malaria-infect/doc/test.Rmd

---
title: "Test"
author: "Pjotr"
date: "24/02/2020"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

## R Markdown

This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.

When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:

```{r cars}
summary(cars)
```

## Including Plots

You can also embed plots, for example:

```{r pressure, echo=FALSE}
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