Tidyverse

README.md

@@ -9,7 +9,7 @@ Install RStudio with R.
 
 With GNU Guix install
 
-    guix package -i r r-markdown r-rmarkdown
+    guix package -i r r-markdown r-rmarkdown r-tidyverse r-hash
 
 # Data
 

doc/rstudio-tips.md

@@ -2,7 +2,6 @@
 
 ## Useful keyboard shortcuts
 
-
 In markdown mode:
 
 Ctrl-Alt-I   Insert code block

doc/test.Rmd

@@ -28,3 +28,55 @@ plot(pressure)
 ```
 
 Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.
+
+## Environments
+
+
+R environments are used to bind names against values. In 
+this case the subjectid is the name.
+
+```{r}
+id <- new.env()
+id$16K0021 = 'first'
+```
+
+oops, can't start with a number
+
+```{r}
+id$m16K0021 = 'first'
+ls(id, all.names = TRUE)
+```
+
+Note that data frames use environment too with the $ notation.
+
+To add material to an environment we create a new environment (a hash of hash). So
+
+```{r}
+mydata <- new.env()
+mydata$days = 21
+mydata$name = "Pjotr Prins"
+id$m16K0021 = mydata
+ls(id$m16K0021, all.names = TRUE)
+id$m16K0021$name
+```
+
+That works well. Step is to be able to parametrize
+
+```{r}
+id[["m16K0021"]]$days
+```
+
+So you can see the dollar notation is just syntactic sugar.
+
+```{r}
+id[["m16Ktest"]] = new.env()
+test = id[["m16Ktest"]]
+test$name = "Jan Wolkers"
+test$days = 22
+ls(id, all.names = TRUE)
+ls(test, all.names=TRUE)
+test$name
+```
+
+
+See also http://adv-r.had.co.nz/Environments.html

doc/using-tidyverse.Rmd

@@ -0,0 +1,33 @@
+---
+title: "using_tidyverse"
+author: "Pjotr"
+date: "03/03/2020"
+output: html_document
+---
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE)
+```
+
+## R Tidyverse
+
+The new way of analysing R data is the tidyverse https://www.tidyverse.org/ which includes the online book 'R for Data Science'. 
+
+Instead of dataframes we use Tibbles now. First import the data - make sure FACTORS is off and tables and columns show.
+
+```{r}
+plot(ind_attr$ELISA ~ ind_attr$Time_to_diagnosis)
+```
+
+we want to turn ind_attr into a tibble with
+
+```{r}
+tb = as_tibble(ind_attr)
+tb
+```
+
+```{r}
+ggplot(data = tb) + geom_point(mapping = aes(y=ELISA, x = Time_to_diagnosis))
+```
+
+