Added (maximum rate of RuBP regeneration) to the list of returned variables by the function. Made and to public functions, exported as part of the rpmodel package.

Author: stineb

DESCRIPTION

@@ -1,14 +1,14 @@
 Package: rpmodel
 Type: Package
 Title: P-Model
-Version: 1.0.4
+Version: 1.0.5
 Authors@R: person( "Benjamin", "Stocker", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-2697-9096") )
 Maintainer: Benjamin Stocker <[email protected]>
-Description: Implements the P-model (Stocker et al., 2019 <doi:10.5194/gmd-2019-200>), predicting acclimated parameters of the enzyme kinetics of C3 photosynthesis, assimilation, and dark respiration rates as a function of the environment (temperature, CO2, vapour pressure deficit, light, atmospheric pressure).
+Description: Implements the P-model (Stocker et al., 2020 <doi:10.5194/gmd-13-1545-2020>), predicting acclimated parameters of the enzyme kinetics of C3 photosynthesis, assimilation, and dark respiration rates as a function of the environment (temperature, CO2, vapour pressure deficit, light, atmospheric pressure).
 License: GPL-3
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.0.0
+RoxygenNote: 7.1.0
 Imports: rlang
 Suggests: dplyr, purrr, tidyr, knitr
 VignetteBuilder: knitr

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(calc_density_h2o)
 export(calc_ftemp_arrh)
 export(calc_ftemp_inst_rd)
 export(calc_ftemp_inst_vcmax)
@@ -8,4 +9,5 @@ export(calc_gammastar)
 export(calc_kmm)
 export(calc_patm)
 export(calc_soilmstress)
+export(calc_viscosity_h2o)
 export(rpmodel)

NEWS.md

@@ -16,3 +16,8 @@
 ## rpmodel 1.0.4
 
 * Bugfix: vectorized all outputs from `rpmodel()`.
+
+## rpmodel 1.0.5
+
+* Added `jmax` (maximum rate of RuBP regeneration) to the list of returned variables by the `rpmodel()` function.
+* Made `calc_viscosity_h2o()` and `calc_density_h2o()` to public functions, exported as part of the rpmodel package.

R/calc_density_h2o.R

@@ -0,0 +1,60 @@
+#' Density of water
+#'
+#' Calculates the density of water as a function of temperature and atmospheric
+#' pressure, using the Tumlirz Equation.
+#'
+#' @param tc numeric, air temperature (tc), degrees C
+#' @param p numeric, atmospheric pressure (p), Pa
+#'
+#' @return numeric, density of water, kg/m^3
+#'
+#' @examples print("Density of water at 20 degrees C and standard atmospheric pressure:")
+#' print(calc_density_h2o(20, 101325))
+#'
+#' @references  F.H. Fisher and O.E Dial, Jr. (1975) Equation of state of
+#' pure water and sea water, Tech. Rept., Marine Physical
+#' Laboratory, San Diego, CA.
+#'
+#' @export
+#'
+calc_density_h2o <- function( tc, p ){
+
+  # Calculate lambda, (bar cm^3)/g:
+  my_lambda <- 1788.316 +
+    21.55053*tc +
+    -0.4695911*tc*tc +
+    (3.096363e-3)*tc*tc*tc +
+    -(7.341182e-6)*tc*tc*tc*tc
+
+  # Calculate po, bar
+  po <- 5918.499 +
+    58.05267*tc +
+    -1.1253317*tc*tc +
+    (6.6123869e-3)*tc*tc*tc +
+    -(1.4661625e-5)*tc*tc*tc*tc
+
+  # Calculate vinf, cm^3/g
+  vinf <- 0.6980547 +
+    -(7.435626e-4)*tc +
+    (3.704258e-5)*tc*tc +
+    -(6.315724e-7)*tc*tc*tc +
+    (9.829576e-9)*tc*tc*tc*tc +
+    -(1.197269e-10)*tc*tc*tc*tc*tc +
+    (1.005461e-12)*tc*tc*tc*tc*tc*tc +
+    -(5.437898e-15)*tc*tc*tc*tc*tc*tc*tc +
+    (1.69946e-17)*tc*tc*tc*tc*tc*tc*tc*tc +
+    -(2.295063e-20)*tc*tc*tc*tc*tc*tc*tc*tc*tc
+
+  # Convert pressure to bars (1 bar <- 100000 Pa)
+  pbar <- (1e-5)*p
+
+  # Calculate the specific volume (cm^3 g^-1):
+  v <- vinf + my_lambda/(po + pbar)
+
+  # Convert to density (g cm^-3) -> 1000 g/kg; 1000000 cm^3/m^3 -> kg/m^3:
+  rho <- (1e3/v)
+
+  return(rho)
+}
+
+

