fix problems in Rmd of Chapter 7

book/07-ligand-based-modelling.Rmd

@@ -1,6 +1,6 @@
 # Encoding and similarity search of chemical structures {#cheminfo}
 
-```{r setup, include=FALSE, message=FALSE, warning=FALSE}
+```{r setup_chapter7, include=FALSE, message=FALSE, warning=FALSE}
 knitr::opts_chunk$set(echo = TRUE, 
                       fig.height=5, fig.width=5)
 library(ribiosUtils)
@@ -215,6 +215,19 @@ ggplot(data=nonld, aes(x=x, y=y, col=z)) +
     
 ```
 
+```{r}
+set.seed(1887)
+library(randomForest)
+library(tree)
+library(caret)
+nonld_train <- sample_frac(nonld, 0.8)
+nonld_test <- nonld %>% filter(!index %in% nonld_train$index)
+rf <- randomForest(z~., data=nonld_train %>% dplyr::select(-index),
+                   ntree=100)
+nonld_test_pred <- predict(rf, nonld_test)
+caret::confusionMatrix(nonld_test_pred, nonld_test$z)
+```
+
 ```{r nonldTrainTest, fig.height=3, fig.width=7}
 nonld_train_test <- rbind(cbind(nonld_train, partition="train"),
                           cbind(nonld_test, partition="test")) %>%
@@ -229,18 +242,6 @@ ggplot(data=nonld_train_test, aes(x=x, y=y, col=z)) +
         panel.background = element_blank()) 
 ```
 
-```{r}
-set.seed(1887)
-library(randomForest)
-library(tree)
-nonld_train <- sample_frac(nonld, 0.8)
-nonld_test <- nonld %>% filter(!index %in% nonld_train$index)
-rf <- randomForest(z~., data=nonld_train %>% dplyr::select(-index),
-                   ntree=100)
-nonld_test_pred <- predict(rf, nonld_test)
-confusionMatrix(nonld_test_pred, nonld_test$z)
-```
-
 ```{r, fig.height=4, fig.width=4}
 {
   compactPar()
@@ -254,6 +255,7 @@ library(reprtree)
 reprtree::plot.getTree(rf, k=1)
 reprtree::plot.getTree(rf, k=20)
 ```
+
 ```{r}
 library(neuralnet)
 nonald_train_nn <- nonld_train %>% dplyr::select(-index) %>%

book/packages.bib

@@ -3,31 +3,31 @@ @Manual{R-base
   author = {{R Core Team}},
   organization = {R Foundation for Statistical Computing},
   address = {Vienna, Austria},
-  year = {2020},
+  year = {2024},
   url = {https://www.R-project.org/},
 }
 
 @Manual{R-bookdown,
   title = {bookdown: Authoring Books and Technical Documents with R Markdown},
   author = {Yihui Xie},
-  year = {2020},
-  note = {R package version 0.20},
+  year = {2023},
+  note = {R package version 0.33},
   url = {https://CRAN.R-project.org/package=bookdown},
 }
 
 @Manual{R-knitr,
   title = {knitr: A General-Purpose Package for Dynamic Report Generation in R},
   author = {Yihui Xie},
-  year = {2020},
-  note = {R package version 1.29},
-  url = {https://CRAN.R-project.org/package=knitr},
+  year = {2023},
+  note = {R package version 1.42},
+  url = {https://yihui.org/knitr/},
 }
 
 @Manual{R-rmarkdown,
   title = {rmarkdown: Dynamic Documents for R},
-  author = {JJ Allaire and Yihui Xie and Jonathan McPherson and Javier Luraschi and Kevin Ushey and Aron Atkins and Hadley Wickham and Joe Cheng and Winston Chang and Richard Iannone},
-  year = {2020},
-  note = {R package version 2.3},
+  author = {JJ Allaire and Yihui Xie and Christophe Dervieux and Jonathan McPherson and Javier Luraschi and Kevin Ushey and Aron Atkins and Hadley Wickham and Joe Cheng and Winston Chang and Richard Iannone},
+  year = {2023},
+  note = {R package version 2.21},
   url = {https://CRAN.R-project.org/package=rmarkdown},
 }
 
@@ -38,7 +38,7 @@ @Book{bookdown2016
   address = {Boca Raton, Florida},
   year = {2016},
   note = {ISBN 978-1138700109},
-  url = {https://github.com/rstudio/bookdown},
+  url = {https://bookdown.org/yihui/bookdown},
 }
 
 @Book{knitr2015,
@@ -60,7 +60,6 @@ @InCollection{knitr2014
   publisher = {Chapman and Hall/CRC},
   year = {2014},
   note = {ISBN 978-1466561595},
-  url = {http://www.crcpress.com/product/isbn/9781466561595},
 }
 
 @Book{rmarkdown2018,
@@ -69,7 +68,17 @@ @Book{rmarkdown2018
   publisher = {Chapman and Hall/CRC},
   address = {Boca Raton, Florida},
   year = {2018},
-  note = {ISBN 9781138359338},
+  isbn = {9781138359338},
   url = {https://bookdown.org/yihui/rmarkdown},
 }
 
+@Book{rmarkdown2020,
+  title = {R Markdown Cookbook},
+  author = {Yihui Xie and Christophe Dervieux and Emily Riederer},
+  publisher = {Chapman and Hall/CRC},
+  address = {Boca Raton, Florida},
+  year = {2020},
+  isbn = {9780367563837},
+  url = {https://bookdown.org/yihui/rmarkdown-cookbook},
+}
+