Package 'TrenchR'

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

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)

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

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)

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

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)

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

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)

Description

The function estimates air pressure (kPa) as a function of elevation (Engineering ToolBox 2003).

Usage

airpressure_from_elev(elev)

Arguments

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)

Description

The function converts angles in radians to degrees or degrees to radians.

Usage

radians_to_degrees(rad)

degrees_to_radians(deg)

Arguments

Value

numeric angle (degrees or radians).

Examples

radians_to_degrees(0.831)
  degrees_to_radians(47.608)

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

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)

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

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)

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

Value

numeric values in units.

Examples

specific_heat_h2o()
  latent_heat_vaporization_h2o()
  stefan_boltzmann_constant()

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

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")

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

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)

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

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)

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

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")

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

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")

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

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)

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

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)

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

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 = -0.17

• 10 cm air temperature: alpha = 1.52, beta = 2.00, gamma = -0.18

• soil surface temperature: alpha = 0.50, beta = 1.81, gamma = 0.49

• 10cm 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)

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

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)

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

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)

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

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)

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

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)

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

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)

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

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)

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

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")

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

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")

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

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")

Description

The function estimates mass (g) from length (m) for a variety of taxa.

Usage

mass_from_length(l, taxon)

Arguments

Details

All models follow (m = a l^b) 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")

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

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)

Description

The function estimates the Nusselt number from the Grashof Number (Gates 1980).

Usage

Nusselt_from_Grashof(Gr)

Arguments

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)

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

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")

Description

The function estimates the Nusselt Number, which describes dimensionless conductance (Gates 1980).

Usage

Nusselt_number(H_L, D, K)

Arguments

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)

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

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)

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

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)

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

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)

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

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)

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

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)

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

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)

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

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)

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

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)

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

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)

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

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")

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

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")

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

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")

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

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)

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

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)

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

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)

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

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)

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

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)

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

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)

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

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)

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

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)

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

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)

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

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)

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

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)

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

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)

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

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)

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)