Merge pull request #82 from TESTgroup-BNL/minor_bugfix

Minor bugfix to address R2 error in the examples
plantphys · Apr 30, 2021 · 3182844 · 3182844
2 parents 709781b + 67f5c58
commit 3182844
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Showing 35 changed files with 87 additions and 87 deletions.
diff --git a/inst/scripts/simple_spectra-trait_plsr_example.R b/inst/scripts/simple_spectra-trait_plsr_example.R
@@ -187,7 +187,7 @@ plsr_data.output <- data.frame(plsr_data[, which(names(plsr_data) %notin% "Spect
 plsr_data.output <- plsr_data.output %>%
   mutate(PLSR_CV_Residuals = PLSR_CV_Predicted-get(inVar))
 head(plsr_data.output)
-cal.R2 <- round(pls::R2(plsr.out)[[1]][nComps],2)
+cal.R2 <- round(pls::R2(plsr.out,intercept=F)[[1]][nComps],2)
 cal.RMSEP <- round(sqrt(mean(plsr_data.output$PLSR_CV_Residuals^2)),2)
 
 rng_quant <- quantile(plsr_data.output[,inVar], probs = c(0.001, 0.999))

diff --git a/inst/scripts/spectra-trait_ely_leafN_plsr_bootstrap_example.R b/inst/scripts/spectra-trait_ely_leafN_plsr_bootstrap_example.R
@@ -209,7 +209,7 @@ cal.plsr.output <- data.frame(cal.plsr.data[, which(names(cal.plsr.data) %notin%
 cal.plsr.output <- cal.plsr.output %>%
   mutate(PLSR_CV_Residuals = PLSR_CV_Predicted-get(inVar))
 head(cal.plsr.output)
-cal.R2 <- round(pls::R2(plsr.out)[[1]][nComps],2)
+cal.R2 <- round(pls::R2(plsr.out,intercept=F)[[1]][nComps],2)
 cal.RMSEP <- round(sqrt(mean(cal.plsr.output$PLSR_CV_Residuals^2)),2)
 
 val.plsr.output <- data.frame(val.plsr.data[, which(names(val.plsr.data) %notin% "Spectra")],
@@ -219,7 +219,7 @@ val.plsr.output <- data.frame(val.plsr.data[, which(names(val.plsr.data) %notin%
 val.plsr.output <- val.plsr.output %>%
   mutate(PLSR_Residuals = PLSR_Predicted-get(inVar))
 head(val.plsr.output)
-val.R2 <- round(pls::R2(plsr.out,newdata=val.plsr.data)[[1]][nComps],2)
+val.R2 <- round(pls::R2(plsr.out,newdata=val.plsr.data,intercept=F)[[1]][nComps],2)
 val.RMSEP <- round(sqrt(mean(val.plsr.output$PLSR_Residuals^2)),2)
 
 rng_quant <- quantile(cal.plsr.output[,inVar], probs = c(0.001, 0.999))
@@ -345,7 +345,7 @@ rmsep_percrmsep <- spectratrait::percent_rmse(plsr_dataset = val.plsr.output,
                                               range="full")
 RMSEP <- rmsep_percrmsep$rmse
 perc_RMSEP <- rmsep_percrmsep$perc_rmse
-r2 <- round(pls::R2(plsr.out, newdata = val.plsr.data)$val[nComps+1],2)
+r2 <- round(pls::R2(plsr.out, newdata = val.plsr.data, intercept=F)$val[nComps],2)
 expr <- vector("expression", 3)
 expr[[1]] <- bquote(R^2==.(r2))
 expr[[2]] <- bquote(RMSEP==.(round(RMSEP,2)))

diff --git a/inst/scripts/spectra-trait_kit_sla_plsr_example.R b/inst/scripts/spectra-trait_kit_sla_plsr_example.R
@@ -235,7 +235,7 @@ cal.plsr.output <- data.frame(cal.plsr.data[, which(names(cal.plsr.data) %notin%
 cal.plsr.output <- cal.plsr.output %>%
   mutate(PLSR_CV_Residuals = PLSR_CV_Predicted-get(inVar))
 head(cal.plsr.output)
-cal.R2 <- round(pls::R2(plsr.out)[[1]][nComps],2)
+cal.R2 <- round(pls::R2(plsr.out,intercept=F)[[1]][nComps],2)
 cal.RMSEP <- round(sqrt(mean(cal.plsr.output$PLSR_CV_Residuals^2)),2)
 
