icb/article-pdf/51/5/666/1757893/icr111.pdf.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Grashof_number()
,
Nusselt_from_Grashof()
,
Nusselt_from_Reynolds()
,
Nusselt_number()
,
Prandtl_number()
,
Qconduction_animal()
,
Qconduction_substrate()
,
Qconvection()
,
Qemitted_thermal_radiation()
,
Qevaporation()
,
Qmetabolism_from_mass_temp()
,
Qmetabolism_from_mass()
,
Qnet_Gates()
,
Qradiation_absorbed()
,
Qthermal_radiation_absorbed()
,
Reynolds_number()
,
T_sky()
,
Tb_CampbellNorman()
,
Tb_Gates2()
,
Tb_Gates()
,
Tb_butterfly()
,
Tb_grasshopper()
,
Tb_limpetBH()
,
Tb_limpet()
,
Tb_lizard_Fei()
,
Tb_mussel()
,
Tb_salamander_humid()
,
Tb_snail()
,
Tbed_mussel()
,
Tsoil()
,
actual_vapor_pressure()
,
boundary_layer_resistance()
,
external_resistance_to_water_vapor_transfer()
,
free_or_forced_convection()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient_simple()
,
heat_transfer_coefficient()
,
saturation_vapor_pressure()
,
saturation_water_vapor_pressure()
Examples
Tb_lizard(T_a = 25,
T_g = 30,
u = 0.1,
svl = 60,
m = 10,
psi = 34,
rho_s = 0.24,
elev = 500,
doy = 200,
sun = TRUE,
surface = TRUE,
a_s = 0.9,
a_l = 0.965,
epsilon_s = 0.965,
F_d = 0.8,
F_r = 0.5,
F_a = 0.5,
F_g = 0.5)
Operative Temperature of a Lizard Using Fei et al. (2012)
Description
The function predicts body temperature (C, operative environmental temperature) of a lizard based on Fei et al. (2012).
Usage
Tb_lizard_Fei(T_a, T_g, S, lw, shade, m, Acondfact, Agradfact)
Arguments
T_a |
|
T_g |
|
S |
|
lw |
|
shade |
|
m |
|
Acondfact |
|
Agradfact |
|
Details
Thermal radiative flux is calculated following Fei et al. (2012) based on Bartlett and Gates (1967) and Porter et al. (1973).
Value
numeric
predicted body (operative environmental) temperature (K).
Author(s)
Ofir Levy
References
Bartlett PN, Gates DM (1967).
“The energy budget of a lizard on a tree trunk.”
Ecology, 48, 316-322.
Fei T, Skidmore AK, Venus V, Wang T, Schlerf M, Toxopeus B, van Overjijk S, Bian M, Liu Y (2012).
“A body temperature model for lizards as estimated from the thermal environment.”
Journal of Thermal Biology, 37(1), 56-64.
ISSN 0306-4565, doi: 10.1016/j.jtherbio.2011.10.013, https://www.sciencedirect.com/science/article/pii/S0306456511001513.
Porter WP, Mitchell JW, Bekman A, DeWitt CB (1973).
“Behavioral implications of mechanistic ecology: thermal and behavioral modeling of desert ectotherms and their microenvironments.”
Oecologia, 13, 1-54.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Grashof_number()
,
Nusselt_from_Grashof()
,
Nusselt_from_Reynolds()
,
Nusselt_number()
,
Prandtl_number()
,
Qconduction_animal()
,
Qconduction_substrate()
,
Qconvection()
,
Qemitted_thermal_radiation()
,
Qevaporation()
,
Qmetabolism_from_mass_temp()
,
Qmetabolism_from_mass()
,
Qnet_Gates()
,
Qradiation_absorbed()
,
Qthermal_radiation_absorbed()
,
Reynolds_number()
,
T_sky()
,
Tb_CampbellNorman()
,
Tb_Gates2()
,
Tb_Gates()
,
Tb_butterfly()
,
Tb_grasshopper()
,
Tb_limpetBH()
,
Tb_limpet()
,
Tb_lizard()
,
Tb_mussel()
,
Tb_salamander_humid()
,
Tb_snail()
,
Tbed_mussel()
,
Tsoil()
,
actual_vapor_pressure()
,
boundary_layer_resistance()
,
external_resistance_to_water_vapor_transfer()
,
free_or_forced_convection()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient_simple()
,
heat_transfer_coefficient()
,
saturation_vapor_pressure()
,
saturation_water_vapor_pressure()
Examples
Tb_lizard_Fei(T_a = 20,
T_g = 27,
S = 1300,
lw = 60,
shade = 0.5,
m = 10.5,
Acondfact = 0.1,
Agradfact = 0.3)
Operative Environmental Temperature of a Mussel
Description
The function estimates body temperature (C, operative environmental temperature) of a mussel. The function implements a steady-state model, which assumes unchanging environmental conditions.
Usage
Tb_mussel(l, h, T_a, T_g, S, k_d, u, psi, cl, evap = FALSE, group = "solitary")
Arguments
l |
|
h |
|
T_a |
|
T_g |
|
S |
|
k_d |
|
u |
|
psi |
|
cl |
|
evap |
|
group |
|
Details
Thermal radiative flux is calculated following Helmuth (1998), Helmuth (1999), and Idso and Jackson (1969).
Value
numeric
predicted body (operative environmental) temperature (C).
References
Helmuth B (1999).
“Thermal biology of rocky intertidal mussels: quantifying body temperatures using climatological data.”
Ecology, 80(1), 15-34.
doi: 10.2307/176977.
Helmuth BST (1998).
“Intertidal Mussel Microclimates: Predicting the Body Temperature of a Sessile Invertebrate.”
Ecological Monographs, 68(1), 51–74.
ISSN 00129615, doi: 10.2307/2657143.
Idso SB, Jackson RD (1969).
“Thermal radiation from the atmosphere.”
Journal of Geophysical Research (1896-1977), 74(23), 5397-5403.
doi: 10.1029/JC074i023p05397.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Grashof_number()
,
Nusselt_from_Grashof()
,
Nusselt_from_Reynolds()
,
Nusselt_number()
,
Prandtl_number()
,
Qconduction_animal()
,
Qconduction_substrate()
,
Qconvection()
,
Qemitted_thermal_radiation()
,
Qevaporation()
,
Qmetabolism_from_mass_temp()
,
Qmetabolism_from_mass()
,
Qnet_Gates()
,
Qradiation_absorbed()
,
Qthermal_radiation_absorbed()
,
Reynolds_number()
,
T_sky()
,
Tb_CampbellNorman()
,
Tb_Gates2()
,
Tb_Gates()
,
Tb_butterfly()
,
Tb_grasshopper()
,
Tb_limpetBH()
,
Tb_limpet()
,
Tb_lizard_Fei()
,
Tb_lizard()
,
Tb_salamander_humid()
,
Tb_snail()
,
Tbed_mussel()
,
Tsoil()
,
actual_vapor_pressure()
,
boundary_layer_resistance()
,
external_resistance_to_water_vapor_transfer()
,
free_or_forced_convection()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient_simple()
,
heat_transfer_coefficient()
,
saturation_vapor_pressure()
,
saturation_water_vapor_pressure()
Examples
Tb_mussel(l = 0.1,
h = 0.05,
T_a = 25,
T_g = 30,
S = 500,
k_d = 0.2,
u = 2,
psi = 30,
evap = FALSE,
cl = 0.5,
group = "solitary")
Humid Operative Environmental Temperature of a Salamander
Description
The function estimates the humid body temperature (C, operative environmental temperature) using an adaptation of Campbell and Norman (1998) described in Riddell et al. (2018).
Usage
Tb_salamander_humid(r_i, r_b, D, T_a, elev, e_a, e_s, Qabs, epsilon = 0.96)
Arguments
r_i |
|
r_b |
|
D |
|
T_a |
|
elev |
|
e_a |
|
e_s |
|
Qabs |
|
epsilon |
|
Value
numeric
humid operative temperature (C).
Author(s)
Eric Riddell
References
Campbell GS, Norman JM (1998).
Introduction to environmental biophysics, 2nd ed. edition.
Springer, New York.
ISBN 0387949372.
Riddell EA, Odom JP, Damm JD, Sears MW (2018).
“Plasticity reveals hidden resistance to extinction under climate change in the global hotspot of salamander diversity.”
Science Advances, 4(4).
doi: 10.1126/sciadv.aar5471.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Grashof_number()
,
Nusselt_from_Grashof()
,
Nusselt_from_Reynolds()
,
Nusselt_number()
,
Prandtl_number()
,
Qconduction_animal()
,
Qconduction_substrate()
,
Qconvection()
,
Qemitted_thermal_radiation()
,
Qevaporation()
,
Qmetabolism_from_mass_temp()
,
Qmetabolism_from_mass()
,
Qnet_Gates()
,
Qradiation_absorbed()
,
Qthermal_radiation_absorbed()
,
Reynolds_number()
,
T_sky()
,
Tb_CampbellNorman()
,
Tb_Gates2()
,
Tb_Gates()
,
Tb_butterfly()
,
Tb_grasshopper()
,
Tb_limpetBH()
,
Tb_limpet()
,
Tb_lizard_Fei()
,
Tb_lizard()
,
Tb_mussel()
,
Tb_snail()
,
Tbed_mussel()
,
Tsoil()
,
actual_vapor_pressure()
,
boundary_layer_resistance()
,
external_resistance_to_water_vapor_transfer()
,
free_or_forced_convection()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient_simple()
,
heat_transfer_coefficient()
,
saturation_vapor_pressure()
,
saturation_water_vapor_pressure()
Examples
Tb_salamander_humid(r_i = 4,
r_b = 1,
D = 0.01,
T_a = 20,
elev = 500,
e_a = 2.0,
e_s = 2.5,
Qabs = 400,
epsilon = 0.96)
Operative Environmental Temperature of a Marine Snail
Description
The function estimates body temperature (C, operative environmental temperature) of a marine snail. The function implements a steady-state model, which assumes unchanging environmental conditions and is based on (Iacarella and Helmuth 2012). Body temperature and desiccation constrain the activity of Littoraria irrorata within the Spartina alterniflora canopy. The function was provided by Brian Helmuth and is a simplified version of the published model.
Usage
Tb_snail(temp, l, S, u, CC, WL, WSH)
Arguments
temp |
|
l |
|
S |
|
u |
|
CC |
|
WL |
|
WSH |
|
Details
Thermal radiative flux is calculated following Helmuth (1998), Helmuth (1999), and Idso and Jackson (1969).
Value
numeric
predicted body (operative environmental) temperature (C).
Author(s)
Brian Helmuth et al.
References
Helmuth B (1999).
“Thermal biology of rocky intertidal mussels: quantifying body temperatures using climatological data.”
Ecology, 80(1), 15-34.
doi: 10.2307/176977.
Helmuth BST (1998).
“Intertidal Mussel Microclimates: Predicting the Body Temperature of a Sessile Invertebrate.”
Ecological Monographs, 68(1), 51–74.
ISSN 00129615, doi: 10.2307/2657143.
Iacarella J, Helmuth B (2012).
“Body temperature and desiccation constrain the activity of Littoraria irrorata within the Spartina alterniflora canopy.”
Journal of Thermal Biology, 37(1).
doi: 10.1016/j.jtherbio.2011.10.003.
Idso SB, Jackson RD (1969).
“Thermal radiation from the atmosphere.”