R/calc_viscosity_h2o.R

@@ -0,0 +1,77 @@
+#' Viscosity of water
+#'
+#' Calculates the viscosity of water as a function of temperature and atmospheric
+#' pressure.
+#'
+#' @param tc numeric, air temperature (tc), degrees C
+#' @param p numeric, atmospheric pressure (p), Pa
+#'
+#' @return numeric, viscosity of water (mu), Pa s
+#'
+#' @examples print("Density of water at 20 degrees C and standard atmospheric pressure:")
+#' print(calc_density_h2o(20, 101325))
+#'
+#' @references  Huber, M. L., R. A. Perkins, A. Laesecke, D. G. Friend, J. V.
+#' Sengers, M. J. Assael, ..., K. Miyagawa (2009) New
+#' international formulation for the viscosity of H2O, J. Phys.
+#' Chem. Ref. Data, Vol. 38(2), pp. 101-125.
+#'
+#' @export
+#'
+calc_viscosity_h2o <- function( tc, p ) {
+
+  # Define reference temperature, density, and pressure values:
+  tk_ast  <- 647.096    # Kelvin
+  rho_ast <- 322.0      # kg/m^3
+  mu_ast  <- 1e-6       # Pa s
+
+  # Get the density of water, kg/m^3
+  rho <- calc_density_h2o(tc, p)
+
+  # Calculate dimensionless parameters:
+  tbar  <- (tc + 273.15)/tk_ast
+  tbarx <- tbar^(0.5)
+  tbar2 <- tbar^2
+  tbar3 <- tbar^3
+  rbar  <- rho/rho_ast
+
+  # Calculate mu0 (Eq. 11 & Table 2, Huber et al., 2009):
+  mu0 <- 1.67752 + 2.20462/tbar + 0.6366564/tbar2 - 0.241605/tbar3
+  mu0 <- 1e2*tbarx/mu0
+
+  # Create Table 3, Huber et al. (2009):
+  h_array <- array(0.0, dim=c(7,6))
+  h_array[1,] <- c(0.520094, 0.0850895, -1.08374, -0.289555, 0.0, 0.0)  # hj0
+  h_array[2,] <- c(0.222531, 0.999115, 1.88797, 1.26613, 0.0, 0.120573) # hj1
+  h_array[3,] <- c(-0.281378, -0.906851, -0.772479, -0.489837, -0.257040, 0.0) # hj2
+  h_array[4,] <- c(0.161913,  0.257399, 0.0, 0.0, 0.0, 0.0) # hj3
+  h_array[5,] <- c(-0.0325372, 0.0, 0.0, 0.0698452, 0.0, 0.0) # hj4
+  h_array[6,] <- c(0.0, 0.0, 0.0, 0.0, 0.00872102, 0.0) # hj5
+  h_array[7,] <- c(0.0, 0.0, 0.0, -0.00435673, 0.0, -0.000593264) # hj6
+
+  # Calculate mu1 (Eq. 12 & Table 3, Huber et al., 2009):
+  mu1 <- 0.0
+  ctbar <- (1.0/tbar) - 1.0
+  # print(paste("ctbar",ctbar))
+  # for i in xrange(6):
+  for (i in 1:6){
+    coef1 <- ctbar^(i-1)
+    # print(paste("i, coef1", i, coef1))
+    coef2 <- 0.0
+    for (j in 1:7){
+      coef2 <- coef2 + h_array[j,i] * (rbar - 1.0)^(j-1)
+    }
+    mu1 <- mu1 + coef1 * coef2
+  }
+  mu1 <- exp( rbar * mu1 )
+  # print(paste("mu1",mu1))
+
+  # Calculate mu_bar (Eq. 2, Huber et al., 2009)
+  #   assumes mu2 = 1
+  mu_bar <- mu0 * mu1
+
+  # Calculate mu (Eq. 1, Huber et al., 2009)
+  mu <- mu_bar * mu_ast    # Pa s
+
+  return( mu )
+}