 val.plsr.output <- data.frame(val.plsr.data[, which(names(val.plsr.data) %notin% "Spectra")],
@@ -245,7 +245,7 @@ val.plsr.output <- data.frame(val.plsr.data[, which(names(val.plsr.data) %notin%
 val.plsr.output <- val.plsr.output %>%
   mutate(PLSR_Residuals = PLSR_Predicted-get(inVar))
 head(val.plsr.output)
-val.R2 <- round(pls::R2(plsr.out,newdata=val.plsr.data)[[1]][nComps],2)
+val.R2 <- round(pls::R2(plsr.out,newdata=val.plsr.data,intercept=F)[[1]][nComps],2)
 val.RMSEP <- round(sqrt(mean(val.plsr.output$PLSR_Residuals^2)),2)
 
 rng_quant <- quantile(cal.plsr.output[,inVar], probs = c(0.001, 0.999))
@@ -371,7 +371,7 @@ rmsep_percrmsep <- spectratrait::percent_rmse(plsr_dataset = val.plsr.output,
                                               range="full")
 RMSEP <- rmsep_percrmsep$rmse
 perc_RMSEP <- rmsep_percrmsep$perc_rmse
-r2 <- round(pls::R2(plsr.out, newdata = val.plsr.data)$val[nComps+1],2)
+r2 <- round(pls::R2(plsr.out, newdata = val.plsr.data, intercept=F)$val[nComps],2)
 expr <- vector("expression", 3)
 expr[[1]] <- bquote(R^2==.(r2))
 expr[[2]] <- bquote(RMSEP==.(round(RMSEP,2)))

diff --git a/inst/scripts/spectra-trait_neon_leafN_canopy_plsr_example.R b/inst/scripts/spectra-trait_neon_leafN_canopy_plsr_example.R
@@ -272,7 +272,7 @@ cal.plsr.output <- data.frame(cal.plsr.data[, which(names(cal.plsr.data) %notin%
 cal.plsr.output <- cal.plsr.output %>%
   mutate(PLSR_CV_Residuals = PLSR_CV_Predicted-get(inVar))
 head(cal.plsr.output)
-cal.R2 <- round(pls::R2(plsr.out)[[1]][nComps],2)
+cal.R2 <- round(pls::R2(plsr.out,intercept=F)[[1]][nComps],2)
 cal.RMSEP <- round(sqrt(mean(cal.plsr.output$PLSR_CV_Residuals^2)),2)
 
 val.plsr.output <- data.frame(val.plsr.data[, which(names(val.plsr.data) %notin% "Spectra")],
@@ -282,7 +282,7 @@ val.plsr.output <- data.frame(val.plsr.data[, which(names(val.plsr.data) %notin%
 val.plsr.output <- val.plsr.output %>%
   mutate(PLSR_Residuals = PLSR_Predicted-get(inVar))
 head(val.plsr.output)
-val.R2 <- round(pls::R2(plsr.out,newdata=val.plsr.data)[[1]][nComps],2)
+val.R2 <- round(pls::R2(plsr.out,newdata=val.plsr.data,intercept=F)[[1]][nComps],2)
 val.RMSEP <- round(sqrt(mean(val.plsr.output$PLSR_Residuals^2)),2)
 
 rng_quant <- quantile(cal.plsr.output[,inVar], probs = c(0.001, 0.999))
@@ -412,7 +412,7 @@ rmsep_percrmsep <- spectratrait::percent_rmse(plsr_dataset = val.plsr.output,
                                               range="full")
 RMSEP <- rmsep_percrmsep$rmse
 perc_RMSEP <- rmsep_percrmsep$perc_rmse
-r2 <- round(pls::R2(plsr.out, newdata = val.plsr.data)$val[nComps+1],2)
+r2 <- round(pls::R2(plsr.out, newdata = val.plsr.data, intercept=F)$val[nComps],2)
 expr <- vector("expression", 3)
 expr[[1]] <- bquote(R^2==.(r2))
 expr[[2]] <- bquote(RMSEP==.(round(RMSEP,2)))