Journal of Geophysical Research (1896-1977), 74(23), 5397-5403.
doi: 10.1029/JC074i023p05397.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Grashof_number()
,
Nusselt_from_Grashof()
,
Nusselt_from_Reynolds()
,
Nusselt_number()
,
Prandtl_number()
,
Qconduction_animal()
,
Qconduction_substrate()
,
Qconvection()
,
Qemitted_thermal_radiation()
,
Qevaporation()
,
Qmetabolism_from_mass_temp()
,
Qmetabolism_from_mass()
,
Qnet_Gates()
,
Qradiation_absorbed()
,
Qthermal_radiation_absorbed()
,
Reynolds_number()
,
T_sky()
,
Tb_CampbellNorman()
,
Tb_Gates2()
,
Tb_Gates()
,
Tb_butterfly()
,
Tb_grasshopper()
,
Tb_limpetBH()
,
Tb_limpet()
,
Tb_lizard_Fei()
,
Tb_lizard()
,
Tb_mussel()
,
Tb_salamander_humid()
,
Tbed_mussel()
,
Tsoil()
,
actual_vapor_pressure()
,
boundary_layer_resistance()
,
external_resistance_to_water_vapor_transfer()
,
free_or_forced_convection()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient_simple()
,
heat_transfer_coefficient()
,
saturation_vapor_pressure()
,
saturation_water_vapor_pressure()
Examples
Tb_snail(temp = 25,
l = 0.012,
S = 800,
u = 1,
CC = 0.5,
WL = 0,
WSH = 10)
Operative Environmental Temperature of a Mussel Bed
Description
The function estimates body temperature of a mussel (C). The function implements a steady-state model, which assumes unchanging environmental conditions. Based on Helmuth (1999).
Usage
Tbed_mussel(l, T_a, S, k_d, u, evap = FALSE, cl = NA)
Arguments
l |
|
T_a |
|
S |
|
k_d |
|
u |
|
evap |
|
cl |
|
Details
Conduction is considered negligible due to a small area of contact.
Thermal radiative flux is calculated following Helmuth (1998), Helmuth (1999), and Idso and Jackson (1969).
Value
numeric
predicted body (operative environmental) temperature (C).
References
Helmuth B (1999).
“Thermal biology of rocky intertidal mussels: quantifying body temperatures using climatological data.”
Ecology, 80(1), 15-34.
doi: 10.2307/176977.
Helmuth BST (1998).
“Intertidal Mussel Microclimates: Predicting the Body Temperature of a Sessile Invertebrate.”
Ecological Monographs, 68(1), 51–74.
ISSN 00129615, doi: 10.2307/2657143.
Idso SB, Jackson RD (1969).
“Thermal radiation from the atmosphere.”
Journal of Geophysical Research (1896-1977), 74(23), 5397-5403.
doi: 10.1029/JC074i023p05397.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Grashof_number()
,
Nusselt_from_Grashof()
,
Nusselt_from_Reynolds()
,
Nusselt_number()
,
Prandtl_number()
,
Qconduction_animal()
,
Qconduction_substrate()
,
Qconvection()
,
Qemitted_thermal_radiation()
,
Qevaporation()
,
Qmetabolism_from_mass_temp()
,
Qmetabolism_from_mass()
,
Qnet_Gates()
,
Qradiation_absorbed()
,
Qthermal_radiation_absorbed()
,
Reynolds_number()
,
T_sky()
,
Tb_CampbellNorman()
,
Tb_Gates2()
,
Tb_Gates()
,
Tb_butterfly()
,
Tb_grasshopper()
,
Tb_limpetBH()
,
Tb_limpet()
,
Tb_lizard_Fei()
,
Tb_lizard()
,
Tb_mussel()
,
Tb_salamander_humid()
,
Tb_snail()
,
Tsoil()
,
actual_vapor_pressure()
,
boundary_layer_resistance()
,
external_resistance_to_water_vapor_transfer()
,
free_or_forced_convection()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient_simple()
,
heat_transfer_coefficient()
,
saturation_vapor_pressure()
,
saturation_water_vapor_pressure()
Examples
Tbed_mussel(l = 0.1,
T_a = 25,
S = 500,
k_d = 0.2,
u = 1,
evap = FALSE)
Approximate Soil Temperature
Description
The function estimates soil temperature (C) at a given depth and hour by approximating diurnal variation as sinusoidal. The function is adapted from Campbell and Norman (1998) and described in Riddell et al. (2018).
Usage
Tsoil(T_g_max, T_g_min, hour, depth)
Arguments
T_g_max |
|
T_g_min |
|
hour |
|
depth |
|
Value
numeric
soil temperature (C).
Author(s)
Eric Riddell
References
Campbell GS, Norman JM (1998).
Introduction to environmental biophysics, 2nd ed. edition.
Springer, New York.
ISBN 0387949372.
Riddell EA, Odom JP, Damm JD, Sears MW (2018).
“Plasticity reveals hidden resistance to extinction under climate change in the global hotspot of salamander diversity.”
Science Advances, 4(4).
doi: 10.1126/sciadv.aar5471.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Grashof_number()
,
Nusselt_from_Grashof()
,
Nusselt_from_Reynolds()
,
Nusselt_number()
,
Prandtl_number()
,
Qconduction_animal()
,
Qconduction_substrate()
,
Qconvection()
,
Qemitted_thermal_radiation()
,
Qevaporation()
,
Qmetabolism_from_mass_temp()
,
Qmetabolism_from_mass()
,
Qnet_Gates()
,
Qradiation_absorbed()
,
Qthermal_radiation_absorbed()
,
Reynolds_number()
,
T_sky()
,
Tb_CampbellNorman()
,
Tb_Gates2()
,
Tb_Gates()
,
Tb_butterfly()
,
Tb_grasshopper()
,
Tb_limpetBH()
,
Tb_limpet()
,
Tb_lizard_Fei()
,
Tb_lizard()
,
Tb_mussel()
,
Tb_salamander_humid()
,
Tb_snail()
,
Tbed_mussel()
,
actual_vapor_pressure()
,
boundary_layer_resistance()
,
external_resistance_to_water_vapor_transfer()
,
free_or_forced_convection()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient_simple()
,
heat_transfer_coefficient()
,
saturation_vapor_pressure()
,
saturation_water_vapor_pressure()
Examples
Tsoil(T_g_max = 30,
T_g_min = 15,
hour = 12,
depth = 5)
Saturation Vapor Pressure
Description
The function calculates saturation vapor pressure for a given air temperature. The program is based on equations from List (1971) and code implementation from NicheMapR (Kearney and Porter 2017; Kearney and Porter 2020).
Usage
VAPPRS(db)
Arguments
db |
|
Value
esat numeric
Saturation vapor pressure (Pa)
References
Kearney MR, Porter WP (2017).
“NicheMapR - an R package for biophysical modelling: the microclimate model.”
Ecography, 40, 664-674.
doi: 10.1111/ecog.02360.
Kearney MR, Porter WP (2020).
“NicheMapR - an R package for biophysical modelling: the ectotherm and Dynamic Energy Budget models.”
Ecography, 43(1), 85-96.
doi: 10.1111/ecog.04680.
List RJ (1971).
“Smithsonian Meteorological Tables.”
Smithsonian Miscellaneous Collections, 114(1), 1-527.
https://repository.si.edu/handle/10088/23746.
Examples
VAPPRS(db = 30)
Properties of Wet Air
Description
The function calculates several properties of humid air described as output variables below. The program is based on equations from List (1971) and code implementation from NicheMapR (Kearney and Porter 2017; Kearney and Porter 2020).
WETAIR must be used in conjunction with VAPPRS
. Input variables are shown below. See Details.
Usage
WETAIR(db, wb = db, rh = 0, dp = 999, bp = 101325)
Arguments
db |
|
wb |
|
rh |
|
dp |
|
bp |
|
Details
The user must supply known values for DB and BP (BP at one standard atmosphere is 101,325 pascals). Values for the remaining variables are determined by whether the user has either (1) psychrometric data (WB or RH), or (2) hygrometric data (DP):
Psychrometric data: If WB is known but not RH, then set RH = -1 and DP = 999. If RH is known but not WB then set WB = 0 and DP = 999
Hygrometric data: If DP is known, set WB = 0 and RH = 0
Value
Named list
with elements
e
:numeric
saturation vapor pressure (Pa)vd
:numeric
vapor density (kg m-3)rw
:numeric
mixing ratio (kg kg-1)tvir
:numeric
virtual temperature (K)tvinc
:numeric
virtual temperature increment (K)denair
:numeric
density of the air (kg m-3)cp
:numeric
specific heat of air at constant pressure (J kg-1 K-1)wtrpot
:numeric
water potential (Pa)rh
:numeric
relative humidity (%)
References
Kearney MR, Porter WP (2017).
“NicheMapR - an R package for biophysical modelling: the microclimate model.”
Ecography, 40, 664-674.
doi: 10.1111/ecog.02360.
Kearney MR, Porter WP (2020).
“NicheMapR - an R package for biophysical modelling: the ectotherm and Dynamic Energy Budget models.”
Ecography, 43(1), 85-96.
doi: 10.1111/ecog.04680.
List RJ (1971).
“Smithsonian Meteorological Tables.”
Smithsonian Miscellaneous Collections, 114(1), 1-527.
https://repository.si.edu/handle/10088/23746.
Examples
WETAIR(db = 30,
wb = 28,
rh = 60,
bp = 100 * 1000)
Actual Vapor Pressure from Dewpoint Temperature
Description
The function calculates actual vapor pressure from dewpoint temperature based on Stull (2000); Riddell et al. (2018).
Usage
actual_vapor_pressure(T_dewpoint)
Arguments
T_dewpoint |
|
Value
numeric
actual vapor pressure (kPa).
Author(s)
Eric Riddell
References
Riddell EA, Odom JP, Damm JD, Sears MW (2018).
“Plasticity reveals hidden resistance to extinction under climate change in the global hotspot of salamander diversity.”
Science Advances, 4(4).
doi: 10.1126/sciadv.aar5471.
Stull RB (2000).
Meteorology for Scientists and Engineers.
Brooks Cole.
ISBN 978-0534372149.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Grashof_number()
,
Nusselt_from_Grashof()
,
Nusselt_from_Reynolds()
,
Nusselt_number()
,
Prandtl_number()
,
Qconduction_animal()
,
Qconduction_substrate()
,
Qconvection()
,
Qemitted_thermal_radiation()
,
Qevaporation()
,
Qmetabolism_from_mass_temp()
,
Qmetabolism_from_mass()
,
Qnet_Gates()
,
Qradiation_absorbed()
,
Qthermal_radiation_absorbed()
,
Reynolds_number()
,
T_sky()
,
Tb_CampbellNorman()
,
Tb_Gates2()
,
Tb_Gates()
,
Tb_butterfly()
,
Tb_grasshopper()
,
Tb_limpetBH()
,
Tb_limpet()
,
Tb_lizard_Fei()
,
Tb_lizard()
,
Tb_mussel()
,
Tb_salamander_humid()
,
Tb_snail()
,
Tbed_mussel()
,
Tsoil()
,
boundary_layer_resistance()
,
external_resistance_to_water_vapor_transfer()
,
free_or_forced_convection()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient_simple()
,
heat_transfer_coefficient()
,
saturation_vapor_pressure()
,
saturation_water_vapor_pressure()
Examples
actual_vapor_pressure(T_dewpoint = 293)
Air Temperature Profile using MICRO Routine
Description
The function estimates air temperature (C) at a specified height (m). Estimates a single, unsegmented temperature profile using the MICRO routine from NicheMapR (Kearney and Porter 2017).
