simulate_error

Contains modeling and analytical tools for plant ecophysiology.
MODELING: Simulate C3 photosynthesis using the Farquhar, von Caemmerer,
Berry (1980) <doi:10.1007/BF00386231> model as described in Buckley and
Diaz-Espejo (2015) <doi:10.1111/pce.12459>. It uses units to ensure that
parameters are properly specified and transformed before calculations.
Temperature response functions get automatically "baked" into all
parameters based on leaf temperature following Bernacchi et al. (2002)
<doi:10.1104/pp.008250>. The package includes boundary layer, cuticular,
stomatal, and mesophyll conductances to CO2, which each can vary on the
upper and lower portions of the leaf. Use straightforward functions to
simulate photosynthesis over environmental gradients such as Photosynthetic
Photon Flux Density (PPFD) and leaf temperature, or over trait gradients
such as CO2 conductance or photochemistry.
ANALYTICAL TOOLS: Fit ACi (Farquhar et al. (1980) <doi:10.1007/BF00386231>)
and AQ curves (Marshall & Biscoe (1980) <doi:10.1093/jxb/31.1.29>),
temperature responses (Heskel et al. (2016) <doi:10.1073/pnas.1520282113>;
Kruse et al. (2008) <doi:10.1111/j.1365-3040.2008.01809.x>, Medlyn et al.
(2002) <doi:10.1046/j.1365-3040.2002.00891.x>, Hobbs et al. (2013)
<doi:10.1021/cb4005029>), respiration in the light (Kok (1956)
<doi:10.1016/0006-3002(56)90003-8>, Walker & Ort (2015) <doi:10.1111/pce.12562>,
Yin et al. (2009) <doi:10.1111/j.1365-3040.2009.01934.x>, Yin et al. (2011)
<doi:10.1093/jxb/err038>), mesophyll conductance (Harley et al. (1992)
<doi:10.1104/pp.98.4.1429>), pressure-volume curves (Koide et al. (2000)
<doi:10.1007/978-94-009-2221-1_9>, Sack et al. (2003)
<doi:10.1046/j.0016-8025.2003.01058.x>, Tyree et al. (1972)
<doi:10.1093/jxb/23.1.267>), hydraulic vulnerability curves (Ogle et al. (2009)
<doi:10.1111/j.1469-8137.2008.02760.x>, Pammenter et al. (1998)
<doi:10.1093/treephys/18.8-9.589>), and tools for running sensitivity
analyses particularly for variables with uncertainty (e.g. g_mc(), gamma_star(),
R_d()).

Chris Muir

photosynthesis

Tools for Plant Ecophysiology & Modeling

Joseph Stinziano

Cassaundra Roback

Demi Sargent

Bridget Murphy

Patrick Hudson

simulate_error function

<dl><dt>ph_out</dt>
<dd>A data frame of output from <code>photo()</code> or <code>photosynthesis()</code>
with units.</dd>
<dt>chamber_pars</dt>
<dd>A data frame with a single row of chamber parameters.
See Note below for table of required parameters.</dd>
<dt>n</dt>
<dd>Integer. Number of replicated simulations per row of <code>ph_out</code>.</dd>
<dt>use_tealeaves</dt>
<dd>Flag. The tealeaves package uses a slightly
different equation to calculate the saturating water content of air as a
function temperature and pressure than LI-COR. If FALSE, the function uses
LI-COR's equation in the LI6800 manual. If TRUE, it uses the tealeaves
function for internal consistency. The function attempts to guess whether
<code>ph_out</code> was run with tealeaves, but this can be manually overridden by
providing a value for the argument.</dd></dl>

Arguments

Simulate gas exchange data with measurement error — simulate_error

<dl>

<dt>ph_out</dt>
<dd>A data frame of output from <code>photo()</code> or <code>photosynthesis()</code>
with units.</dd>


<dt>chamber_pars</dt>
<dd>A data frame with a single row of chamber parameters.
See Note below for table of required parameters.</dd>


<dt>n</dt>
<dd>Integer. Number of replicated simulations per row of <code>ph_out</code>.</dd>


<dt>use_tealeaves</dt>
<dd>Flag. The tealeaves package uses a slightly
different equation to calculate the saturating water content of air as a
function temperature and pressure than LI-COR. If FALSE, the function uses
LI-COR's equation in the LI6800 manual. If TRUE, it uses the tealeaves
function for internal consistency. The function attempts to guess whether
<code>ph_out</code> was run with tealeaves, but this can be manually overridden by
providing a value for the argument.</dd>

</dl>

column name	assumed or derived?	description
`flow`	assumed	chamber flow rate
`leaf_area`	assumed	leaf area in chamber
`sigma_CO2_r`	assumed	standard deviation of measurement error in CO2_r
`sigma_CO2_s`	assumed	standard deviation of measurement error in CO2_s
`sigma_H2O_r`	assumed	standard deviation of measurement error in H2O_r
`sigma_H2O_s`	assumed	standard deviation of measurement error in H2O_s
`c_0`	derived	CO $_{2}$ concentration before entering chamber [ $μ$ mol / mol]
`w_i`	derived	Water vapor concentration within leaf [mmol / mol]
`w_a`	derived	Water vapor concentration in chamber [mmol / mol]
`w_0`	derived	Water vapor concentration before entering chamber [mmol / mol]
`g_tw`	derived	Leaf conductance to water vapor [mol/m $^{2}$ /s]
`E_area`	derived	Evaporation rate per area [mmol/m $^{2}$ /s]
`E`	derived	Total evaporation rate [mmol/s]
`CO2_r`	derived	CO $_{2}$ concentration before entering chamber with measurement error [ $μ$ mol / mol]
`CO2_s`	derived	CO $_{2}$ concentration in chamber with measurement error [ $μ$ mol / mol]
`H2O_s`	derived	Water vapor concentration in chamber with measurement error [mmol / mol]
`H2O_r`	derived	Water vapor concentration before entering chamber with measurement error [mmol / mol]
`E_meas`	derived	Total evaporation rate (measured) [mmol/s]
`E_area_meas`	derived	Evaporation rate per area (measured) [mmol/m $^{2}$ /s]
`g_tw_meas`	derived	Leaf conductance to water vapor (measured) [mol/m $^{2}$ /s]
`g_sc_meas`	derived	Stomatal conductance to CO $_{2}$ (measured) [mol/m $^{2}$ /s]
`g_tc_meas`	derived	Leaf conductance to CO $_{2}$ (measured) [mol/m $^{2}$ /s]
`A_meas`	derived	Net photosynthetic CO $_{2}$ assimilation (measured) [ $μ$ mol/m $^{2}$ /s]
`C_i`	derived	Intercellular CO $_{2}$ concentration (measured) [ $μ$ mol/mol]

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simulate_error: Simulate gas exchange data with measurement error

Description

Usage

Value

Arguments

Examples