diff --git a/inst/scripts/spectra-trait_neon_lma_plsr_example.R b/inst/scripts/spectra-trait_neon_lma_plsr_example.R
@@ -236,7 +236,7 @@ cal.plsr.output <- data.frame(cal.plsr.data[, which(names(cal.plsr.data) %notin%
 cal.plsr.output <- cal.plsr.output %>%
   mutate(PLSR_CV_Residuals = PLSR_CV_Predicted-get(inVar))
 head(cal.plsr.output)
-cal.R2 <- round(pls::R2(plsr.out)[[1]][nComps],2)
+cal.R2 <- round(pls::R2(plsr.out,intercept=F)[[1]][nComps],2)
 cal.RMSEP <- round(sqrt(mean(cal.plsr.output$PLSR_CV_Residuals^2)),2)
 
 val.plsr.output <- data.frame(val.plsr.data[, which(names(val.plsr.data) %notin% "Spectra")],
@@ -246,7 +246,7 @@ val.plsr.output <- data.frame(val.plsr.data[, which(names(val.plsr.data) %notin%
 val.plsr.output <- val.plsr.output %>%
   mutate(PLSR_Residuals = PLSR_Predicted-get(inVar))
 head(val.plsr.output)
-val.R2 <- round(pls::R2(plsr.out,newdata=val.plsr.data)[[1]][nComps],2)
+val.R2 <- round(pls::R2(plsr.out,newdata=val.plsr.data,intercept=F)[[1]][nComps],2)
 val.RMSEP <- round(sqrt(mean(val.plsr.output$PLSR_Residuals^2)),2)
 
 rng_quant <- quantile(cal.plsr.output[,inVar], probs = c(0.001, 0.999))
@@ -376,7 +376,7 @@ rmsep_percrmsep <- spectratrait::percent_rmse(plsr_dataset = val.plsr.output,
                                               range="full")
 RMSEP <- rmsep_percrmsep$rmse
 perc_RMSEP <- rmsep_percrmsep$perc_rmse
-r2 <- round(pls::R2(plsr.out, newdata = val.plsr.data)$val[nComps+1],2)
+r2 <- round(pls::R2(plsr.out, newdata = val.plsr.data, intercept=F)$val[nComps],2)
 expr <- vector("expression", 3)
 expr[[1]] <- bquote(R^2==.(r2))
 expr[[2]] <- bquote(RMSEP==.(round(RMSEP,2)))

diff --git a/inst/scripts/spectra-trait_reseco_leafN_plsr_bootstrap_example.R b/inst/scripts/spectra-trait_reseco_leafN_plsr_bootstrap_example.R
@@ -237,7 +237,7 @@ cal.plsr.output <- data.frame(cal.plsr.data[, which(names(cal.plsr.data) %notin%
 cal.plsr.output <- cal.plsr.output %>%
   mutate(PLSR_CV_Residuals = PLSR_CV_Predicted-get(inVar))
 head(cal.plsr.output)
-cal.R2 <- round(pls::R2(plsr.out)[[1]][nComps],2)
+cal.R2 <- round(pls::R2(plsr.out, intercept=F)[[1]][nComps],2)
 cal.RMSEP <- round(sqrt(mean(cal.plsr.output$PLSR_CV_Residuals^2)),2)
 
 val.plsr.output <- data.frame(val.plsr.data[, which(names(val.plsr.data) %notin% "Spectra")],
@@ -247,7 +247,7 @@ val.plsr.output <- data.frame(val.plsr.data[, which(names(val.plsr.data) %notin%
 val.plsr.output <- val.plsr.output %>%
   mutate(PLSR_Residuals = PLSR_Predicted-get(inVar))
 head(val.plsr.output)
-val.R2 <- round(pls::R2(plsr.out,newdata=val.plsr.data)[[1]][nComps],2)
+val.R2 <- round(pls::R2(plsr.out,newdata=val.plsr.data, intercept=F)[[1]][nComps],2)
 val.RMSEP <- round(sqrt(mean(val.plsr.output$PLSR_Residuals^2)),2)
 