Usage
air_temp_profile(T_r, u_r, zr, z0, z, T_s)
Arguments
T_r |
|
u_r |
|
zr |
|
z0 |
|
z |
|
T_s |
|
Value
numeric
air temperature (C).
References
Kearney MR, Porter WP (2017). “NicheMapR - an R package for biophysical modelling: the microclimate model.” Ecography, 40, 664-674. doi: 10.1111/ecog.02360.
See Also
Other microclimate functions:
air_temp_profile_neutral()
,
air_temp_profile_segment()
,
degree_days()
,
direct_solar_radiation()
,
diurnal_radiation_variation()
,
diurnal_temp_variation_sineexp()
,
diurnal_temp_variation_sinesqrt()
,
diurnal_temp_variation_sine()
,
monthly_solar_radiation()
,
partition_solar_radiation()
,
proportion_diffuse_solar_radiation()
,
solar_radiation()
,
surface_roughness()
,
wind_speed_profile_neutral()
,
wind_speed_profile_segment()
Examples
air_temp_profile(T_r = 20,
u_r = 0.1,
zr = 0.1,
z0 = 0.2,
z = 0.15,
T_s = 25)
Air Temperature at a Specified Height Under Neutral Conditions
Description
The function calculates air temperature (C) at a specified height (m) within a boundary layer near the surface. The velocity profile is the neutral profile described by Sellers (1965). Function is included as equations (2) and (3) of Porter et al. (1973).
Usage
air_temp_profile_neutral(T_r, zr, z0, z, T_s)
Arguments
T_r |
|
zr |
|
z0 |
|
z |
|
T_s |
|
Value
numeric
air temperature (C).
References
Porter WP, Mitchell JW, Bekman A, DeWitt CB (1973).
“Behavioral implications of mechanistic ecology: thermal and behavioral modeling of desert ectotherms and their microenvironments.”
Oecologia, 13, 1-54.
Sellers WD (1965).
Physical climatology.
University of Chicago Press, Chicago, IL, USA.
See Also
Other microclimate functions:
air_temp_profile_segment()
,
air_temp_profile()
,
degree_days()
,
direct_solar_radiation()
,
diurnal_radiation_variation()
,
diurnal_temp_variation_sineexp()
,
diurnal_temp_variation_sinesqrt()
,
diurnal_temp_variation_sine()
,
monthly_solar_radiation()
,
partition_solar_radiation()
,
proportion_diffuse_solar_radiation()
,
solar_radiation()
,
surface_roughness()
,
wind_speed_profile_neutral()
,
wind_speed_profile_segment()
Examples
air_temp_profile_neutral(T_r = 20,
zr = 0.1,
z0 = 0.2,
z = 0.15,
T_s = 25)
Air Temperature at a Specified Height
Description
The function calculates air temperature (C) at a specified height (m). Estimates a three segment velocity and temperature profile based on user-specified, experimentally determined values for 3 roughness heights and reference heights. Multiple heights are appropriate in heterogenous areas with, for example, a meadow, bushes, and rocks. Implements the MICROSEGMT routine from NicheMapR as described in Kearney and Porter (2017).
Usage
air_temp_profile_segment(T_r, u_r, zr, z0, z, T_s)
Arguments
T_r |
|
u_r |
|
zr |
|
z0 |
|
z |
|
T_s |
|
Value
numeric
air temperature (C).
References
Kearney MR, Porter WP (2017). “NicheMapR - an R package for biophysical modelling: the microclimate model.” Ecography, 40, 664-674. doi: 10.1111/ecog.02360.
See Also
Other microclimate functions:
air_temp_profile_neutral()
,
air_temp_profile()
,
degree_days()
,
direct_solar_radiation()
,
diurnal_radiation_variation()
,
diurnal_temp_variation_sineexp()
,
diurnal_temp_variation_sinesqrt()
,
diurnal_temp_variation_sine()
,
monthly_solar_radiation()
,
partition_solar_radiation()
,
proportion_diffuse_solar_radiation()
,
solar_radiation()
,
surface_roughness()
,
wind_speed_profile_neutral()
,
wind_speed_profile_segment()
Examples
air_temp_profile_segment(T_r = c(25, 22, 20),
u_r = c(0.01, 0.025, 0.05),
zr = c(0.05, 0.25, 0.5),
z0 = c(0.01, 0.15, 0.2),
z = 0.3,
T_s = 27)
Air Pressure from Elevation
Description
The function estimates air pressure (kPa) as a function of elevation (Engineering ToolBox 2003).
Usage
airpressure_from_elev(elev)
Arguments
elev |
|
Value
numeric
air pressure (kPa).
References
Engineering ToolBox (2003). Atmospheric Pressure vs. Elevation above Sea Level. https://www.engineeringtoolbox.com/air-altitude-pressure-d_462.html.
See Also
Other utility functions:
azimuth_angle()
,
day_of_year()
,
daylength()
,
dec_angle()
,
solar_noon()
,
temperature conversions
,
zenith_angle()
Examples
airpressure_from_elev(elev = 1500)
Convert Angles Between Radians and Degrees
Description
The function converts angles in radians to degrees or degrees to radians.
Usage
radians_to_degrees(rad)
degrees_to_radians(deg)
Arguments
rad |
|
deg |
|
Value
numeric
angle (degrees or radians).
Examples
radians_to_degrees(0.831)
degrees_to_radians(47.608)
Azimuth Angle
Description
The function calculates the azimuth angle, the angle (degrees) from which the sunlight is coming measured from true north or south measured in the horizontal plane. The azimuth angle is measured with respect to due south, increasing in the counter clockwise direction so 90 degrees is east (Campbell and Norman 1998).
Usage
azimuth_angle(doy, lat, lon, hour, offset = NA)
Arguments
doy |
|
lat |
|
lon |
|
hour |
|
offset |
|
Value
numeric
azimuth angle (degrees).
References
Campbell GS, Norman JM (1998). Introduction to environmental biophysics, 2nd ed. edition. Springer, New York. ISBN 0387949372.
See Also
Other utility functions:
airpressure_from_elev()
,
day_of_year()
,
daylength()
,
dec_angle()
,
solar_noon()
,
temperature conversions
,
zenith_angle()
Examples
azimuth_angle(doy = 112,
lat = 47.61,
lon = -122.33,
hour = 12,
offset = -8)
Boundary Layer Resistance
Description
The function estimates boundary layer resistance under free convection based on the function in Riddell et al. (2018).
Usage
boundary_layer_resistance(T_a, e_s, e_a, elev, D, u = NA)
Arguments
T_a |
|
e_s |
|
e_a |
|
elev |
|
D |
|
u |
|
Value
numeric
boundary layer resistance (s cm-1).
Author(s)
Eric Riddell
References
Riddell EA, Odom JP, Damm JD, Sears MW (2018). “Plasticity reveals hidden resistance to extinction under climate change in the global hotspot of salamander diversity.” Science Advances, 4(4). doi: 10.1126/sciadv.aar5471.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Grashof_number()
,
Nusselt_from_Grashof()
,
Nusselt_from_Reynolds()
,
Nusselt_number()
,
Prandtl_number()
,
Qconduction_animal()
,
Qconduction_substrate()
,
Qconvection()
,
Qemitted_thermal_radiation()
,
Qevaporation()
,
Qmetabolism_from_mass_temp()
,
Qmetabolism_from_mass()
,
Qnet_Gates()
,
Qradiation_absorbed()
,
Qthermal_radiation_absorbed()
,
Reynolds_number()
,
T_sky()
,
Tb_CampbellNorman()
,
Tb_Gates2()
,
Tb_Gates()
,
Tb_butterfly()
,
Tb_grasshopper()
,
Tb_limpetBH()
,
Tb_limpet()
,
Tb_lizard_Fei()
,
Tb_lizard()
,
Tb_mussel()
,
Tb_salamander_humid()
,
Tb_snail()
,
Tbed_mussel()
,
Tsoil()
,
actual_vapor_pressure()
,
external_resistance_to_water_vapor_transfer()
,
free_or_forced_convection()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient_simple()
,
heat_transfer_coefficient()
,
saturation_vapor_pressure()
,
saturation_water_vapor_pressure()
Examples
boundary_layer_resistance(T_a = 293,
e_s = 2.5,
e_a = 2.0,
elev = 500,
D = 0.007,
u = 2)
General Use Constants
Description
Basic functions for numerical constants for conversions.
Usage
specific_heat_h2o(units = "J_kg-1_K-1")
latent_heat_vaporization_h2o(units = "J_kg-1")
stefan_boltzmann_constant(units = "W_m-2_K-4")
von_karman_constant(units = "")
Arguments
units |
|
Value
numeric
values in units
.
Examples
specific_heat_h2o()
latent_heat_vaporization_h2o()
stefan_boltzmann_constant()
Calendar Day from Date
Description
The function converts a date (day, month, year) to Calendar Day (day of year).
Usage
day_of_year(day, format = "%Y-%m-%d")
Arguments
day |
|
format |
|
Value
numeric
Julian day number, 1-366 (e.g. 1 for January 1st).
See Also
Other utility functions:
airpressure_from_elev()
,
azimuth_angle()
,
daylength()
,
dec_angle()
,
solar_noon()
,
temperature conversions
,
zenith_angle()
Examples
day_of_year(day = "2017-04-22",
format = "%Y-%m-%d")
day_of_year(day = "2017-04-22")
day_of_year(day = "04/22/2017",
format = "%m/%d/%Y")
Day Length
Description
The function calculates daylength in hours as a function of latitude and day of year. Uses the CMB model (Campbell and Norman 1998).
Usage
daylength(lat, doy)
Arguments
lat |
|
doy |
|
Value
numeric
day length (hours).
References
Campbell GS, Norman JM (1998). Introduction to environmental biophysics, 2nd ed. edition. Springer, New York. ISBN 0387949372.
See Also
Other utility functions:
airpressure_from_elev()
,
azimuth_angle()
,
day_of_year()
,
dec_angle()
,
solar_noon()
,
temperature conversions
,
zenith_angle()
Examples
daylength(lat = 47.61,
doy = 112)
Solar Declination in Radians
Description
The function calculates solar declination, which is the angular distance of the sun north or south of the earth’s equator, based on the day of year (Campbell and Norman 1998).
Usage
dec_angle(doy)
Arguments
doy |
|
Value
numeric
declination angle (radians).
References
Campbell GS, Norman JM (1998). Introduction to environmental biophysics, 2nd ed. edition. Springer, New York. ISBN 0387949372.
See Also
Other utility functions:
airpressure_from_elev()
,
azimuth_angle()
,
day_of_year()
,
daylength()
,
solar_noon()
,
temperature conversions
,
zenith_angle()
Examples
dec_angle(doy = 112)
dec_angle(doy = 360)
Degree Days
Description
The function calculates degree days using the following approximations: single or double sine wave, single or double triangulation (University of California Integrated Pest Management Program 2016). Double approximation methods assume symmetry, such that a day's thermal minimum is equal to that of the previous day. Double sine wave approximation of degree days from Allen (1976).
Usage
degree_days(T_min, T_max, LDT = NA, UDT = NA, method = "single.sine")
Arguments
T_min |
|
T_max |
|
LDT |
|
UDT |
|
method |
|
Value
numeric
degree days (C).
References
Allen JC (1976).
“A Modified Sine Wave Method for Calculating Degree Days.”
Environmental Entomology, 5(3), 388-396.
doi: 10.1093/ee/5.3.388.
University of California Integrated Pest Management Program (2016).
Degree Days: Methods.
https://ipm.ucanr.edu/WEATHER/ddfigindex.html.
