Updates (#108)

plantphys · Jun 17, 2024 · 8454110 · 8454110
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diff --git a/inst/doc/ely_etal_ex1.pdf b/inst/doc/ely_etal_ex1.pdf
diff --git a/inst/doc/ely_etal_ex2.pdf b/inst/doc/ely_etal_ex2.pdf
diff --git a/inst/doc/kit_sla_ex3.pdf b/inst/doc/kit_sla_ex3.pdf
diff --git a/inst/doc/neon_canopy_leafN_ex5.pdf b/inst/doc/neon_canopy_leafN_ex5.pdf
diff --git a/inst/doc/neon_canopy_lma_ex10.pdf b/inst/doc/neon_canopy_lma_ex10.pdf
diff --git a/inst/doc/neon_lma_ex4.pdf b/inst/doc/neon_lma_ex4.pdf
diff --git a/inst/doc/reseco_leafN_ex6.pdf b/inst/doc/reseco_leafN_ex6.pdf
diff --git a/inst/doc/reseco_leafN_ex7.pdf b/inst/doc/reseco_leafN_ex7.pdf
diff --git a/inst/doc/reseco_lma_ex8.pdf b/inst/doc/reseco_lma_ex8.pdf
diff --git a/inst/doc/sserbin2019_plsr_ex9.pdf b/inst/doc/sserbin2019_plsr_ex9.pdf
diff --git a/inst/docs/ely_etal_ex1.pdf b/inst/docs/ely_etal_ex1.pdf
diff --git a/inst/docs/ely_etal_ex2.pdf b/inst/docs/ely_etal_ex2.pdf
diff --git a/inst/docs/kit_sla_ex3.pdf b/inst/docs/kit_sla_ex3.pdf
diff --git a/inst/docs/neon_canopy_leafN_ex5.pdf b/inst/docs/neon_canopy_leafN_ex5.pdf
diff --git a/inst/docs/neon_lma_ex4.pdf b/inst/docs/neon_lma_ex4.pdf
diff --git a/inst/docs/reseco_leafN_ex6.pdf b/inst/docs/reseco_leafN_ex6.pdf
diff --git a/inst/docs/reseco_leafN_ex7.pdf b/inst/docs/reseco_leafN_ex7.pdf
diff --git a/inst/docs/reseco_lma_ex8.pdf b/inst/docs/reseco_lma_ex8.pdf
diff --git a/inst/docs/sserbin2019_plsr_ex9.pdf b/inst/docs/sserbin2019_plsr_ex9.pdf
diff --git a/spectratrait_1.2.1.pdf → spectratrait_1.2.5.pdf b/spectratrait_1.2.1.pdf → spectratrait_1.2.5.pdf
diff --git a/vignettes/ely_etal_ex1.Rmd b/vignettes/ely_etal_ex1.Rmd
@@ -4,11 +4,11 @@ author: "Shawn P. Serbin, Julien Lamour, & Jeremiah Anderson"
 date: "`r Sys.Date()`"
 output:
   github_document: default
-  pdf_document: default
-  html_notebook: default
   html_document:
     df_print: paged
     keep_md: true
+  pdf_document: default
+  html_notebook: default
   rmarkdown: html_vignette
 vignette: >
   %\VignetteIndexEntry{Spectra-trait PLSR example using leaf-level spectra and leaf nitrogen content (Narea, g/m2) data from eight different crop species growing in a glasshouse at Brookhaven National Laboratory}

diff --git a/vignettes/ely_etal_ex1.md b/vignettes/ely_etal_ex1.md
@@ -3,13 +3,13 @@ content (Narea, g/m2) data from eight different crop species growing in
 a glasshouse at Brookhaven National Laboratory
 ================
 Shawn P. Serbin, Julien Lamour, & Jeremiah Anderson
-2022-03-17
+2024-06-17
 