 rng_quant <- quantile(cal.plsr.output[,inVar], probs = c(0.001, 0.999))
@@ -372,7 +372,7 @@ rmsep_percrmsep <- spectratrait::percent_rmse(plsr_dataset = val.plsr.output,
                                               range="full")
 RMSEP <- rmsep_percrmsep$rmse
 perc_RMSEP <- rmsep_percrmsep$perc_rmse
-r2 <- round(pls::R2(plsr.out, newdata = val.plsr.data)$val[nComps+1],2)
+r2 <- round(pls::R2(plsr.out, newdata = val.plsr.data, intercept=F)$val[nComps],2)
 expr <- vector("expression", 3)
 expr[[1]] <- bquote(R^2==.(r2))
 expr[[2]] <- bquote(RMSEP==.(round(RMSEP,2)))

diff --git a/inst/scripts/spectra-trait_reseco_leafN_plsr_example.R b/inst/scripts/spectra-trait_reseco_leafN_plsr_example.R
@@ -239,7 +239,7 @@ cal.plsr.output <- data.frame(cal.plsr.data[, which(names(cal.plsr.data) %notin%
 cal.plsr.output <- cal.plsr.output %>%
   mutate(PLSR_CV_Residuals = PLSR_CV_Predicted-get(inVar))
 head(cal.plsr.output)
-cal.R2 <- round(pls::R2(plsr.out)[[1]][nComps],2)
+cal.R2 <- round(pls::R2(plsr.out, intercept=F)[[1]][nComps],2)
 cal.RMSEP <- round(sqrt(mean(cal.plsr.output$PLSR_CV_Residuals^2)),2)
 
 val.plsr.output <- data.frame(val.plsr.data[, which(names(val.plsr.data) %notin% "Spectra")],
@@ -249,7 +249,7 @@ val.plsr.output <- data.frame(val.plsr.data[, which(names(val.plsr.data) %notin%
 val.plsr.output <- val.plsr.output %>%
   mutate(PLSR_Residuals = PLSR_Predicted-get(inVar))
 head(val.plsr.output)
-val.R2 <- round(pls::R2(plsr.out,newdata=val.plsr.data)[[1]][nComps],2)
+val.R2 <- round(pls::R2(plsr.out,newdata=val.plsr.data, intercept=F)[[1]][nComps],2)
 val.RMSEP <- round(sqrt(mean(val.plsr.output$PLSR_Residuals^2)),2)
 
 rng_quant <- quantile(cal.plsr.output[,inVar], probs = c(0.001, 0.999))
@@ -377,7 +377,7 @@ rmsep_percrmsep <- spectratrait::percent_rmse(plsr_dataset = val.plsr.output,
                                               range="full")
 RMSEP <- rmsep_percrmsep$rmse
 perc_RMSEP <- rmsep_percrmsep$perc_rmse
-r2 <- round(pls::R2(plsr.out, newdata = val.plsr.data)$val[nComps+1],2)
+r2 <- round(pls::R2(plsr.out, newdata = val.plsr.data, intercept=F)$val[nComps],2)
 expr <- vector("expression", 3)
 expr[[1]] <- bquote(R^2==.(r2))
 expr[[2]] <- bquote(RMSEP==.(round(RMSEP,2)))

diff --git a/inst/scripts/spectra-trait_reseco_lma_plsr_example.R b/inst/scripts/spectra-trait_reseco_lma_plsr_example.R
@@ -288,7 +288,7 @@ cal.plsr.output <- data.frame(cal.plsr.data[, which(names(cal.plsr.data) %notin%
 cal.plsr.output <- cal.plsr.output %>%
   mutate(PLSR_CV_Residuals = PLSR_CV_Predicted-get(inVar))
 head(cal.plsr.output)
-cal.R2 <- round(pls::R2(plsr.out)[[1]][nComps],2)
+cal.R2 <- round(pls::R2(plsr.out, intercept=F)[[1]][nComps],2)
 cal.RMSEP <- round(sqrt(mean(cal.plsr.output$PLSR_CV_Residuals^2)),2)
 
