Problem with multiple htmlwidgets within an R Markdown document

test_qtlcharts.Rmd

---
title: "test qtlcharts"
author: "Karl Broman"
date: "February 23, 2015"
output: html_document
---

```{r load_lib}
library(devtools)
install_github("kbroman/qtlcharts", ref="htmlwidgets")
library(qtlcharts)
```

If I include multiple htmlwidgets charts within an R Markdown document,
only the resources for the first of them gets included.

For example, in the following, the two `iplot` examples will be shown,
but the `iplotPXG` example gives an error, `Uncaught ReferenceError: iplotPXG is not defined`.

If I move the `iplotPXG` chunk to before the `iplot` chunks, then
the `iplotPXG` example works, but the `iplot` examples give an error.

```{r iplot}
x <- rnorm(100)
grp <- sample(1:3, 100, replace=TRUE)
y <- x*grp + rnorm(100)
iplot(x, y, grp)
```

```{r iplot2}
iplot(y, x, grp)
```

```{r iplotPXG}
library(qtl)
data(hyper)
iplotPXG(hyper, "D4Mit164")
```

test_qtlcharts_v2.Rmd

---
title: "test qtlcharts"
author: "Karl Broman"
date: "February 23, 2015"
output: html_document
---

```{r load_lib}
library(devtools)
install_github("kbroman/qtlcharts", ref="htmlwidgets")
library(qtlcharts)
```

If I include multiple htmlwidgets charts within an R Markdown document,
only the resources for the first of them gets included.

For example, in the following, the `iplotPXG` example will be shown,
but the `iplot` examples give an error.

If I move the `iplot` chunks to before the `iplotPXG` chunk, then
the `iplot` examples work, but the `iplotPXG` example give an error.

```{r iplotPXG}
library(qtl)
data(hyper)
iplotPXG(hyper, "D4Mit164")
```

```{r iplot}
x <- rnorm(100)
grp <- sample(1:3, 100, replace=TRUE)
y <- x*grp + rnorm(100)
iplot(x, y, grp)
```

```{r iplot2}
iplot(y, x, grp)
```

An example for array of scripts is here https://github.com/htmlwidgets/iquiz/blob/master/inst/htmlwidgets/iquiz.yaml#L13.

@timelyportfolio Thanks! That's understandable.

I guess the thing for me to do is to have a separate chunk of yaml for each of the basic bits, so it loads just what's necessary, and only once.

Yes, I think that is the best option.