See Also
Other microclimate functions:
air_temp_profile_neutral()
,
air_temp_profile_segment()
,
air_temp_profile()
,
direct_solar_radiation()
,
diurnal_radiation_variation()
,
diurnal_temp_variation_sineexp()
,
diurnal_temp_variation_sinesqrt()
,
diurnal_temp_variation_sine()
,
monthly_solar_radiation()
,
partition_solar_radiation()
,
proportion_diffuse_solar_radiation()
,
solar_radiation()
,
surface_roughness()
,
wind_speed_profile_neutral()
,
wind_speed_profile_segment()
Examples
degree_days(T_min = 7,
T_max = 14,
LDT = 12,
UDT = 33,
method = "single.sine")
degree_days(T_min = 7,
T_max = 14,
LDT = 12,
UDT = 33,
method = "single.triangulation")
Direct Solar Radiation
Description
The function estimates direct solar radiation (W/m2) based on latitude, day of year, elevation, and time. The function uses two methods (McCullough and Porter 1971; Campbell and Norman 1998) compiled in Tracy et al. (1983).
Usage
direct_solar_radiation(lat, doy, elev, t, t0, method = "Campbell 1977")
Arguments
lat |
|
doy |
|
elev |
|
t |
|
t0 |
|
method |
|
Value
numeric
direct solar radiation (W/m2).
References
Campbell GS, Norman JM (1998).
Introduction to environmental biophysics, 2nd ed. edition.
Springer, New York.
ISBN 0387949372.
McCullough EC, Porter WP (1971).
“Computing Clear Day Solar Radiation Spectra for the Terrestrial Ecological Environment.”
Ecology, 52(6), 1008-1015.
doi: 10.2307/1933806.
Tracy CR, Hammond KA, Lechleitner RA, II WJS, Thompson DB, Whicker AD, Williamson SC (1983).
“Estimating clear-day solar radiation: an evaluation of three models.”
Journal of Thermal Biology, 8(3), 247-251.
doi: 10.1016/0306-4565(83)90003-7.
See Also
Other microclimate functions:
air_temp_profile_neutral()
,
air_temp_profile_segment()
,
air_temp_profile()
,
degree_days()
,
diurnal_radiation_variation()
,
diurnal_temp_variation_sineexp()
,
diurnal_temp_variation_sinesqrt()
,
diurnal_temp_variation_sine()
,
monthly_solar_radiation()
,
partition_solar_radiation()
,
proportion_diffuse_solar_radiation()
,
solar_radiation()
,
surface_roughness()
,
wind_speed_profile_neutral()
,
wind_speed_profile_segment()
Examples
direct_solar_radiation(lat = 47.61,
doy = 112,
elev = 1500,
t = 9,
t0 = 12,
method = "Campbell 1977")
Hourly Solar Radiation
Description
The function estimates hourly solar radiation (W m-2 hr-1) as a function of daily global solar radiation (W m-2 d-1). Based on Tham et al. (2010) and Tham et al. (2011).
Usage
diurnal_radiation_variation(doy, S, hour, lon, lat)
Arguments
doy |
|
S |
|
hour |
|
lon |
|
lat |
|
Value
numeric
hourly solar radiation (W m-2).
References
Tham Y, Muneer T, Davison B (2010).
“Estimation of hourly averaged solar irradiation: evaluation of models.”
Building Services Engingeering Research Technology, 31(1).
doi: 10.1177/0143624409350547.
Tham Y, Muneer T, Davison B (2011).
“Prediction of hourly solar radiation on horizontal and inclined surfaces for Muscat/Oman.”
The Journal of Engineering Research, 8(2), 19-31.
doi: 10.24200/tjer.vol8iss2pp19-31.
See Also
Other microclimate functions:
air_temp_profile_neutral()
,
air_temp_profile_segment()
,
air_temp_profile()
,
degree_days()
,
direct_solar_radiation()
,
diurnal_temp_variation_sineexp()
,
diurnal_temp_variation_sinesqrt()
,
diurnal_temp_variation_sine()
,
monthly_solar_radiation()
,
partition_solar_radiation()
,
proportion_diffuse_solar_radiation()
,
solar_radiation()
,
surface_roughness()
,
wind_speed_profile_neutral()
,
wind_speed_profile_segment()
Examples
diurnal_radiation_variation(doy = 112,
S = 8000,
hour = 12,
lon = -122.33,
lat = 47.61)
Hourly Temperature Variation assuming a Sine Interpolation
Description
The function estimates temperature for a specified hour using the sine interpolation in Campbell and Norman (1998).
Usage
diurnal_temp_variation_sine(T_max, T_min, t)
Arguments
T_max , T_min |
|
t |
|
Value
numeric
temperature (C) at a specified hour.
References
Campbell GS, Norman JM (1998). Introduction to environmental biophysics, 2nd ed. edition. Springer, New York. ISBN 0387949372.
See Also
Other microclimate functions:
air_temp_profile_neutral()
,
air_temp_profile_segment()
,
air_temp_profile()
,
degree_days()
,
direct_solar_radiation()
,
diurnal_radiation_variation()
,
diurnal_temp_variation_sineexp()
,
diurnal_temp_variation_sinesqrt()
,
monthly_solar_radiation()
,
partition_solar_radiation()
,
proportion_diffuse_solar_radiation()
,
solar_radiation()
,
surface_roughness()
,
wind_speed_profile_neutral()
,
wind_speed_profile_segment()
Examples
diurnal_temp_variation_sine(T_max = 30,
T_min = 10,
t = 11)
Hourly Temperature Variation assuming Sine and Exponential Components
Description
The function estimates temperature across hours using a diurnal temperature variation function incorporating sine and exponential components (Parton and Logan 1981).
Usage
diurnal_temp_variation_sineexp(
T_max,
T_min,
t,
t_r,
t_s,
alpha = 2.59,
beta = 1.55,
gamma = 2.2
)
Arguments
T_max , T_min |
|
t |
|
t_r , t_s |
|
alpha |
|
beta |
|
gamma |
|
Details
Default alpha
, beta
, and gamma
values are the average of 5 North Carolina sites (Wann et al. 1985).
Other alpha
, beta
, and gamma
parameterizations include values for Denver, Colorado from Parton and Logan (1981):
150 cm air temperature:
alpha
= 1.86,beta
= 2.20,gamma
= -0.1710 cm air temperature:
alpha
= 1.52,beta
= 2.00,gamma
= -0.18soil surface temperature:
alpha
= 0.50,beta
= 1.81,gamma
= 0.4910cm soil temperature:
alpha
= 0.45,beta
= 2.28,gamma
= 1.83
Value
numeric
temperature (C) at a specified hour.
References
Parton WJ, Logan JA (1981).
“A model for diurnal variation in soil and air temperature.”
Agricultural Meteorology, 23, 205-216.
doi: 10.1016/0002-1571(81)90105-9, https://www.sciencedirect.com/science/article/abs/pii/0002157181901059.
Wann M, Yen D, Gold HJ (1985).
“Evaluation and calibration of three models for daily cycle of air temperature.”
Agricultural and Forest Meteorology, 34, 121-128.
https://doi.org/10.1016/0168-1923(85)90013-9.
See Also
Other microclimate functions:
air_temp_profile_neutral()
,
air_temp_profile_segment()
,
air_temp_profile()
,
degree_days()
,
direct_solar_radiation()
,
diurnal_radiation_variation()
,
diurnal_temp_variation_sinesqrt()
,
diurnal_temp_variation_sine()
,
monthly_solar_radiation()
,
partition_solar_radiation()
,
proportion_diffuse_solar_radiation()
,
solar_radiation()
,
surface_roughness()
,
wind_speed_profile_neutral()
,
wind_speed_profile_segment()
Examples
diurnal_temp_variation_sineexp(T_max = 30,
T_min = 10,
t = 11,
t_r = 6,
t_s = 18,
alpha = 2.59,
beta = 1.55,
gamma = 2.2)
Hourly Temperature Variation using Sine and Square Root Functions
Description
The function estimates temperature for a specified hour using sine and square root functions (Cesaraccio et al. 2001).
Usage
diurnal_temp_variation_sinesqrt(t, t_r, t_s, T_max, T_min, T_minp)
Arguments
t |
|
t_r , t_s |
|
T_max , T_min |
|
T_minp |
|
Value
numeric
temperature (C) at a specified hour.
References
Cesaraccio C, Spano D, Duce P, Snyder RL (2001). “An improved model for determining degree-day values from daily temperature data.” International Journal of Biometeorology, 45, 161-169. doi: 10.1007/s004840100104.
See Also
Other microclimate functions:
air_temp_profile_neutral()
,
air_temp_profile_segment()
,
air_temp_profile()
,
degree_days()
,
direct_solar_radiation()
,
diurnal_radiation_variation()
,
diurnal_temp_variation_sineexp()
,
diurnal_temp_variation_sine()
,
monthly_solar_radiation()
,
partition_solar_radiation()
,
proportion_diffuse_solar_radiation()
,
solar_radiation()
,
surface_roughness()
,
wind_speed_profile_neutral()
,
wind_speed_profile_segment()
Examples
diurnal_temp_variation_sinesqrt(t = 8,
t_r = 6,
t_s = 18,
T_max = 30,
T_min = 10,
T_minp = 12)
External Resistance to Water Vapor Transfer
Description
The function estimate external resistance to water vapor transfer using the Lewis rule relating heat and mass transport (Spotila et al. 1992)
Usage
external_resistance_to_water_vapor_transfer(H, ecp = 12000)
Arguments
H |
|
ecp |
|
Value
numeric
external resistance to water vapor transfer (s m-1).
References
Spotila JR, Feder ME, Burggren WW (1992). “Biophysics of Heat and Mass Transfer.” Environmental Physiology of the Amphibians. https://press.uchicago.edu/ucp/books/book/chicago/E/bo3636401.html.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Grashof_number()
,
Nusselt_from_Grashof()
,
Nusselt_from_Reynolds()
,
Nusselt_number()
,
Prandtl_number()
,
Qconduction_animal()
,
Qconduction_substrate()
,
Qconvection()
,
Qemitted_thermal_radiation()
,
Qevaporation()
,
Qmetabolism_from_mass_temp()
,
Qmetabolism_from_mass()
,
Qnet_Gates()
,
Qradiation_absorbed()
,
Qthermal_radiation_absorbed()
,
Reynolds_number()
,
T_sky()
,
Tb_CampbellNorman()
,
Tb_Gates2()
,
Tb_Gates()
,
Tb_butterfly()
,
Tb_grasshopper()
,
Tb_limpetBH()
,
Tb_limpet()
,
Tb_lizard_Fei()
,
Tb_lizard()
,
Tb_mussel()
,
Tb_salamander_humid()
,
Tb_snail()
,
Tbed_mussel()
,
Tsoil()
,
actual_vapor_pressure()
,
boundary_layer_resistance()
,
free_or_forced_convection()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient_simple()
,
heat_transfer_coefficient()
,
saturation_vapor_pressure()
,
saturation_water_vapor_pressure()
Examples
external_resistance_to_water_vapor_transfer(H = 20)
Determine if Convection is Free or Forced
Description
The function compares the Grashof and Reynolds numbers to determine whether convection is free or forced (Gates 1980).
Usage
free_or_forced_convection(Gr, Re)
Arguments
Gr |
|
Re |
|
Value
character
"free"
, "forced"
, or "intermediate"
.