 val.plsr.output <- data.frame(val.plsr.data[, which(names(val.plsr.data) %notin% "Spectra")],
@@ -298,7 +298,7 @@ val.plsr.output <- data.frame(val.plsr.data[, which(names(val.plsr.data) %notin%
 val.plsr.output <- val.plsr.output %>%
   mutate(PLSR_Residuals = PLSR_Predicted-get(inVar))
 head(val.plsr.output)
-val.R2 <- round(pls::R2(plsr.out,newdata=val.plsr.data)[[1]][nComps],2)
+val.R2 <- round(pls::R2(plsr.out,newdata=val.plsr.data, intercept=F)[[1]][nComps],2)
 val.RMSEP <- round(sqrt(mean(val.plsr.output$PLSR_Residuals^2)),2)
 
 rng_quant <- quantile(cal.plsr.output[,inVar], probs = c(0.001, 0.999))
@@ -447,7 +447,7 @@ rmsep_percrmsep <- spectratrait::percent_rmse(plsr_dataset = val.plsr.output,
                                               range="full")
 RMSEP <- rmsep_percrmsep$rmse
 perc_RMSEP <- rmsep_percrmsep$perc_rmse
-r2 <- round(pls::R2(plsr.out, newdata = val.plsr.data)$val[nComps+1],2)
+r2 <- round(pls::R2(plsr.out, newdata = val.plsr.data, intercept=F)$val[nComps],2)
 expr <- vector("expression", 3)
 expr[[1]] <- bquote(R^2==.(r2))
 expr[[2]] <- bquote(RMSEP==.(round(RMSEP,2)))

diff --git a/vignettes/ely_leafN_bootstrap_plsr_example.Rmd b/vignettes/ely_leafN_bootstrap_plsr_example.Rmd
@@ -4,9 +4,9 @@ author: "Shawn P. Serbin, Julien Lamour, & Jeremiah Anderson"
 output:
   github_document: default
   html_notebook: default
+  pdf_document: default
   html_document:
     df_print: paged
-  pdf_document: default
 params:
   date: !r Sys.Date()
 ---
@@ -211,7 +211,7 @@ cal.plsr.output <- data.frame(cal.plsr.data[, which(names(cal.plsr.data) %notin%
 cal.plsr.output <- cal.plsr.output %>%
   mutate(PLSR_CV_Residuals = PLSR_CV_Predicted-get(inVar))
 head(cal.plsr.output)
-cal.R2 <- round(pls::R2(plsr.out)[[1]][nComps],2)
+cal.R2 <- round(pls::R2(plsr.out,intercept=F)[[1]][nComps],2)
 cal.RMSEP <- round(sqrt(mean(cal.plsr.output$PLSR_CV_Residuals^2)),2)
 
 val.plsr.output <- data.frame(val.plsr.data[, which(names(val.plsr.data) %notin% "Spectra")],
@@ -221,7 +221,7 @@ val.plsr.output <- data.frame(val.plsr.data[, which(names(val.plsr.data) %notin%
 val.plsr.output <- val.plsr.output %>%
   mutate(PLSR_Residuals = PLSR_Predicted-get(inVar))
 head(val.plsr.output)
-val.R2 <- round(pls::R2(plsr.out,newdata=val.plsr.data)[[1]][nComps],2)
+val.R2 <- round(pls::R2(plsr.out,newdata=val.plsr.data,intercept=F)[[1]][nComps],2)
 val.RMSEP <- round(sqrt(mean(val.plsr.output$PLSR_Residuals^2)),2)
 
