rcontroll 0.2.0.9021:

- parameters: update TROLLv4_input.txt and generate_parameters according to the last discussion with IM
- dailyvar: update dailyvar day index to avoid bissextile years extra days

NEWS.md

@@ -1,3 +1,8 @@
+# rcontroll 0.2.0.9021
+
+- parameters: update TROLLv4_input.txt and generate_parameters according to the last discussion with IM
+- dailyvar: update dailyvar day index to avoid bissextile years extra days
+
 # rcontroll 0.2.0.9020
 
 - CPP: TROLL version 4.0.1 following discussion with IM, updating treefall time normalisation

R/generate_dailyvar.R

@@ -37,13 +37,13 @@ generate_dailyvar <- function(hourly_data,
   Snet <- VPD <- WS <- time_numeric <- Temp <- NULL # nolint
 
   # dailyvar
+  ndays <- length(unique(date(hourly_data$time)))
   hourly_data %>%
     rename(Temp = temperature, Snet = snet, VPD = vpd, WS = ws) %>%
     mutate(time_hour = hour(time)) %>%
     filter(time_hour >= daytime_start, time_hour < daytime_end) %>%
     select(-time_hour) %>%
     mutate(time_numeric = hour(time) + minute(time) / 60) %>%
-    mutate(DayJulian = date(time) - date(first(time)) + 1) %>%
-    mutate(DayJulian = as.numeric(DayJulian)) %>%
+    mutate(DayJulian = rep(1:ndays, each = 24)) %>% 
     select(DayJulian, time_numeric, Temp, Snet, VPD, WS)
 }

R/generate_parameters.R

@@ -122,7 +122,7 @@ generate_parameters <- function(cols = 200,
                                 SWtoPPFD = 2.27, # nolint
                                 p_nonvert = 0.05,
                                 klight = 0.5,
-                                phi = 0.093,
+                                phi = 0.10625,
                                 absorptance_leaves = 0.83,
                                 theta = 0.7,
                                 g1 = 3.77,
@@ -134,8 +134,8 @@ generate_parameters <- function(cols = 200,
                                 DBH0 = 0.005, # nolint
                                 H0 = 0.950, # nolint
                                 CR_min = 0.3, # nolint
-                                CR_a = 2.13, # nolint
-                                CR_b = 0.63, # nolint
+                                CR_a = 1.85, # nolint
+                                CR_b = 0.4445, # nolint
                                 CD_a = 0, # nolint
                                 CD_b = 0.2, # nolint
                                 CD0 = 0.3, # nolint
@@ -163,8 +163,8 @@ generate_parameters <- function(cols = 200,
                                 p_tfsecondary = 1,
                                 hurt_decay = 0,
                                 crown_gap_fraction = 0.15,
-                                m = 0.025,
-                                m1 = 0.025,
+                                m = 0.045,
+                                m1 = 0.045,
                                 Cair = 375, # nolint
                                 PRESS = 101.0, # nolint
                                 SOIL_LAYER_WEIGHT = 2, # nolint

inst/extdata/TROLLv4_input.txt

@@ -11,7 +11,7 @@ nbspp	109	/* Number of species */
 SWtoPPFD	2.27	/* convert short wave irradiance to PAR photons (cf. code) */
 p_nonvert	0.05	/* light incidence param (diff through turbid medium) */
 klight	0.5	/* light attenuation in the canopy Beer-Lambert */
-phi	0.093	/*  quantum yield (in micromol C/micromol photon) */
+phi	0.10625	/*  quantum yield (in micromol C/micromol photon) */
 absorptance_leaves	0.83	/* absorptance of individual leaves */
 theta	0.7	/* parameter of the Farquhar model */
 g1	3.77	/* parameter g1 of Medlyn et al ’s stomatal conductance model */
@@ -23,8 +23,8 @@ vC	0.021	/* variance of the flexion moment */
 DBH0	0.005	/* initial dbh (m) */
 H0	0.95	/* initial height (m) */
 CR_min 	0.3	/* minimum crown radius (in m) */
-CR_a	2.13	/* CR log intercept or Michaelis Menten initial growth */
-CR_b	0.63	/* CR log slope or Michaelis Menten asymptotic CR */
+CR_a	1.85	/* CR log intercept or Michaelis Menten initial growth */
+CR_b	0.4445	/* CR log slope or Michaelis Menten asymptotic CR */
 CD_a	0.0	/* CD intercept (absolute value) */
 CD_b	0.2	/* CD slope (as fraction of tree height) */
 CD0	0.3	/* initial crown depth(in m) */
@@ -52,8 +52,8 @@ leafdem_resolution	1	/* resolution of leaf demography model */
 p_tfsecondary	1.0	/* probability of secondary treefall */
 hurt_decay	0	/*  parameter determining how tree damages are repaired */
 crown_gap_fraction	0.15	/* fraction of gaps in the crown */
-m	0.025	/* minimal death rate */
-m1	0.025	/* m1 (slope of death rate) */
+m	0.045	/* minimal death rate */
+m1	0.045	/* m1 (slope of death rate) */
 Cair	375	/* atmospheric CO2 concentration in micromol/mol */
 PRESS	101.0	/* atmospheric pressure in kPa
 _SOIL_LAYER_WEIGHT	2	/* soil layer weights: relative biomass, conductance, max transpiration (0,1, 2) */
@@ -62,7 +62,7 @@ _LL_parameterization	0	/* LL parameterizations: empirical, Kikuzawa model, and K
 _LA_regulation	2	/* dynamic LA regulation: off, 1.0, 0.75, or 0.5 (0,1,2,3) */
 _sapwood	1	/* sapwood parameterizations: constant thickness (0.04), Fyllas percentage, Fyllas lower limit (0,1,2) */
 _seedsadditional	0	/* excess biomass into seeds after maturation (0,1) */
-_NONRANDOM	0	/* If _NONRANDOM == 1, the seeds for the random number generators will be kept fixed at 1, default for bug fixing */
+_NONRANDOM	1	/* If _NONRANDOM == 1, the seeds for the random number generators will be kept fixed at 1, default for bug fixing */
 _GPPcrown	0	/* This defines an option to compute only GPP from the topmost value of PPFD and GPP, instead of looping within the crown. */
 _BASICTREEFALL	1	/* if defined: treefall is a source of tree death */
 _SEEDTRADEOFF	0	/* if defined: the number of seeds produced is determined by NPP allocated to reproduction and seed mass, otherwise the number of seeds is fixed */