References
Gates DM (1980). Biophysical Ecology. Springer-Verlag, New York, NY, USA.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Grashof_number()
,
Nusselt_from_Grashof()
,
Nusselt_from_Reynolds()
,
Nusselt_number()
,
Prandtl_number()
,
Qconduction_animal()
,
Qconduction_substrate()
,
Qconvection()
,
Qemitted_thermal_radiation()
,
Qevaporation()
,
Qmetabolism_from_mass_temp()
,
Qmetabolism_from_mass()
,
Qnet_Gates()
,
Qradiation_absorbed()
,
Qthermal_radiation_absorbed()
,
Reynolds_number()
,
T_sky()
,
Tb_CampbellNorman()
,
Tb_Gates2()
,
Tb_Gates()
,
Tb_butterfly()
,
Tb_grasshopper()
,
Tb_limpetBH()
,
Tb_limpet()
,
Tb_lizard_Fei()
,
Tb_lizard()
,
Tb_mussel()
,
Tb_salamander_humid()
,
Tb_snail()
,
Tbed_mussel()
,
Tsoil()
,
actual_vapor_pressure()
,
boundary_layer_resistance()
,
external_resistance_to_water_vapor_transfer()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient_simple()
,
heat_transfer_coefficient()
,
saturation_vapor_pressure()
,
saturation_water_vapor_pressure()
Examples
free_or_forced_convection(Gr = 100,
Re = 5)
Estimate the Heat Transfer Coefficient Empirically
Description
The function estimates the heat transfer coefficient for various taxa based on empirical measurements (Mitchell 1976).
Usage
heat_transfer_coefficient(u, D, K, nu, taxon = "cylinder")
Arguments
u |
|
D |
|
K |
|
nu |
|
taxon |
|
Value
numeric
heat transfer coefficient, H_L
(W K-1 m-2).
References
Mitchell JW (1976). “Heat transfer from spheres and other animal forms.” Biophysical Journal, 16(6), 561-569. ISSN 0006-3495, doi: 10.1016/S0006-3495(76)85711-6.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Grashof_number()
,
Nusselt_from_Grashof()
,
Nusselt_from_Reynolds()
,
Nusselt_number()
,
Prandtl_number()
,
Qconduction_animal()
,
Qconduction_substrate()
,
Qconvection()
,
Qemitted_thermal_radiation()
,
Qevaporation()
,
Qmetabolism_from_mass_temp()
,
Qmetabolism_from_mass()
,
Qnet_Gates()
,
Qradiation_absorbed()
,
Qthermal_radiation_absorbed()
,
Reynolds_number()
,
T_sky()
,
Tb_CampbellNorman()
,
Tb_Gates2()
,
Tb_Gates()
,
Tb_butterfly()
,
Tb_grasshopper()
,
Tb_limpetBH()
,
Tb_limpet()
,
Tb_lizard_Fei()
,
Tb_lizard()
,
Tb_mussel()
,
Tb_salamander_humid()
,
Tb_snail()
,
Tbed_mussel()
,
Tsoil()
,
actual_vapor_pressure()
,
boundary_layer_resistance()
,
external_resistance_to_water_vapor_transfer()
,
free_or_forced_convection()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient_simple()
,
saturation_vapor_pressure()
,
saturation_water_vapor_pressure()
Examples
heat_transfer_coefficient(u = 0.5,
D = 0.05,
K = 25.7 * 10^(-3),
nu = 15.3 * 10^(-6),
taxon = "cylinder")
Estimate the Heat Transfer Coefficient Using a Spherical Approximation
Description
The function estimates the heat transfer coefficient for various taxa. Approximates forced convective heat transfer for animal shapes using the convective relationship for a sphere (Mitchell 1976).
Usage
heat_transfer_coefficient_approximation(u, D, K, nu, taxon = "sphere")
Arguments
u |
|
D |
|
K |
|
nu |
|
taxon |
|
Value
numeric
heat transfer coefficient, H_L
(W m-2 K-1).
References
Mitchell JW (1976). “Heat transfer from spheres and other animal forms.” Biophysical Journal, 16(6), 561-569. ISSN 0006-3495, doi: 10.1016/S0006-3495(76)85711-6.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Grashof_number()
,
Nusselt_from_Grashof()
,
Nusselt_from_Reynolds()
,
Nusselt_number()
,
Prandtl_number()
,
Qconduction_animal()
,
Qconduction_substrate()
,
Qconvection()
,
Qemitted_thermal_radiation()
,
Qevaporation()
,
Qmetabolism_from_mass_temp()
,
Qmetabolism_from_mass()
,
Qnet_Gates()
,
Qradiation_absorbed()
,
Qthermal_radiation_absorbed()
,
Reynolds_number()
,
T_sky()
,
Tb_CampbellNorman()
,
Tb_Gates2()
,
Tb_Gates()
,
Tb_butterfly()
,
Tb_grasshopper()
,
Tb_limpetBH()
,
Tb_limpet()
,
Tb_lizard_Fei()
,
Tb_lizard()
,
Tb_mussel()
,
Tb_salamander_humid()
,
Tb_snail()
,
Tbed_mussel()
,
Tsoil()
,
actual_vapor_pressure()
,
boundary_layer_resistance()
,
external_resistance_to_water_vapor_transfer()
,
free_or_forced_convection()
,
heat_transfer_coefficient_simple()
,
heat_transfer_coefficient()
,
saturation_vapor_pressure()
,
saturation_water_vapor_pressure()
Examples
heat_transfer_coefficient_approximation(u = 3,
D = 0.05,
K = 25.7 * 10^(-3),
nu = 15.3 * 10^(-6),
taxon = "sphere")
Estimate the Heat Transfer Coefficient using Simple Relationships
Description
The function estimates the heat transfer coefficient (Mitchell 1976) using either the relationship in Spotila et al. (1992) or that in Gates (1980).
Usage
heat_transfer_coefficient_simple(u, D, type)
Arguments
u |
|
D |
|
type |
|
Value
numeric
heat transfer coefficient, H_L (W m-2 K-1).
References
Gates DM (1980).
Biophysical Ecology.
Springer-Verlag, New York, NY, USA.
Mitchell JW (1976).
“Heat transfer from spheres and other animal forms.”
Biophysical Journal, 16(6), 561-569.
ISSN 0006-3495, doi: 10.1016/S0006-3495(76)85711-6.
Spotila JR, Feder ME, Burggren WW (1992).
“Biophysics of Heat and Mass Transfer.”
Environmental Physiology of the Amphibians.
https://press.uchicago.edu/ucp/books/book/chicago/E/bo3636401.html.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Grashof_number()
,
Nusselt_from_Grashof()
,
Nusselt_from_Reynolds()
,
Nusselt_number()
,
Prandtl_number()
,
Qconduction_animal()
,
Qconduction_substrate()
,
Qconvection()
,
Qemitted_thermal_radiation()
,
Qevaporation()
,
Qmetabolism_from_mass_temp()
,
Qmetabolism_from_mass()
,
Qnet_Gates()
,
Qradiation_absorbed()
,
Qthermal_radiation_absorbed()
,
Reynolds_number()
,
T_sky()
,
Tb_CampbellNorman()
,
Tb_Gates2()
,
Tb_Gates()
,
Tb_butterfly()
,
Tb_grasshopper()
,
Tb_limpetBH()
,
Tb_limpet()
,
Tb_lizard_Fei()
,
Tb_lizard()
,
Tb_mussel()
,
Tb_salamander_humid()
,
Tb_snail()
,
Tbed_mussel()
,
Tsoil()
,
actual_vapor_pressure()
,
boundary_layer_resistance()
,
external_resistance_to_water_vapor_transfer()
,
free_or_forced_convection()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient()
,
saturation_vapor_pressure()
,
saturation_water_vapor_pressure()
Examples
heat_transfer_coefficient_simple(u = 0.5,
D = 0.05,
type = "Gates")
Organism Mass from Length
Description
The function estimates mass (g) from length (m) for a variety of taxa.
Usage
mass_from_length(l, taxon)
Arguments
l |
|
taxon |
|
Details
All models follow (m = a lb) with mass in grams and length in meters.
Lizards: Meiri (2010):
a = 16368.17
b = 3.022
Salamanders: Pough (1980):
a = 13654.4
b = 2.94
Frogs: Pough (1980):
a = 181197.1
b = 3.24
Snakes: Pough (1980):
a = 723.6756
b = 3.02
Turtles: Pough (1980):
a = 93554.48
b = 2.69
Insects: Sample et al. (1993):
a = 806.0827
b = 2.494
Value
numeric
mass (g).
References
Meiri S (2010).
“Length - weight allometries in lizards.”
Journal of Zoology, 281(3), 218-226.
doi: 10.1111/j.1469-7998.2010.00696.x.
Pough FH (1980).
“The Advantages of Ectothermy for Tetrapods.”
The American Naturalist, 115(1), 92–112.
ISSN 00030147, 15375323.
Sample BE, Cooper RJ, Greer RD, Whitmore RC (1993).
“Estimation of Insect Biomass by Length and Width.”
The American Midland Naturalist, 129(2), 234–240.
ISSN 00030031, 19384238, doi: 10.2307/2426503.
See Also
Other allometric functions:
proportion_silhouette_area_shapes()
,
proportion_silhouette_area()
,
surface_area_from_length()
,
surface_area_from_mass()
,
surface_area_from_volume()
,
volume_from_length()
Examples
mass_from_length(l = 0.04,
taxon = "insect")
mass_from_length(l = 0.04,
taxon = "lizard")
mass_from_length(l = 0.04,
taxon = "salamander")
mass_from_length(l = 0.04,
taxon = "frog")
mass_from_length(l = 0.04,
taxon = "snake")
mass_from_length(l = 0.04,
taxon = "turtle")
Average Monthly Solar Radiation
Description
The function estimates average monthly solar radiation (W m-2 d-1) using basic topographic and climatic information as input. Cloudiness is stochastically modeled, so output will vary between functional calls. Based on Nikolov and Zeller (1992).
Usage
monthly_solar_radiation(lat, lon, doy, elev, T_a, hp, P)
Arguments
lat |
|
lon |
|
doy |
|
elev |
|
T_a |
|
hp |
|
P |
|
Value
numeric
average monthly solar radiation (W m-2).
References
Nikolov NT, Zeller K (1992). “A solar radiation algorithm for ecosystem dynamic models.” Ecological Modelling, 61(3-4), 149-168. doi: 10.24200/tjer.vol8iss2pp19-31.
See Also
Other microclimate functions:
air_temp_profile_neutral()
,
air_temp_profile_segment()
,
air_temp_profile()
,
degree_days()
,
direct_solar_radiation()
,
diurnal_radiation_variation()
,
diurnal_temp_variation_sineexp()
,
diurnal_temp_variation_sinesqrt()
,
diurnal_temp_variation_sine()
,
partition_solar_radiation()
,
proportion_diffuse_solar_radiation()
,
solar_radiation()
,
surface_roughness()
,
wind_speed_profile_neutral()
,
wind_speed_profile_segment()
Examples
monthly_solar_radiation(lat = 47.61,
lon = -122.33,
doy = 112,
elev = 1500,
T_a = 15,
hp = 50,
P = 50)
Diffuse Fraction for Partitioning Solar Radiation
Description
The function partitions solar radiation (W m-2) into direct and diffuse components by estimating the diffuse fraction (k_d). The function uses the models presented in Wong and Chow (2001).
Usage
partition_solar_radiation(method, kt, lat = NA, sol.elev = NA)
Arguments
method |
|
kt |
|
lat |
|
sol.elev |
|
Value
numeric
diffuse fraction.
References
Wong LT, Chow WK (2001). “Solar radiation model.” Applied Energy, 69(3), 191-224. ISSN 0306-2619, doi: 10.1016/S0306-2619(01)00012-5, https://www.sciencedirect.com/science/article/pii/S0306261901000125.