 rng_quant <- quantile(cal.plsr.output[,inVar], probs = c(0.001, 0.999))
@@ -355,7 +355,7 @@ rmsep_percrmsep <- spectratrait::percent_rmse(plsr_dataset = val.plsr.output,
                                               range="full")
 RMSEP <- rmsep_percrmsep$rmse
 perc_RMSEP <- rmsep_percrmsep$perc_rmse
-r2 <- round(pls::R2(plsr.out, newdata = val.plsr.data)$val[nComps+1],2)
+r2 <- round(pls::R2(plsr.out, newdata = val.plsr.data, intercept=F)$val[nComps],2)
 expr <- vector("expression", 3)
 expr[[1]] <- bquote(R^2==.(r2))
 expr[[2]] <- bquote(RMSEP==.(round(RMSEP,2)))

diff --git a/vignettes/ely_leafN_bootstrap_plsr_example.md b/vignettes/ely_leafN_bootstrap_plsr_example.md
@@ -103,7 +103,7 @@ inVar <- "N_g_m2"
 
 ### Set working directory (scratch space)
 
-    ## [1] "/private/var/folders/xp/h3k9vf3n2jx181ts786_yjrn9c2gjq/T/RtmpqlTXi1"
+    ## [1] "/private/var/folders/xp/h3k9vf3n2jx181ts786_yjrn9c2gjq/T/RtmpTADBVi"
 
 ### Full PLSR dataset
 
@@ -448,7 +448,7 @@ head(cal.plsr.output)
     ## 10    Cal       1.358638          1.365181        0.06107105
 
 ``` r
-cal.R2 <- round(pls::R2(plsr.out)[[1]][nComps],2)
+cal.R2 <- round(pls::R2(plsr.out,intercept=F)[[1]][nComps],2)
 cal.RMSEP <- round(sqrt(mean(cal.plsr.output$PLSR_CV_Residuals^2)),2)
 
 val.plsr.output <- data.frame(val.plsr.data[, which(names(val.plsr.data) %notin% "Spectra")],
@@ -476,7 +476,7 @@ head(val.plsr.output)
     ## 15    Val      1.1267054    0.002059572
 
 ``` r
-val.R2 <- round(pls::R2(plsr.out,newdata=val.plsr.data)[[1]][nComps],2)
+val.R2 <- round(pls::R2(plsr.out,newdata=val.plsr.data,intercept=F)[[1]][nComps],2)
 val.RMSEP <- round(sqrt(mean(val.plsr.output$PLSR_Residuals^2)),2)
 
