Package: TrenchR 1.1.1

Lauren Buckley

TrenchR: Tools for Microclimate and Biophysical Ecology

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>.

Authors:Lauren Buckley [aut, cre], Bryan Briones Ortiz [aut], Isaac Caruso [aut], Aji John [aut], Ofir Levy [aut], Abigail Meyer [aut], Eric Riddell [aut], Yutaro Sakairi [aut], Juniper Simonis [aut], Brian Helmuth [ctb]

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TrenchR.pdf |TrenchR.html✨
TrenchR/json (API)
NEWS

# Install 'TrenchR' in R:
install.packages('TrenchR', repos = c('https://trenchproject.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/trenchproject/trenchr/issues

On CRAN:

6.83 score 12 stars 40 scripts 189 downloads 92 exports 22 dependencies

Last updated 1 years agofrom:ca58d44041. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 12 2024
R-4.5-winNOTENov 12 2024
R-4.5-linuxNOTENov 12 2024
R-4.4-winNOTENov 12 2024
R-4.4-macNOTENov 12 2024
R-4.3-winOKNov 12 2024
R-4.3-macOKNov 12 2024

Exports:actual_vapor_pressureair_temp_profileair_temp_profile_neutralair_temp_profile_segmentairpressure_from_elevazimuth_angleboundary_layer_resistancecelsius_to_kelvinday_of_yeardaylengthdec_angledegree_daysdegrees_to_radiansdirect_solar_radiationdiurnal_radiation_variationdiurnal_temp_variation_sinediurnal_temp_variation_sineexpdiurnal_temp_variation_sinesqrtDRYAIRexternal_resistance_to_water_vapor_transferfahrenheit_to_celsiusfahrenheit_to_kelvinfree_or_forced_convectionGrashof_numberGrashof_number_Gatesheat_transfer_coefficientheat_transfer_coefficient_approximationheat_transfer_coefficient_simplekelvin_to_celsiuslatent_heat_vaporization_h2omass_from_lengthmonthly_solar_radiationNusselt_from_GrashofNusselt_from_ReynoldsNusselt_numberpartition_solar_radiationPrandtl_numberproportion_diffuse_solar_radiationproportion_silhouette_areaproportion_silhouette_area_shapesQconduction_animalQconduction_substrateQconvectionQemitted_thermal_radiationQevaporationQmetabolism_from_massQmetabolism_from_mass_tempQnet_GatesQradiation_absorbedQthermal_radiation_absorbedradians_to_degreesReynolds_numbersaturation_vapor_pressuresaturation_water_vapor_pressuresoil_conductivitysoil_specific_heatsoil_temperaturesoil_temperature_equationsoil_temperature_functionsoil_temperature_integrandsolar_noonsolar_radiationspecific_heat_h2ostefan_boltzmann_constantsurface_area_from_lengthsurface_area_from_masssurface_area_from_volumesurface_roughnessT_skyTb_butterflyTb_CampbellNormanTb_GatesTb_Gates2Tb_grasshopperTb_limpetTb_limpetBHTb_lizardTb_lizard_FeiTb_musselTb_salamander_humidTb_snailTbed_musselTPCTPC_betaTsoilVAPPRSvolume_from_lengthvon_karman_constantWETAIRwind_speed_profile_neutralwind_speed_profile_segmentzenith_angle

Dependencies:clideSolveexpmfansigenericsgluelatticelifecyclemagrittrMatrixmsmmvtnormpillarpkgconfigrbibutilsRdpackrlangsurvivaltibbleutf8vctrszoo

Allometries and conversions

Lauren Buckley and the TrEnCh project, Department of Biology, University of Washington

Rendered fromAllometryAndConversionsTutorial.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2022-10-14
Started: 2018-09-14

Estimating microclimates

Lauren Buckley and the TrEnCh project, Department of Biology, University of Washington

Rendered fromMicroclimateTutorial.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2023-09-06
Started: 2018-09-13

List of symbols

TrEnCh project, Buckley Lab, Department of Biology, University of Washington

Rendered fromSymbols.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2022-10-14
Started: 2019-12-11

Using energy balances to estimate body temperatures

Lauren Buckley and the TrEnCh project, Department of Biology, University of Washington

Rendered fromTeTutorial.Rmdusingknitr::rmarkdownon Nov 12 2024.