See Also
Other microclimate functions:
air_temp_profile_neutral()
,
air_temp_profile_segment()
,
air_temp_profile()
,
degree_days()
,
direct_solar_radiation()
,
diurnal_radiation_variation()
,
diurnal_temp_variation_sineexp()
,
diurnal_temp_variation_sinesqrt()
,
diurnal_temp_variation_sine()
,
monthly_solar_radiation()
,
proportion_diffuse_solar_radiation()
,
solar_radiation()
,
surface_roughness()
,
wind_speed_profile_neutral()
,
wind_speed_profile_segment()
Examples
partition_solar_radiation(method = "Erbs",
kt = 0.5,
lat = 40,
sol.elev = 60)
Ratio of Diffuse to Direct Solar Radiation
Description
The function estimates the ratio of diffuse to direct solar radiation based on the approximation of the SOLRAD model (McCullough and Porter 1971) described in Tracy et al. (1983).
Usage
proportion_diffuse_solar_radiation(psi, p_a, rho)
Arguments
psi |
|
p_a |
|
rho |
|
Value
numeric
diffuse fraction.
References
McCullough EC, Porter WP (1971).
“Computing Clear Day Solar Radiation Spectra for the Terrestrial Ecological Environment.”
Ecology, 52(6), 1008-1015.
doi: 10.2307/1933806.
Tracy CR, Hammond KA, Lechleitner RA, II WJS, Thompson DB, Whicker AD, Williamson SC (1983).
“Estimating clear-day solar radiation: an evaluation of three models.”
Journal of Thermal Biology, 8(3), 247-251.
doi: 10.1016/0306-4565(83)90003-7.
See Also
Other microclimate functions:
air_temp_profile_neutral()
,
air_temp_profile_segment()
,
air_temp_profile()
,
degree_days()
,
direct_solar_radiation()
,
diurnal_radiation_variation()
,
diurnal_temp_variation_sineexp()
,
diurnal_temp_variation_sinesqrt()
,
diurnal_temp_variation_sine()
,
monthly_solar_radiation()
,
partition_solar_radiation()
,
solar_radiation()
,
surface_roughness()
,
wind_speed_profile_neutral()
,
wind_speed_profile_segment()
Examples
proportion_diffuse_solar_radiation(psi = 60,
p_a = 86.1,
rho = 0.25)
Organism Silhouette Area
Description
The function estimates the projected (silhouette) area as a portion of the surface area of the organism as a function of zenith angle. The function is useful for estimating absorbed solar radiation.
Usage
proportion_silhouette_area(psi, taxon, raz = 0, posture = "prostrate")
Arguments
psi |
|
taxon |
|
raz |
|
posture |
|
Details
Relationships come from
Lizards: Muth (1977)
Frogs: Tracy (1976)
Grasshoppers: Anderson et al. (1979)
Value
numeric
silhouette area as a proportion.
References
Anderson RV, Tracy CR, Abramsky Z (1979).
“Habitat Selection in Two Species of Short-Horned Grasshoppers. The Role of Thermal and Hydric Stresses.”
Oecologia, 38(3), 359–374.
doi: 10.1007/BF00345194.
Muth A (1977).
“Thermoregulatory Postures and Orientation to the Sun: A Mechanistic Evaluation for the Zebra-Tailed Lizard, Callisaurus draconoides.”
Copeia, 4, 710 - 720.
Tracy CR (1976).
“A Model of the Dynamic Exchanges of Water and Energy between a Terrestrial Amphibian and Its Environment.”
Ecological Monographs, 46(3), 293-326.
doi: 10.2307/1942256.
See Also
Other allometric functions:
mass_from_length()
,
proportion_silhouette_area_shapes()
,
surface_area_from_length()
,
surface_area_from_mass()
,
surface_area_from_volume()
,
volume_from_length()
Examples
proportion_silhouette_area(psi = 60,
taxon = "frog")
proportion_silhouette_area(psi = 60,
taxon = "grasshopper")
proportion_silhouette_area(psi = 60,
taxon = "lizard",
posture = "prostrate",
raz = 90)
proportion_silhouette_area(psi = 60,
taxon = "lizard",
posture = "elevated",
raz = 180)
Organism Silhouette Area using Shape Approximations
Description
The function estimates the projected (silhouette) area as a portion of the surface area of the organism. The function estimates the projected area as a function of the dimensions and the angle between the solar beam and the longitudinal axis of the solid, using Figure 11.6 in Campbell and Norman (1998). The function is useful for estimating absorbed solar radiation.
Usage
proportion_silhouette_area_shapes(shape, theta, h, d)
Arguments
shape |
|
theta |
|
h |
|
d |
|
Value
numeric
silhouette area as a proportion.
References
Campbell GS, Norman JM (1998). Introduction to environmental biophysics, 2nd ed. edition. Springer, New York. ISBN 0387949372.
See Also
Other allometric functions:
mass_from_length()
,
proportion_silhouette_area()
,
surface_area_from_length()
,
surface_area_from_mass()
,
surface_area_from_volume()
,
volume_from_length()
Examples
proportion_silhouette_area_shapes(shape = "spheroid",
theta = 60,
h = 0.01,
d = 0.001)
proportion_silhouette_area_shapes(shape = "cylinder flat ends",
theta = 60,
h = 0.01,
d = 0.001)
proportion_silhouette_area_shapes(shape = "cylinder hemisphere ends",
theta = 60,
h = 0.01,
d = 0.001)
Saturation Vapor Pressure
Description
The function calculates saturation vapor pressure (kPa) based on the Clausius-Clapeyron equation (Stull 2000; Riddell et al. 2018).
Usage
saturation_vapor_pressure(T_a)
Arguments
T_a |
|
Value
numeric
saturation vapor pressure, e_s
(kPa).
Author(s)
Eric Riddell
References
Riddell EA, Odom JP, Damm JD, Sears MW (2018).
“Plasticity reveals hidden resistance to extinction under climate change in the global hotspot of salamander diversity.”
Science Advances, 4(4).
doi: 10.1126/sciadv.aar5471.
Stull RB (2000).
Meteorology for Scientists and Engineers.
Brooks Cole.
ISBN 978-0534372149.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Grashof_number()
,
Nusselt_from_Grashof()
,
Nusselt_from_Reynolds()
,
Nusselt_number()
,
Prandtl_number()
,
Qconduction_animal()
,
Qconduction_substrate()
,
Qconvection()
,
Qemitted_thermal_radiation()
,
Qevaporation()
,
Qmetabolism_from_mass_temp()
,
Qmetabolism_from_mass()
,
Qnet_Gates()
,
Qradiation_absorbed()
,
Qthermal_radiation_absorbed()
,
Reynolds_number()
,
T_sky()
,
Tb_CampbellNorman()
,
Tb_Gates2()
,
Tb_Gates()
,
Tb_butterfly()
,
Tb_grasshopper()
,
Tb_limpetBH()
,
Tb_limpet()
,
Tb_lizard_Fei()
,
Tb_lizard()
,
Tb_mussel()
,
Tb_salamander_humid()
,
Tb_snail()
,
Tbed_mussel()
,
Tsoil()
,
actual_vapor_pressure()
,
boundary_layer_resistance()
,
external_resistance_to_water_vapor_transfer()
,
free_or_forced_convection()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient_simple()
,
heat_transfer_coefficient()
,
saturation_water_vapor_pressure()
Examples
saturation_vapor_pressure(T_a = 293)
Saturation Water Vapor Pressure
Description
The function approximates saturation water vapor pressure as a function of ambient temperature for temperatures from 0 to 40 C using Rosenberg (1974) in Spotila et al. (1992). See also NicheMapR WETAIR
and DRYAIR
(Kearney and Porter 2020).
Usage
saturation_water_vapor_pressure(T_a)
Arguments
T_a |
|
Value
numeric
Saturation water vapor pressure, e_s
(Pa).
References
Kearney MR, Porter WP (2020).
“NicheMapR - an R package for biophysical modelling: the ectotherm and Dynamic Energy Budget models.”
Ecography, 43(1), 85-96.
doi: 10.1111/ecog.04680.
Rosenberg NJ (1974).
Microclimate: the biological environment.
Wiley, New York.
Spotila JR, Feder ME, Burggren WW (1992).
“Biophysics of Heat and Mass Transfer.”
Environmental Physiology of the Amphibians.
https://press.uchicago.edu/ucp/books/book/chicago/E/bo3636401.html.
See Also
Other biophysical models:
Grashof_number_Gates()
,
Grashof_number()
,
Nusselt_from_Grashof()
,
Nusselt_from_Reynolds()
,
Nusselt_number()
,
Prandtl_number()
,
Qconduction_animal()
,
Qconduction_substrate()
,
Qconvection()
,
Qemitted_thermal_radiation()
,
Qevaporation()
,
Qmetabolism_from_mass_temp()
,
Qmetabolism_from_mass()
,
Qnet_Gates()
,
Qradiation_absorbed()
,
Qthermal_radiation_absorbed()
,
Reynolds_number()
,
T_sky()
,
Tb_CampbellNorman()
,
Tb_Gates2()
,
Tb_Gates()
,
Tb_butterfly()
,
Tb_grasshopper()
,
Tb_limpetBH()
,
Tb_limpet()
,
Tb_lizard_Fei()
,
Tb_lizard()
,
Tb_mussel()
,
Tb_salamander_humid()
,
Tb_snail()
,
Tbed_mussel()
,
Tsoil()
,
actual_vapor_pressure()
,
boundary_layer_resistance()
,
external_resistance_to_water_vapor_transfer()
,
free_or_forced_convection()
,
heat_transfer_coefficient_approximation()
,
heat_transfer_coefficient_simple()
,
heat_transfer_coefficient()
,
saturation_vapor_pressure()
Examples
saturation_water_vapor_pressure(T_a = 20)
Soil Thermal Conductivity
Description
The function estimates soil thermal conductivity (W m-1 K-1) using the methods of deVries (1963).
Usage
soil_conductivity(x, lambda, g_a)
Arguments
x |
|
lambda |
|
g_a |
|
Value
numeric
soil thermal conductivity (W m-1 K-1).
Author(s)
Joseph Grigg
References
deVries DA (1952).
“Thermal Conductivity of Soil.”
Nature, 178, 1074.
doi: 10.1038/1781074a0.
deVries DA (1963).
“Thermal Properties of Soils.”
In Physics of Plant Environment.
North Holland Publishing Company.
doi: 10.1002/qj.49709038628.
See Also
Other soil temperature functions:
soil_specific_heat()
,
soil_temperature_equation()
,
soil_temperature_function()
,
soil_temperature_integrand()
,
soil_temperature()
Examples
soil_conductivity(x = c(0.10, 0.40, 0.11, 0.01, 0.2, 0.18),
lambda = c(0.10, 0.40, 0.11, 0.01, 0.2, 0.18),
g_a = 0.125)
Soil Specific Heat
Description
The function estimates soil specific heat (J kg-1 K-1) using the methods of deVries (1963). The function incorporates the volume fraction of organic material, minerals, and water in soil.
Usage
soil_specific_heat(x_o, x_m, x_w, rho_so)
Arguments
x_o |
|
x_m |
|
x_w |
|
rho_so |
|
Value
numeric
soil specific heat (J kg-1 K-1).
Author(s)
Joseph Grigg
References
deVries DA (1963). “Thermal Properties of Soils.” In Physics of Plant Environment. North Holland Publishing Company. doi: 10.1002/qj.49709038628.