 ### Overview
 
 This is an [R Markdown](http://rmarkdown.rstudio.com) Notebook to
-illustrate how to load an internal dataset (“ely\_plsr\_data”), choose
-the “optimal” number of plsr components, and fit a plsr model for leaf
+illustrate how to load an internal dataset (“ely_plsr_data”), choose the
+“optimal” number of plsr components, and fit a plsr model for leaf
 nitrogen content (Narea, g/m2)
 
 ### Getting Started
@@ -21,14 +21,16 @@ list.of.packages <- c("pls","dplyr","here","plotrix","ggplot2","gridExtra","spec
 invisible(lapply(list.of.packages, library, character.only = TRUE))
 ```
 
+    ## Warning: package 'pls' was built under R version 4.3.1
+
     ## 
     ## Attaching package: 'pls'
 
     ## The following object is masked from 'package:stats':
     ## 
     ##     loadings
 
-    ## Warning: package 'dplyr' was built under R version 4.0.5
+    ## Warning: package 'dplyr' was built under R version 4.3.1
 
     ## 
     ## Attaching package: 'dplyr'
@@ -41,7 +43,11 @@ invisible(lapply(list.of.packages, library, character.only = TRUE))
     ## 
     ##     intersect, setdiff, setequal, union
 
-    ## here() starts at /Users/sserbin/Data/GitHub/spectratrait
+    ## here() starts at /Users/sserbin/Library/CloudStorage/OneDrive-NASA/Data/Github/spectratrait
+
+    ## Warning: package 'plotrix' was built under R version 4.3.1
+
+    ## Warning: package 'ggplot2' was built under R version 4.3.1
 
     ## 
     ## Attaching package: 'gridExtra'
@@ -103,7 +109,7 @@ inVar <- "N_g_m2"
 
 ### Set working directory (scratch space)
 
-    ## [1] "/private/var/folders/xp/h3k9vf3n2jx181ts786_yjrn9c2gjq/T/RtmpP2S4KY"
+    ## [1] "/private/var/folders/th/fpt_z3417gn8xgply92pvy6r0000gq/T/RtmpJ3BBUV"
 
 ### Full PLSR dataset
 
@@ -219,6 +225,14 @@ cal_hist_plot <- qplot(cal.plsr.data[,paste0(inVar)],geom="histogram",
                        main = paste0("Cal. Histogram for ",inVar),
                        xlab = paste0(inVar),ylab = "Count",fill=I("grey50"),col=I("black"),
                        alpha=I(.7))
+```
+
+    ## Warning: `qplot()` was deprecated in ggplot2 3.4.0.
+    ## This warning is displayed once every 8 hours.
+    ## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
+    ## generated.
+
+``` r
 val_hist_plot <- qplot(val.plsr.data[,paste0(inVar)],geom="histogram",
                        main = paste0("Val. Histogram for ",inVar),
                        xlab = paste0(inVar),ylab = "Count",fill=I("grey50"),col=I("black"),
@@ -495,7 +509,21 @@ cal_scatter_plot <- ggplot(cal.plsr.output, aes(x=PLSR_CV_Predicted, y=get(inVar
         axis.title=element_text(size=20, face="bold"), 
         axis.text.x = element_text(angle = 0,vjust = 0.5),
         panel.border = element_rect(linetype = "solid", fill = NA, size=1.5))
+```
+
+    ## Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
+    ## ℹ Please use `linewidth` instead.
+    ## This warning is displayed once every 8 hours.
+    ## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
+    ## generated.
 
+    ## Warning: The `size` argument of `element_rect()` is deprecated as of ggplot2 3.4.0.
+    ## ℹ Please use the `linewidth` argument instead.
+    ## This warning is displayed once every 8 hours.
+    ## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
+    ## generated.
+
+``` r
 cal_resid_histogram <- ggplot(cal.plsr.output, aes(x=PLSR_CV_Residuals)) +
   geom_histogram(alpha=.5, position="identity") + 
   geom_vline(xintercept = 0, color="black", 
@@ -534,8 +562,11 @@ scatterplots <- grid.arrange(cal_scatter_plot, val_scatter_plot, cal_resid_histo
                              val_resid_histogram, nrow=2,ncol=2)
 ```
 
-    ## Warning: Removed 3 rows containing missing values (geom_point).
-    ## Removed 3 rows containing missing values (geom_point).
+    ## Warning: Removed 3 rows containing missing values or values outside the scale range
+    ## (`geom_point()`).
+
+    ## Warning: Removed 3 rows containing missing values or values outside the scale range
+    ## (`geom_point()`).
 
     ## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
     ## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
@@ -754,7 +785,7 @@ write.csv(out.jk.coefs,file=file.path(outdir,paste0(inVar,
 print(paste("Output directory: ", outdir))
 ```
 
-    ## [1] "Output directory:  /var/folders/xp/h3k9vf3n2jx181ts786_yjrn9c2gjq/T//RtmpP2S4KY"
+    ## [1] "Output directory:  /var/folders/th/fpt_z3417gn8xgply92pvy6r0000gq/T//RtmpJ3BBUV"
 
 ``` r
 # Observed versus predicted

diff --git a/vignettes/ely_etal_ex1.pdf b/vignettes/ely_etal_ex1.pdf
diff --git a/vignettes/ely_etal_ex1_files/figure-gfm/unnamed-chunk-10-1.png b/vignettes/ely_etal_ex1_files/figure-gfm/unnamed-chunk-10-1.png
diff --git a/vignettes/ely_etal_ex1_files/figure-gfm/unnamed-chunk-11-1.png b/vignettes/ely_etal_ex1_files/figure-gfm/unnamed-chunk-11-1.png
diff --git a/vignettes/ely_etal_ex1_files/figure-gfm/unnamed-chunk-12-1.png b/vignettes/ely_etal_ex1_files/figure-gfm/unnamed-chunk-12-1.png
diff --git a/vignettes/ely_etal_ex1_files/figure-gfm/unnamed-chunk-14-1.png b/vignettes/ely_etal_ex1_files/figure-gfm/unnamed-chunk-14-1.png
diff --git a/vignettes/ely_etal_ex1_files/figure-gfm/unnamed-chunk-15-1.png b/vignettes/ely_etal_ex1_files/figure-gfm/unnamed-chunk-15-1.png
diff --git a/vignettes/ely_etal_ex1_files/figure-gfm/unnamed-chunk-6-1.png b/vignettes/ely_etal_ex1_files/figure-gfm/unnamed-chunk-6-1.png
diff --git a/vignettes/ely_etal_ex1_files/figure-gfm/unnamed-chunk-8-1.png b/vignettes/ely_etal_ex1_files/figure-gfm/unnamed-chunk-8-1.png
diff --git a/vignettes/ely_etal_ex1_files/figure-gfm/unnamed-chunk-9-1.png b/vignettes/ely_etal_ex1_files/figure-gfm/unnamed-chunk-9-1.png
diff --git a/vignettes/ely_etal_ex2.Rmd b/vignettes/ely_etal_ex2.Rmd
@@ -3,9 +3,9 @@ title: Spectra-trait PLSR example using leaf-level spectra and leaf nitrogen con
 author: "Shawn P. Serbin, Julien Lamour, & Jeremiah Anderson"
 date: "`r Sys.Date()`"
 output:
-  github_document: default
-  html_notebook: default
   pdf_document: default
+  html_notebook: default
+  github_document: default
   html_document:
     df_print: paged
     keep_md: true

diff --git a/vignettes/ely_etal_ex2.md b/vignettes/ely_etal_ex2.md
@@ -4,13 +4,13 @@ a glasshouse at Brookhaven National Laboratory. This example illustrates
 running the PLSR permutation by group
 ================
 Shawn P. Serbin, Julien Lamour, & Jeremiah Anderson
-2022-03-17
+2024-06-17
 
 ### Overview
 
 This is an [R Markdown](http://rmarkdown.rstudio.com) Notebook to
-illustrate how to load an internal dataset (“ely\_plsr\_data”), choose
-the “optimal” number of plsr components, and fit a plsr model for leaf
+illustrate how to load an internal dataset (“ely_plsr_data”), choose the
+“optimal” number of plsr components, and fit a plsr model for leaf
 nitrogen content (Narea, g/m2)
 