Last update: 2022-10-28
Started: 2018-08-10

Readme and manuals

Help Manual

Help pageTopics
Actual Vapor Pressure from Dewpoint Temperatureactual_vapor_pressure
Air Temperature Profile using MICRO Routineair_temp_profile
Air Temperature at a Specified Height Under Neutral Conditionsair_temp_profile_neutral
Air Temperature at a Specified Heightair_temp_profile_segment
Air Pressure from Elevationairpressure_from_elev
Convert Angles Between Radians and Degreesangle conversions degrees_to_radians radians_to_degrees
Azimuth Angleazimuth_angle
Boundary Layer Resistanceboundary_layer_resistance
General Use Constantsconstants latent_heat_vaporization_h2o specific_heat_h2o stefan_boltzmann_constant von_karman_constant
Calendar Day from Dateday_of_year
Day Lengthdaylength
Solar Declination in Radiansdec_angle
Degree Daysdegree_days
Direct Solar Radiationdirect_solar_radiation
Hourly Solar Radiationdiurnal_radiation_variation
Hourly Temperature Variation assuming a Sine Interpolationdiurnal_temp_variation_sine
Hourly Temperature Variation assuming Sine and Exponential Componentsdiurnal_temp_variation_sineexp
Hourly Temperature Variation using Sine and Square Root Functionsdiurnal_temp_variation_sinesqrt
Properties of Dry AirDRYAIR
External Resistance to Water Vapor Transferexternal_resistance_to_water_vapor_transfer
Determine if Convection is Free or Forcedfree_or_forced_convection
Grashof NumberGrashof_number
Grashof Number as in Gates (1980)Grashof_number_Gates
Estimate the Heat Transfer Coefficient Empiricallyheat_transfer_coefficient
Estimate the Heat Transfer Coefficient Using a Spherical Approximationheat_transfer_coefficient_approximation
Estimate the Heat Transfer Coefficient using Simple Relationshipsheat_transfer_coefficient_simple
Organism Mass from Lengthmass_from_length
Average Monthly Solar Radiationmonthly_solar_radiation
Nusselt Number from the Grashof NumberNusselt_from_Grashof
Nusselt Number from the Reynolds NumberNusselt_from_Reynolds
Nusselt NumberNusselt_number
Diffuse Fraction for Partitioning Solar Radiationpartition_solar_radiation
Prandtl NumberPrandtl_number
Ratio of Diffuse to Direct Solar Radiationproportion_diffuse_solar_radiation
Organism Silhouette Areaproportion_silhouette_area
Organism Silhouette Area using Shape Approximationsproportion_silhouette_area_shapes
Conductance Assuming Animal Thermal Conductivity is Rate LimitingQconduction_animal
Conductance Assuming Substrate Thermal Conductivity is Rate LimitingQconduction_substrate
Organismal ConvectionQconvection
Emitted Thermal RadiationQemitted_thermal_radiation
Heat Loss Associated with Evaporative Water LossQevaporation
Metabolism as a Function of MassQmetabolism_from_mass
Metabolism as a Function of Mass and Body TemperatureQmetabolism_from_mass_temp
Net Energy Exchange Between an Animal and the EnvironmentQnet_Gates
Absorbed Solar and Thermal RadiationQradiation_absorbed
Absorbed Thermal RadiationQthermal_radiation_absorbed
Reynolds NumberReynolds_number
Saturation Vapor Pressuresaturation_vapor_pressure
Saturation Water Vapor Pressuresaturation_water_vapor_pressure
Soil Thermal Conductivitysoil_conductivity
Soil Specific Heatsoil_specific_heat
Calculate Soil Temperature using ODEssoil_temperature
Core Function Called to Solve Equation for Soil Temperaturesoil_temperature_equation
Core Function for Calculating Soil Temperaturesoil_temperature_function
Solve Equation for Soil Temperaturesoil_temperature_integrand
Time of Solar Noonsolar_noon
Estimate the Three Components of Solar Radiation (Direct, Diffuse and Reflected)solar_radiation
Organism Surface Area from Lengthsurface_area_from_length
Organism Surface Area from Masssurface_area_from_mass
Organism Surface Area from Volumesurface_area_from_volume
Surface Roughness from Empirical Measurementssurface_roughness
Effective radiant temperature of sky (K)T_sky
Operative Environmental Temperature of a ButterflyTb_butterfly
Operative Environmental Temperature of an Ectotherm based on Campbell and Norman (1988)Tb_CampbellNorman
Operative Environmental Temperature of an Ectotherm Based on Gates (1980)Tb_Gates
Operative Environmental Temperature of an Ectotherm Based on a Variant of Gates (1980)Tb_Gates2
Operative Environmental Temperature of a GrasshopperTb_grasshopper
Operative Environmental Temperature of a LimpetTb_limpet
Operative Environmental Temperature of a Limpet Based on a Model by HelmuthTb_limpetBH
Operative Environmental Temperature of a LizardTb_lizard
Operative Temperature of a Lizard Using Fei et al. (2012)Tb_lizard_Fei
Operative Environmental Temperature of a MusselTb_mussel
Humid Operative Environmental Temperature of a SalamanderTb_salamander_humid
Operative Environmental Temperature of a Marine SnailTb_snail
Operative Environmental Temperature of a Mussel BedTbed_mussel
Convert Among Temperature Scalescelsius_to_kelvin fahrenheit_to_celsius fahrenheit_to_kelvin kelvin_to_celsius temperature conversions
Gaussian-Quadratic Function Thermal Performance CurveTPC
Beta Function Thermal Performance CurveTPC_beta
Approximate Soil TemperatureTsoil
Saturation Vapor PressureVAPPRS
Organism Volume from Lengthvolume_from_length
Properties of Wet AirWETAIR
Wind Speed at a Specific Height Under Neutral Conditionswind_speed_profile_neutral
Wind Speed at a Specified Heightwind_speed_profile_segment
Zenith Anglezenith_angle