See Also
Other soil temperature functions:
soil_conductivity()
,
soil_temperature_equation()
,
soil_temperature_function()
,
soil_temperature_integrand()
,
soil_temperature()
Examples
soil_specific_heat(x_o = 0.01,
x_m = 0.6,
x_w = 0.2,
rho_so = 1620)
Calculate Soil Temperature using ODEs
Description
This function is called to calculate soil temperature (C) as in Beckman et al. (1973). This function calls soil_temperature_function
, which uses ODEs to calculate a soil profile using equations from deVries (1963)
Usage
soil_temperature(
z_r.intervals = 12,
z_r,
z,
T_a,
u,
Tsoil0,
z0,
SSA,
TimeIn,
S,
water_content = 0.2,
air_pressure,
rho_so = 1620,
shade = FALSE
)
Arguments
z_r.intervals |
|
z_r |
|
z |
|
T_a |
|
u |
|
Tsoil0 |
|
z0 |
|
SSA |
|
TimeIn |
|
S |
|
water_content |
|
air_pressure |
|
rho_so |
|
shade |
|
Value
numeric
soil temperature (C).
Author(s)
Joseph Grigg
References
Beckman WA, Mitchell JW, Porter WP (1973).
“Thermal Model for Prediction of a Desert Iguana's Daily and Seasonal Behavior.”
Journal of Heat Transfer, 95(2), 257-262.
doi: 10.1115/1.3450037.
deVries DA (1963).
“Thermal Properties of Soils.”
In Physics of Plant Environment.
North Holland Publishing Company.
doi: 10.1002/qj.49709038628.
See Also
Other soil temperature functions:
soil_conductivity()
,
soil_specific_heat()
,
soil_temperature_equation()
,
soil_temperature_function()
,
soil_temperature_integrand()
Examples
set.seed(123)
temp_vector <- runif(48, min = -10, max = 10)
wind_speed_vector <- runif(48, min = 0, max = 0.4)
time_vector <- rep(1:24, 2)
solrad_vector <- rep(c(rep(0, 6),
seq(10, 700, length.out = 6),
seq(700, 10, length.out = 6),
rep(0, 6)),
2)
soil_temperature(z_r.intervals = 12,
z_r = 1.5,
z = 2,
T_a = temp_vector,
u = wind_speed_vector,
Tsoil0 = 20,
z0 = 0.02,
SSA = 0.7,
TimeIn = time_vector,
S = solrad_vector,
water_content = 0.2,
air_pressure = 85,
rho_so = 1620,
shade = FALSE)
Core Function Called to Solve Equation for Soil Temperature
Description
The function called by soil_temperature_function
to solve equation for soil temperature from Beckman et al. (1973).
Usage
soil_temperature_equation(L, rho_a, c_a, u_inst, z_r, z0, T_inst, T_s)
Arguments
L |
|
rho_a |
|
c_a |
|
u_inst |
|
z_r |
|
z0 |
|
T_inst |
|
T_s |
|
Value
numeric
soil temperature (C).
Author(s)
Joseph Grigg
References
Beckman WA, Mitchell JW, Porter WP (1973). “Thermal Model for Prediction of a Desert Iguana's Daily and Seasonal Behavior.” Journal of Heat Transfer, 95(2), 257-262. doi: 10.1115/1.3450037.
See Also
Other soil temperature functions:
soil_conductivity()
,
soil_specific_heat()
,
soil_temperature_function()
,
soil_temperature_integrand()
,
soil_temperature()
Examples
soil_temperature_equation(L = -10,
rho_a = 1.177,
c_a = 1006,
u_inst = 0.3,
z_r = 1.5,
z0 = 0.02,
T_inst = 8,
T_s = 20)
Core Function for Calculating Soil Temperature
Description
This function is called to calculate soil temperature as in Beckman et al. (1973). Parameters are passed as a list to facilitating solving the equations. This function is not intended to be called directly. The energy balance equations are from Porter et al. (1973) and Kingsolver (1979)
Usage
soil_temperature_function(j, T_so, params)
Arguments
j |
|
T_so |
|
params |
|
Value
Soil temperature profile as a list
.
Author(s)
Joseph Grigg
References
Beckman WA, Mitchell JW, Porter WP (1973).
“Thermal Model for Prediction of a Desert Iguana's Daily and Seasonal Behavior.”
Journal of Heat Transfer, 95(2), 257-262.
doi: 10.1115/1.3450037.
Kingsolver JG (1979).
“Thermal and hydric aspects of environmental hetergeneity in the pitcher plant mosquito.”
Ecological Monographs, 49, 357-376.
Porter WP, Mitchell JW, Bekman A, DeWitt CB (1973).
“Behavioral implications of mechanistic ecology: thermal and behavioral modeling of desert ectotherms and their microenvironments.”
Oecologia, 13, 1-54.
See Also
Other soil temperature functions:
soil_conductivity()
,
soil_specific_heat()
,
soil_temperature_equation()
,
soil_temperature_integrand()
,
soil_temperature()
Examples
set.seed(123)
temp_vector <- runif(96, min = -10, max = 10)
wind_speed_vector <- runif(96, min = 0, max = 0.4)
time_vector <- rep(1:24, 4)
solrad_vector <- rep(c(rep(0, 6),
seq(10, 700, length.out = 6),
seq(700, 10, length.out = 6),
rep(0, 6)),
4)
params <- list(SSA = 0.7,
epsilon_so = 0.98,
k_so = 0.293,
c_so = 800,
dz = 0.05,
z_r = 1.5,
z0 = 0.02,
S = solrad_vector,
T_a = temp_vector,
u = wind_speed_vector,
rho_a = 1.177,
rho_so = 1620,
c_a = 1006,
TimeIn = time_vector,
dt = 60 * 60,
shade = FALSE)
soil_temperature_function(j = 1,
T_so = rep(20,13),
params = params)
Solve Equation for Soil Temperature
Description
This function is called by soil_temperature_equation
to solve the equation for soil temperature from Beckman et al. (1973). The function represents the integrand in the equation. It is not intended to be called directly.
Usage
soil_temperature_integrand(x, L, z0)
Arguments
x |
|
L |
|
z0 |
|
Value
numeric
integrand for soil temperature function.
Author(s)
Joseph Grigg
References
Beckman WA, Mitchell JW, Porter WP (1973). “Thermal Model for Prediction of a Desert Iguana's Daily and Seasonal Behavior.” Journal of Heat Transfer, 95(2), 257-262. doi: 10.1115/1.3450037.
See Also
Other soil temperature functions:
soil_conductivity()
,
soil_specific_heat()
,
soil_temperature_equation()
,
soil_temperature_function()
,
soil_temperature()
Examples
soil_temperature_integrand(x = c(0.10, 0.40, 0.11, 0.01, 0.2, 0.18),
L = -10,
z0 = 0.2)
Time of Solar Noon
Description
The function calculates the time of solar noon in hours as a function of the day of year and longitude (Campbell and Norman 1998).
Usage
solar_noon(lon, doy, offset = NA)
Arguments
lon |
|
doy |
|
offset |
|
Value
numeric
time of solar noon (hours).
References
Campbell GS, Norman JM (1998). Introduction to environmental biophysics, 2nd ed. edition. Springer, New York. ISBN 0387949372.
See Also
Other utility functions:
airpressure_from_elev()
,
azimuth_angle()
,
day_of_year()
,
daylength()
,
dec_angle()
,
temperature conversions
,
zenith_angle()
Examples
solar_noon(lon = -122.335,
doy = 112)
Estimate the Three Components of Solar Radiation (Direct, Diffuse and Reflected)
Description
The function estimate direct, diffuse, and reflected components of solar radiation (W m-2) as a function of day of year using the model in Campbell and Norman (1998).
Usage
solar_radiation(doy, psi, tau, elev, rho = 0.7)
Arguments
doy |
|
psi |
|
tau |
|
elev |
|
rho |
|
Value
numeric
radiation components - direct, diffused and reflected (W m-2).
References
Campbell GS, Norman JM (1998). Introduction to environmental biophysics, 2nd ed. edition. Springer, New York. ISBN 0387949372.
See Also
Other microclimate functions:
air_temp_profile_neutral()
,
air_temp_profile_segment()
,
air_temp_profile()
,
degree_days()
,
direct_solar_radiation()
,
diurnal_radiation_variation()
,
diurnal_temp_variation_sineexp()
,
diurnal_temp_variation_sinesqrt()
,
diurnal_temp_variation_sine()
,
monthly_solar_radiation()
,
partition_solar_radiation()
,
proportion_diffuse_solar_radiation()
,
surface_roughness()
,
wind_speed_profile_neutral()
,
wind_speed_profile_segment()
Examples
solar_radiation(doy = 112,
psi = 1,
tau = 0.6,
elev = 1500,
rho = 0.7)
Organism Surface Area from Length
Description
This function estimates surface area (m2) from length (m) by approximating the animal's body as a rotational ellipsoid with half the body length as the semi-major axis.
Usage
surface_area_from_length(l)
Arguments
l |
|
Details
Following Samietz et al. (2005) and Lactin and Johnson (1998).
Value
numeric
surface area (m2).
References
Lactin DJ, Johnson DL (1998).
“Convective heat loss and change in body temperature of grasshopper and locust nymphs: Relative importance of wind speed, insect size and insect orientation.”
Journal of Thermal Biology, 23(1), 5-13.
ISSN 0306-4565, doi: 10.1016/S0306-4565(97)00037-5, https://www.sciencedirect.com/science/article/pii/S0306456597000375.
Samietz J, Salser MA, Dingle H (2005).
“Altitudinal variation in behavioural thermoregulation: local adaptation vs. plasticity in California grasshoppers.”
Journal of Evolutionary Biology, 18(4), 1087-1096.
doi: 10.1111/j.1420-9101.2005.00893.x.
See Also
Other allometric functions:
mass_from_length()
,
proportion_silhouette_area_shapes()
,
proportion_silhouette_area()
,
surface_area_from_mass()
,
surface_area_from_volume()
,
volume_from_length()
Examples
surface_area_from_length(l = 0.04)
Organism Surface Area from Mass
Description
The function estimates surface area (m2) from mass (g) for one of a variety of taxa.
Usage
surface_area_from_mass(m, taxon)
Arguments
m |
|
taxon |
|
Details
All models follow (SA = a Mb) with mass in grams and surface area in meters2.
Lizards (Norris 1965; Porter and James 1979; Roughgarden 1981; O'Connor 1999; Fei et al. 2012):
a = 0.000314 \pi
b = 2/3
Salamanders (Whitford and Hutchison 1967; Riddell et al. 2017):
a = 0.000842
b = 0.694
Frogs (McClanahan and Baldwin 1969):
a = 0.00099
b = 0.56
Insects (Lactin and Johnson 1997):
a = 0.0013
b = 0.8
Value
numeric
surface area (m2).
References
Fei T, Skidmore AK, Venus V, Wang T, Schlerf M, Toxopeus B, van Overjijk S, Bian M, Liu Y (2012).
“A body temperature model for lizards as estimated from the thermal environment.”
Journal of Thermal Biology, 37(1), 56-64.
ISSN 0306-4565, doi: 10.1016/j.jtherbio.2011.10.013, https://www.sciencedirect.com/science/article/pii/S0306456511001513.
Lactin DJ, Johnson DL (1997).
“Response of body temperature to solar radiation in restrained nymphal migratory grasshoppers (Orthoptera: Acrididae): influences of orientation and body size.”
Physiological Entomology, 22(2), 131-139.
doi: 10.1111/j.1365-3032.1997.tb01150.x.