 ### Getting Started
@@ -22,14 +22,16 @@ list.of.packages <- c("pls","dplyr","here","plotrix","ggplot2","gridExtra","spec
 invisible(lapply(list.of.packages, library, character.only = TRUE))
 ```
 
+    ## Warning: package 'pls' was built under R version 4.3.1
+
     ## 
     ## Attaching package: 'pls'
 
     ## The following object is masked from 'package:stats':
     ## 
     ##     loadings
 
-    ## Warning: package 'dplyr' was built under R version 4.0.5
+    ## Warning: package 'dplyr' was built under R version 4.3.1
 
     ## 
     ## Attaching package: 'dplyr'
@@ -42,7 +44,11 @@ invisible(lapply(list.of.packages, library, character.only = TRUE))
     ## 
     ##     intersect, setdiff, setequal, union
 
-    ## here() starts at /Users/sserbin/Data/GitHub/spectratrait
+    ## here() starts at /Users/sserbin/Library/CloudStorage/OneDrive-NASA/Data/Github/spectratrait
+
+    ## Warning: package 'plotrix' was built under R version 4.3.1
+
+    ## Warning: package 'ggplot2' was built under R version 4.3.1
 
     ## 
     ## Attaching package: 'gridExtra'
@@ -104,7 +110,7 @@ inVar <- "N_g_m2"
 
 ### Set working directory (scratch space)
 
-    ## [1] "/private/var/folders/xp/h3k9vf3n2jx181ts786_yjrn9c2gjq/T/RtmpX6UzBl"
+    ## [1] "/private/var/folders/th/fpt_z3417gn8xgply92pvy6r0000gq/T/RtmpXZoXO6"
 
 ### Full PLSR dataset
 
@@ -220,6 +226,14 @@ cal_hist_plot <- qplot(cal.plsr.data[,paste0(inVar)],geom="histogram",
                        main = paste0("Cal. Histogram for ",inVar),
                        xlab = paste0(inVar),ylab = "Count",fill=I("grey50"),col=I("black"),
                        alpha=I(.7))
+```
+
+    ## Warning: `qplot()` was deprecated in ggplot2 3.4.0.
+    ## This warning is displayed once every 8 hours.
+    ## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
+    ## generated.
+
+``` r
 val_hist_plot <- qplot(val.plsr.data[,paste0(inVar)],geom="histogram",
                        main = paste0("Val. Histogram for ",inVar),
                        xlab = paste0(inVar),ylab = "Count",fill=I("grey50"),col=I("black"),
@@ -493,7 +507,21 @@ cal_scatter_plot <- ggplot(cal.plsr.output, aes(x=PLSR_CV_Predicted, y=get(inVar
         axis.title=element_text(size=20, face="bold"), 
         axis.text.x = element_text(angle = 0,vjust = 0.5),
         panel.border = element_rect(linetype = "solid", fill = NA, size=1.5))
+```
+
+    ## Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
+    ## ℹ Please use `linewidth` instead.
+    ## This warning is displayed once every 8 hours.
+    ## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
+    ## generated.
 
+    ## Warning: The `size` argument of `element_rect()` is deprecated as of ggplot2 3.4.0.
+    ## ℹ Please use the `linewidth` argument instead.
+    ## This warning is displayed once every 8 hours.
+    ## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
+    ## generated.
+
+``` r
 cal_resid_histogram <- ggplot(cal.plsr.output, aes(x=PLSR_CV_Residuals)) +
   geom_histogram(alpha=.5, position="identity") + 
   geom_vline(xintercept = 0, color="black", 
@@ -532,9 +560,11 @@ scatterplots <- grid.arrange(cal_scatter_plot, val_scatter_plot, cal_resid_histo
                              val_resid_histogram, nrow=2,ncol=2)
 ```
 
-    ## Warning: Removed 5 rows containing missing values (geom_point).
+    ## Warning: Removed 5 rows containing missing values or values outside the scale range
+    ## (`geom_point()`).
 
