From 15a737b8d28fb4aae85d8c25c1e13dfc8115b196 Mon Sep 17 00:00:00 2001 From: mrke Date: Fri, 7 Jun 2024 17:34:33 +1000 Subject: [PATCH] updating vignettes --- inst/doc/endotherm-model-tutorial.html | 4 ++-- inst/doc/leaf-temperature-tutorial.Rmd | 2 +- inst/doc/leaf-temperature-tutorial.html | 20 ++++++++++---------- 3 files changed, 13 insertions(+), 13 deletions(-) diff --git a/inst/doc/endotherm-model-tutorial.html b/inst/doc/endotherm-model-tutorial.html index a44da62..6b19ecd 100644 --- a/inst/doc/endotherm-model-tutorial.html +++ b/inst/doc/endotherm-model-tutorial.html @@ -800,7 +800,7 @@

Metabolic chamber example

}) # run endoR across environments proc.time() - ptm # stop timing 
##    user  system elapsed 
-##     0.1     0.0     0.1
+## 0.24 0.02 0.25 
# extract the output
 endo.out1 <- do.call("rbind", lapply(endo.out, data.frame))
 
@@ -959,7 +959,7 @@ 
Microclimate model integration example

 })
 proc.time() - ptm  # end timing
##    user  system elapsed 
-##    0.47    0.00    0.47
+## 1.05 0.00 1.05 
# extract the output
 endo.out1 <- do.call("rbind", lapply(endo.out, data.frame))
 
diff --git a/inst/doc/leaf-temperature-tutorial.Rmd b/inst/doc/leaf-temperature-tutorial.Rmd
index 055bdbf..11c6ab8 100644
--- a/inst/doc/leaf-temperature-tutorial.Rmd
+++ b/inst/doc/leaf-temperature-tutorial.Rmd
@@ -4,7 +4,7 @@ author: "Michael Kearney"
 date: "`r Sys.Date()`"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{Leaf Temperature Tutorial}
+  %\VignetteIndexEntry{Leaf Temperature Simulations}
   %\VignetteEncoding{UTF-8}
   %\VignetteEngine{knitr::rmarkdown}
 urlcolor: blue    
diff --git a/inst/doc/leaf-temperature-tutorial.html b/inst/doc/leaf-temperature-tutorial.html
index cca2e9e..081c085 100644
--- a/inst/doc/leaf-temperature-tutorial.html
+++ b/inst/doc/leaf-temperature-tutorial.html
@@ -507,7 +507,7 @@ 
Run the NicheMapR ectotherm model

     postur = postur, preshr = P_a, PDIF = PDIFs)
 print(proc.time() - ptm)  # Stop the clock
##    user  system elapsed 
-##    0.01    0.00    0.02
+## 0.03 0.00 0.03 
environ <- as.data.frame(ecto$environ)
 T_leaf_NMR <- environ$TC

Now plot the results against air temperature at leaf height and at @@ -575,7 +575,7 @@

Run NicheMapR ectoR_devel model

} print(proc.time() - ptm) # Stop the clock 
##    user  system elapsed 
-##    0.49    0.00    0.50
+## 0.59 0.02 0.61 
# plot
 plot(seq(0, 23), T_air_1cm[sub], type = 'l', col = 'blue', ylab = 'temperature, deg C', xlab = 'hour of day', ylim = c(15, 50))
 points(seq(0, 23), T_air_1.2m[sub], type = 'l', col = 'blue', lty = 2)
@@ -644,7 +644,7 @@ 
Run the Campbell and Norman model

 )})) # run leaf_temperature across environments
 print(proc.time() - ptm) # Stop the clock
##    user  system elapsed 
-##    0.63    0.11    0.81
+## 0.79 0.21 1.06 
# plot
 plot(seq(0, 23), T_air_1cm[sub], type = 'l', col = 'blue', ylab = 'temperature, deg C', xlab = 'hour of day', ylim = c(15, 50))
 points(seq(0, 23), T_air_1.2m[sub], type = 'l', col = 'blue', lty = 2)
@@ -681,7 +681,7 @@ 
Run the plantecophys leaf temperature model

   LeafAbs = alpha_L)})) # run FindTleaf across environments
 print(proc.time() - ptm) # Stop the clock
##    user  system elapsed 
-##    0.72    0.17    1.00
+## 0.92 0.33 1.31 
# plot
 plot(seq(0, 23), T_air_1cm[sub], type = 'l', col = 'blue', ylab = 'temperature, deg C', xlab = 'hour of day', ylim = c(15, 50))
 points(seq(0, 23), T_air_1.2m[sub], type = 'l', col = 'blue', lty = 2)
@@ -726,7 +726,7 @@ 
Run the tealeaves model

 }
 print(proc.time() - ptm)  # Stop the clock
##    user  system elapsed 
-##   40.22    0.99   41.99
+## 37.59 0.90 39.64 
colnames(T_leaf_tealeaves) <- colnames(T_leaf)
 T_leaf_tealeaves <- as.data.frame(T_leaf_tealeaves)$T_leaf -
     273.15
@@ -824,7 +824,7 @@ 
Incorporating stomatal dynamics with the plantecophys package

     postur = postur, preshr = P_a, PDIF = PDIFs)
 print(proc.time() - ptm)  # Stop the clock
##    user  system elapsed 
-##    0.02    0.00    0.01
+## 0.02 0.00 0.02 
environ <- as.data.frame(ecto$environ)
 T_leaf_NMR_plantecophys <- environ$TC

Compare the two calculations of leaf temperature. Stomatal closure in @@ -983,7 +983,7 @@

Simulate microclimate in the Mojave Desert

## running micro_global to get clear sky solar ## running microclimate model for 731 days from 01/01/2016 to 31/12/2017 at site long -116.53 lat 33.83 ## user system elapsed -## 36.57 0.20 36.88 +## 38.55 0.16 38.72 
# define time zone
 tz <- paste0("Etc/GMT-", floor(micro$longlat[1]/15 * -1))
 dates <- micro$dates
@@ -1054,7 +1054,7 @@ 
Compute stomatal dynamics with Photosyn

     postur = postur, preshr = P_a, PDIF = PDIFs)
 print(proc.time() - ptm)  # Stop the clock
##    user  system elapsed 
-##    1.38    0.08    1.46
+## 1.05 0.08 1.12 
environ <- as.data.frame(ecto$environ)
 T_leaf_photosyn <- environ$TC
 plot(dates[sub], T_leaf_photosyn[sub], type = "l", ylim = c(-5,
@@ -1088,7 +1088,7 @@ 
Impose effects of water stress on stomatal dynamics

     postur = postur, preshr = P_a, PDIF = PDIFs)
 print(proc.time() - ptm)  # Stop the clock
##    user  system elapsed 
-##    1.34    0.05    1.39
+## 0.98 0.08 1.09 
environ <- as.data.frame(ecto$environ)
 T_leaf <- environ$TC
 # plot(dates[sub], T_leaf[sub], type = 'l', ylim = c(-5,
@@ -1124,7 +1124,7 @@ 
Impose effects of water stress on stomatal dynamics

     postur = postur, preshr = P_a, PDIF = PDIFs)
 print(proc.time() - ptm)  # Stop the clock
##    user  system elapsed 
-##    1.66    0.10    1.75
+## 1.33 0.04 1.38 
environ <- as.data.frame(ecto$environ)
 T_leaf <- environ$TC
 plot(dates[sub], T_leaf[sub], type = "l", ylim = c(-5, 70), ylab = "leaf temperature, deg C",