 rng_quant <- quantile(cal.plsr.output[,inVar], probs = c(0.001, 0.999))
@@ -677,7 +677,7 @@ rmsep_percrmsep <- spectratrait::percent_rmse(plsr_dataset = val.plsr.output,
                                               range="full")
 RMSEP <- rmsep_percrmsep$rmse
 perc_RMSEP <- rmsep_percrmsep$perc_rmse
-r2 <- round(pls::R2(plsr.out, newdata = val.plsr.data)$val[nComps+1],2)
+r2 <- round(pls::R2(plsr.out, newdata = val.plsr.data, intercept=F)$val[nComps],2)
 expr <- vector("expression", 3)
 expr[[1]] <- bquote(R^2==.(r2))
 expr[[2]] <- bquote(RMSEP==.(round(RMSEP,2)))
@@ -752,7 +752,7 @@ 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//RtmpqlTXi1"
+    ## [1] "Output directory:  /var/folders/xp/h3k9vf3n2jx181ts786_yjrn9c2gjq/T//RtmpTADBVi"
 
 ``` r
 # Observed versus predicted

diff --git a/vignettes/ely_leafN_bootstrap_plsr_example.pdf b/vignettes/ely_leafN_bootstrap_plsr_example.pdf
diff --git a/vignettes/ely_leafN_bootstrap_plsr_example_files/figure-gfm/unnamed-chunk-11-1.png b/vignettes/ely_leafN_bootstrap_plsr_example_files/figure-gfm/unnamed-chunk-11-1.png
diff --git a/vignettes/kit_sla_plsr_example.Rmd b/vignettes/kit_sla_plsr_example.Rmd
@@ -3,10 +3,10 @@ title: Spectra-trait PLSR example using leaf-level spectra and specific leaf are
 author: "Shawn P. Serbin, Julien Lamour, & Jeremiah Anderson"
 output:
   github_document: default
-  pdf_document: default
-  html_notebook: default
   html_document:
     df_print: paged
+  html_notebook: default
+  pdf_document: default
 params:
   date: !r Sys.Date()
 ---
@@ -229,7 +229,7 @@ cal.plsr.output <- data.frame(cal.plsr.data[, which(names(cal.plsr.data) %notin%
 cal.plsr.output <- cal.plsr.output %>%
   mutate(PLSR_CV_Residuals = PLSR_CV_Predicted-get(inVar))
 head(cal.plsr.output)
-cal.R2 <- round(pls::R2(plsr.out)[[1]][nComps],2)
+cal.R2 <- round(pls::R2(plsr.out,intercept=F)[[1]][nComps],2)
 cal.RMSEP <- round(sqrt(mean(cal.plsr.output$PLSR_CV_Residuals^2)),2)
 
 val.plsr.output <- data.frame(val.plsr.data[, which(names(val.plsr.data) %notin% "Spectra")],
@@ -239,7 +239,7 @@ val.plsr.output <- data.frame(val.plsr.data[, which(names(val.plsr.data) %notin%
 val.plsr.output <- val.plsr.output %>%
   mutate(PLSR_Residuals = PLSR_Predicted-get(inVar))
 head(val.plsr.output)
-val.R2 <- round(pls::R2(plsr.out,newdata=val.plsr.data)[[1]][nComps],2)
+val.R2 <- round(pls::R2(plsr.out,newdata=val.plsr.data,intercept=F)[[1]][nComps],2)
 val.RMSEP <- round(sqrt(mean(val.plsr.output$PLSR_Residuals^2)),2)
 
 rng_quant <- quantile(cal.plsr.output[,inVar], probs = c(0.001, 0.999))
@@ -372,7 +372,7 @@ rmsep_percrmsep <- spectratrait::percent_rmse(plsr_dataset = val.plsr.output,
                                               range="full")
 RMSEP <- rmsep_percrmsep$rmse
 perc_RMSEP <- rmsep_percrmsep$perc_rmse
-r2 <- round(pls::R2(plsr.out, newdata = val.plsr.data)$val[nComps+1],2)
+r2 <- round(pls::R2(plsr.out, newdata = val.plsr.data, intercept=F)$val[nComps],2)
 expr <- vector("expression", 3)
 expr[[1]] <- bquote(R^2==.(r2))
 expr[[2]] <- bquote(RMSEP==.(round(RMSEP,2)))

diff --git a/vignettes/kit_sla_plsr_example.md b/vignettes/kit_sla_plsr_example.md
@@ -85,7 +85,7 @@ output_dir <- "tempdir"
 
 ### Set working directory (scratch space)
 
-    ## [1] "Output directory: /private/var/folders/xp/h3k9vf3n2jx181ts786_yjrn9c2gjq/T/Rtmpm4d2mF"
+    ## [1] "Output directory: /private/var/folders/xp/h3k9vf3n2jx181ts786_yjrn9c2gjq/T/RtmpktUPJx"
 
 ### Grab data from EcoSIS
 
@@ -626,7 +626,7 @@ head(cal.plsr.output)
     ## 6       277.2292          274.2644       -113.974044
 
 ``` r
-cal.R2 <- round(pls::R2(plsr.out)[[1]][nComps],2)
+cal.R2 <- round(pls::R2(plsr.out,intercept=F)[[1]][nComps],2)
 cal.RMSEP <- round(sqrt(mean(cal.plsr.output$PLSR_CV_Residuals^2)),2)
 