-    ## Warning: Removed 4 rows containing missing values (geom_point).
+    ## Warning: Removed 4 rows containing missing values or values outside the scale range
+    ## (`geom_point()`).
 
     ## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
     ## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
@@ -755,7 +785,7 @@ write.csv(out.jk.coefs,file=file.path(outdir,paste0(inVar,
 print(paste("Output directory: ", outdir))
 ```
 
-    ## [1] "Output directory:  /var/folders/xp/h3k9vf3n2jx181ts786_yjrn9c2gjq/T//RtmpX6UzBl"
+    ## [1] "Output directory:  /var/folders/th/fpt_z3417gn8xgply92pvy6r0000gq/T//RtmpXZoXO6"
 
 ``` r
 # Observed versus predicted

diff --git a/vignettes/ely_etal_ex2.pdf b/vignettes/ely_etal_ex2.pdf
diff --git a/vignettes/ely_etal_ex2_files/figure-gfm/unnamed-chunk-10-1.png b/vignettes/ely_etal_ex2_files/figure-gfm/unnamed-chunk-10-1.png
diff --git a/vignettes/ely_etal_ex2_files/figure-gfm/unnamed-chunk-11-1.png b/vignettes/ely_etal_ex2_files/figure-gfm/unnamed-chunk-11-1.png
diff --git a/vignettes/ely_etal_ex2_files/figure-gfm/unnamed-chunk-12-1.png b/vignettes/ely_etal_ex2_files/figure-gfm/unnamed-chunk-12-1.png
diff --git a/vignettes/ely_etal_ex2_files/figure-gfm/unnamed-chunk-14-1.png b/vignettes/ely_etal_ex2_files/figure-gfm/unnamed-chunk-14-1.png
diff --git a/vignettes/ely_etal_ex2_files/figure-gfm/unnamed-chunk-15-1.png b/vignettes/ely_etal_ex2_files/figure-gfm/unnamed-chunk-15-1.png
diff --git a/vignettes/ely_etal_ex2_files/figure-gfm/unnamed-chunk-6-1.png b/vignettes/ely_etal_ex2_files/figure-gfm/unnamed-chunk-6-1.png
diff --git a/vignettes/ely_etal_ex2_files/figure-gfm/unnamed-chunk-8-1.png b/vignettes/ely_etal_ex2_files/figure-gfm/unnamed-chunk-8-1.png
diff --git a/vignettes/ely_etal_ex2_files/figure-gfm/unnamed-chunk-9-1.png b/vignettes/ely_etal_ex2_files/figure-gfm/unnamed-chunk-9-1.png
diff --git a/vignettes/kit_sla_ex3.Rmd b/vignettes/kit_sla_ex3.Rmd
@@ -3,8 +3,8 @@ title: Spectra-trait PLSR example using leaf-level spectra and specific leaf are
 author: "Shawn P. Serbin, Julien Lamour, & Jeremiah Anderson"
 date: "`r Sys.Date()`"
 output:
-  github_document: default
   pdf_document: default
+  github_document: default
   html_notebook: default
   html_document:
     df_print: paged
@@ -145,12 +145,10 @@ write.csv(val.plsr.data,file=file.path(outdir,paste0(inVar,'_Val_PLSR_Dataset.cs
 cal_spec <- as.matrix(cal.plsr.data[, which(names(cal.plsr.data) %in% paste0("Wave_",wv))])
 cal.plsr.data <- data.frame(cal.plsr.data[, which(names(cal.plsr.data) %notin% paste0("Wave_",wv))],
                             Spectra=I(cal_spec))
-head(cal.plsr.data)[1:5]
 
 val_spec <- as.matrix(val.plsr.data[, which(names(val.plsr.data) %in% paste0("Wave_",wv))])
 val.plsr.data <- data.frame(val.plsr.data[, which(names(val.plsr.data) %notin% paste0("Wave_",wv))],
                             Spectra=I(val_spec))
-head(val.plsr.data)[1:5]
 ```
 
 ### plot cal and val spectra