McClanahan L, Baldwin R (1969).
“Rate of water uptake through the integument of the desert toad, Bufo punctatus.”
Comparative Biochemistry and Physiology, 28(1), 381-389.
ISSN 0010-406X, doi: 10.1016/0010-406X(69)91351-6.
Norris KS (1965).
“Color adaptation in desert reptiles and its thermal relationships.”
In Symposium on Lizard Ecology, 162- 229.
U. Missouri Press.
O'Connor M (1999).
“Physiological and ecological implications of a simple model of heating and cooling in reptiles.”
Journal of Thermal Biology, 24, 113-136.
Porter WP, James FC (1979).
“Behavioral Implications of Mechanistic Ecology II: The African Rainbow Lizard, Agama agama.”
Copeia, 1979(4), 594–619.
ISSN 00458511, 19385110, doi: 10.2307/1443867.
Riddell EA, Apanovitch EK, Odom JP, Sears MW (2017).
“Physical calculations of resistance to water loss improve predictions of species range models.”
Ecological Monographs, 87(1), 21-33.
doi: 10.1002/ecm.1240.
Roughgarden J (1981).
“Resource partitioning of space and its relationship to body temperature in Anolis lizard populations.”
Oecologia, 50, 256 – 264.
https://link.springer.com/article/10.1007/BF00348048.
Whitford WG, Hutchison VH (1967).
“Body Size and Metabolic Rate in Salamanders.”
Physiological Zoology, 40(2), 127-133.
doi: 10.1086/physzool.40.2.30152447.
See Also
Other allometric functions:
mass_from_length()
,
proportion_silhouette_area_shapes()
,
proportion_silhouette_area()
,
surface_area_from_length()
,
surface_area_from_volume()
,
volume_from_length()
Examples
surface_area_from_mass(m = 1:50,
taxon = "lizard")
surface_area_from_mass(m = 1:50,
taxon = "salamander")
surface_area_from_mass(m = 1:50,
taxon = "frog")
surface_area_from_mass(m = seq(0.1, 5, 0.1),
taxon = "insect")
Organism Surface Area from Volume
Description
The function estimates surface area (m2) from volume (m3) for a variety of taxa following Mitchell (1976).
Usage
surface_area_from_volume(V, taxon)
Arguments
V |
|
taxon |
|
Details
All models follow (SA = Ka V2/3) with surface area and volume in meters.
Lizards: Norris (1965):
Ka = 11.0
Frogs: Tracy (1972):
Ka = 11.0
Sphere: Mitchell (1976):
Ka = 4.83
Value
numeric
surface area (m2).
References
Mitchell JW (1976).
“Heat transfer from spheres and other animal forms.”
Biophysical Journal, 16(6), 561-569.
ISSN 0006-3495, doi: 10.1016/S0006-3495(76)85711-6.
Norris KS (1965).
“Color adaptation in desert reptiles and its thermal relationships.”
In Symposium on Lizard Ecology, 162- 229.
U. Missouri Press.
Tracy CR (1972).
“Newton's Law: Its Application for Expressing Heat Losses from Homeotherms.”
BioScience, 22(11), 656-659.
ISSN 0006-3568, doi: 10.2307/1296267.
See Also
Other allometric functions:
mass_from_length()
,
proportion_silhouette_area_shapes()
,
proportion_silhouette_area()
,
surface_area_from_length()
,
surface_area_from_mass()
,
volume_from_length()
Examples
surface_area_from_volume(V = 0.001,
taxon = "lizard")
surface_area_from_volume(V = 0.001,
taxon = "frog")
surface_area_from_volume(V = 0.001,
taxon = "sphere")
Surface Roughness from Empirical Measurements
Description
The function estimates surface roughness (m) from empirical wind speed (m s-1) data collected at a vector of heights (m) (Kingsolver and Buckley 2015; Campbell and Norman 1998; Porter and James 1979).
Usage
surface_roughness(u_r, zr)
Arguments
u_r |
|
zr |
|
Value
numeric
surface roughness (m).
References
Campbell GS, Norman JM (1998).
Introduction to environmental biophysics, 2nd ed. edition.
Springer, New York.
ISBN 0387949372.
Kingsolver JG, Buckley LB (2015).
“Climate variability slows evolutionary responses of Colias butterflies to recent climate change.”
Proceedings of the Royal Society B, 282(1802).
doi: 10.1098/rspb.2014.2470.
Porter WP, James FC (1979).
“Behavioral Implications of Mechanistic Ecology II: The African Rainbow Lizard, Agama agama.”
Copeia, 1979(4), 594–619.
ISSN 00458511, 19385110, doi: 10.2307/1443867.
See Also
Other microclimate functions:
air_temp_profile_neutral()
,
air_temp_profile_segment()
,
air_temp_profile()
,
degree_days()
,
direct_solar_radiation()
,
diurnal_radiation_variation()
,
diurnal_temp_variation_sineexp()
,
diurnal_temp_variation_sinesqrt()
,
diurnal_temp_variation_sine()
,
monthly_solar_radiation()
,
partition_solar_radiation()
,
proportion_diffuse_solar_radiation()
,
solar_radiation()
,
wind_speed_profile_neutral()
,
wind_speed_profile_segment()
Examples
surface_roughness(u_r = c(0.01, 0.025, 0.05, 0.1, 0.2),
zr = c(0.05, 0.25, 0.5, 0.75, 1))
Convert Among Temperature Scales
Description
The function converts temperatures among Celsius, Fahrenheit, and Kelvin (J. Blischak et al. 2016).
Usage
fahrenheit_to_kelvin(temperature)
kelvin_to_celsius(temperature)
celsius_to_kelvin(temperature)
fahrenheit_to_celsius(temperature)
Arguments
temperature |
|
Value
numeric
temperature (Celsius, Fahrenheit, or Kelvin).
References
J. Blischak, D. Chen, H. Dashnow, Haine D (2016). Software Carpentry: Programming with R. doi: 10.5281/zenodo.57541, Version 2016.06, June 2016.
See Also
Other utility functions:
airpressure_from_elev()
,
azimuth_angle()
,
day_of_year()
,
daylength()
,
dec_angle()
,
solar_noon()
,
zenith_angle()
Examples
kelvin_to_celsius(temperature = 270)
fahrenheit_to_kelvin(temperature = 85)
fahrenheit_to_celsius(temperature = 85)
celsius_to_kelvin(temperature = -10)
Organism Volume from Length
Description
The function estimates volume (m3) from length (m) for a variety of taxa following Mitchell (1976).
Usage
volume_from_length(l, taxon)
Arguments
l |
|
taxon |
|
Details
Relationships come from
Lizards: Norris (1965)
Frogs: Tracy (1972)
Sphere: Mitchell (1976)
Value
numeric
volume (m3).
References
Mitchell JW (1976).
“Heat transfer from spheres and other animal forms.”
Biophysical Journal, 16(6), 561-569.
ISSN 0006-3495, doi: 10.1016/S0006-3495(76)85711-6.
Norris KS (1965).
“Color adaptation in desert reptiles and its thermal relationships.”
In Symposium on Lizard Ecology, 162- 229.
U. Missouri Press.
Tracy CR (1972).
“Newton's Law: Its Application for Expressing Heat Losses from Homeotherms.”
BioScience, 22(11), 656-659.
ISSN 0006-3568, doi: 10.2307/1296267.
See Also
Other allometric functions:
mass_from_length()
,
proportion_silhouette_area_shapes()
,
proportion_silhouette_area()
,
surface_area_from_length()
,
surface_area_from_mass()
,
surface_area_from_volume()
Examples
volume_from_length(l = 0.05,
taxon = "lizard")
volume_from_length(l = 0.05,
taxon = "frog")
volume_from_length(l = 0.05,
taxon = "sphere")
Wind Speed at a Specific Height Under Neutral Conditions
Description
The function calculates wind speed (m s-1) at a specified height (m) within a boundary layer near the surface. The profile assumes neutral conditions. The velocity profile is the neutral profile described by Sellers (1965). Function is equations (2) and (3) of Porter et al. (1973).
Usage
wind_speed_profile_neutral(u_r, zr, z0, z)
Arguments
u_r |
|
zr |
|
z0 |
|
z |
|
Value
numeric
windspeed (m s-1).
References
Porter WP, Mitchell JW, Bekman A, DeWitt CB (1973).
“Behavioral implications of mechanistic ecology: thermal and behavioral modeling of desert ectotherms and their microenvironments.”
Oecologia, 13, 1-54.
Sellers WD (1965).
Physical climatology.
University of Chicago Press, Chicago, IL, USA.
See Also
Other microclimate functions:
air_temp_profile_neutral()
,
air_temp_profile_segment()
,
air_temp_profile()
,
degree_days()
,
direct_solar_radiation()
,
diurnal_radiation_variation()
,
diurnal_temp_variation_sineexp()
,
diurnal_temp_variation_sinesqrt()
,
diurnal_temp_variation_sine()
,
monthly_solar_radiation()
,
partition_solar_radiation()
,
proportion_diffuse_solar_radiation()
,
solar_radiation()
,
surface_roughness()
,
wind_speed_profile_segment()
Examples
wind_speed_profile_neutral(u_r = 0.1,
zr = 0.1,
z0 = 0.2,
z = 0.15)
Wind Speed at a Specified Height
Description
The function calculates wind speed (m s-1) at a specified height (m). The function estimates a three segment velocity and temperature profile based on user-specified, experimentally determined values for 3 roughness heights and reference heights. Multiple heights are appropriate in heterogenous areas with, for example, a meadow, bushes, and rocks. Implements the MICROSEGMT routine from NicheMapR as described in Kearney and Porter (2017).
Usage
wind_speed_profile_segment(u_r, zr, z0, z)
Arguments
u_r |
|
zr |
|
z0 |
|
z |
|
Value
numeric
wind speed (m s-1).
References
Kearney MR, Porter WP (2017). “NicheMapR - an R package for biophysical modelling: the microclimate model.” Ecography, 40, 664-674. doi: 10.1111/ecog.02360.
See Also
Other microclimate functions:
air_temp_profile_neutral()
,
air_temp_profile_segment()
,
air_temp_profile()
,
degree_days()
,
direct_solar_radiation()
,
diurnal_radiation_variation()
,
diurnal_temp_variation_sineexp()
,
diurnal_temp_variation_sinesqrt()
,
diurnal_temp_variation_sine()
,
monthly_solar_radiation()
,
partition_solar_radiation()
,
proportion_diffuse_solar_radiation()
,
solar_radiation()
,
surface_roughness()
,
wind_speed_profile_neutral()
Examples
wind_speed_profile_segment(u_r = c(0.01, 0.025, 0.05),
zr = c(0.05, 0.25, 0.5),
z0 = c(0.01, 0.15, 0.2),
z = 0.3)
Zenith Angle
Description
The function calculates the zenith angle, the location of the sun as an angle (in degrees) measured from vertical (Campbell and Norman 1998).
Usage
zenith_angle(doy, lat, lon, hour, offset = NA)
Arguments
doy |
|
lat |
|
lon |
|
hour |
|
offset |
|
Value
numeric
zenith angle (degrees)
References
Campbell GS, Norman JM (1998). Introduction to environmental biophysics, 2nd ed. edition. Springer, New York. ISBN 0387949372.
See Also
Other utility functions:
airpressure_from_elev()
,
azimuth_angle()
,
day_of_year()
,
daylength()
,
dec_angle()
,
solar_noon()
,
temperature conversions
Examples
zenith_angle(doy = 112,
lat = 47.61,
lon = -122.33,
hour = 12)