 val.plsr.output <- data.frame(val.plsr.data[, which(names(val.plsr.data) %notin% "Spectra")],
@@ -654,7 +654,7 @@ head(val.plsr.output)
     ## 47       274.2311     -37.170622
 
 ``` r
-val.R2 <- round(pls::R2(plsr.out,newdata=val.plsr.data)[[1]][nComps],2)
+val.R2 <- round(pls::R2(plsr.out,newdata=val.plsr.data,intercept=F)[[1]][nComps],2)
 val.RMSEP <- round(sqrt(mean(val.plsr.output$PLSR_Residuals^2)),2)
 
 rng_quant <- quantile(cal.plsr.output[,inVar], probs = c(0.001, 0.999))
@@ -849,7 +849,7 @@ rmsep_percrmsep <- spectratrait::percent_rmse(plsr_dataset = val.plsr.output,
                                               range="full")
 RMSEP <- rmsep_percrmsep$rmse
 perc_RMSEP <- rmsep_percrmsep$perc_rmse
-r2 <- round(pls::R2(plsr.out, newdata = val.plsr.data)$val[nComps+1],2)
+r2 <- round(pls::R2(plsr.out, newdata = val.plsr.data, intercept=F)$val[nComps],2)
 expr <- vector("expression", 3)
 expr[[1]] <- bquote(R^2==.(r2))
 expr[[2]] <- bquote(RMSEP==.(round(RMSEP,2)))

diff --git a/vignettes/kit_sla_plsr_example.pdf b/vignettes/kit_sla_plsr_example.pdf
diff --git a/vignettes/kit_sla_plsr_example_files/figure-gfm/unnamed-chunk-12-1.png b/vignettes/kit_sla_plsr_example_files/figure-gfm/unnamed-chunk-12-1.png
diff --git a/vignettes/neon_leafN_canopy_plsr_example.Rmd b/vignettes/neon_leafN_canopy_plsr_example.Rmd
@@ -2,11 +2,11 @@
 title: Spectra-trait PLSR example using NEON AOP pixel spectra and field-sampled leaf nitrogen content from CONUS NEON sites
 author: "Shawn P. Serbin, Julien Lamour, & Jeremiah Anderson"
 output:
-  github_document: default
-  html_notebook: default
   pdf_document: default
+  html_notebook: default
   html_document:
     df_print: paged
+  github_document: default
 params:
   date: !r Sys.Date()
 ---
@@ -263,7 +263,7 @@ cal.plsr.output <- data.frame(cal.plsr.data[, which(names(cal.plsr.data) %notin%
 cal.plsr.output <- cal.plsr.output %>%
   mutate(PLSR_CV_Residuals = PLSR_CV_Predicted-get(inVar))
 head(cal.plsr.output)
-cal.R2 <- round(pls::R2(plsr.out)[[1]][nComps],2)
+cal.R2 <- round(pls::R2(plsr.out,intercept=F)[[1]][nComps],2)
 cal.RMSEP <- round(sqrt(mean(cal.plsr.output$PLSR_CV_Residuals^2)),2)
 
 val.plsr.output <- data.frame(val.plsr.data[, which(names(val.plsr.data) %notin% "Spectra")],
@@ -273,7 +273,7 @@ val.plsr.output <- data.frame(val.plsr.data[, which(names(val.plsr.data) %notin%
 val.plsr.output <- val.plsr.output %>%
   mutate(PLSR_Residuals = PLSR_Predicted-get(inVar))
 head(val.plsr.output)
-val.R2 <- round(pls::R2(plsr.out,newdata=val.plsr.data)[[1]][nComps],2)
+val.R2 <- round(pls::R2(plsr.out,newdata=val.plsr.data,intercept=F)[[1]][nComps],2)
 val.RMSEP <- round(sqrt(mean(val.plsr.output$PLSR_Residuals^2)),2)
 
 rng_quant <- quantile(cal.plsr.output[,inVar], probs = c(0.001, 0.999))
@@ -407,7 +407,7 @@ rmsep_percrmsep <- spectratrait::percent_rmse(plsr_dataset = val.plsr.output,
                                               range="full")
 RMSEP <- rmsep_percrmsep$rmse
 perc_RMSEP <- rmsep_percrmsep$perc_rmse
-r2 <- round(pls::R2(plsr.out, newdata = val.plsr.data)$val[nComps+1],2)
+r2 <- round(pls::R2(plsr.out, newdata = val.plsr.data, intercept=F)$val[nComps],2)
 expr <- vector("expression", 3)
 expr[[1]] <- bquote(R^2==.(r2))
 expr[[2]] <- bquote(RMSEP==.(round(RMSEP,2)))