SMHS Usage Rfundamentals - Revision history

Dinov at 18:38, 24 June 2016

2016-06-24T18:38:12Z

Dinov: /* Example: Generate an R HTML Export using the SOCR PD Data */

2016-04-12T13:17:17Z

‎Example: Generate an R HTML Export using the SOCR PD Data

Dinov at 13:16, 12 April 2016

2016-04-12T13:16:12Z

Dinov: /* Example: Generate an R HTML Export using the SOCR PD Data */

2016-04-12T13:11:18Z

‎Example: Generate an R HTML Export using the SOCR PD Data

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Dinov: /* Saving R commands/scripts and HTML outputs */

2016-04-12T12:52:12Z

‎Saving R commands/scripts and HTML outputs

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Dinov: Created page with "==SMHS_Usage: SMHS EBook Usage - Some R Fundamentals== ===Command-line Help=== > apropos("nova") # within R keyword search/help ===Saving R commands/scripts and HTML o..."

2016-04-12T12:44:55Z

Created page with "==SMHS_Usage: SMHS EBook Usage - Some R Fundamentals== ===Command-line Help=== > apropos("nova") # within R keyword search/help ===Saving R commands/scripts and HTML o..."

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==[[SMHS_Usage: SMHS EBook Usage]] - Some R Fundamentals==

===Command-line Help===
> apropos("nova") # within R keyword search/help

===Saving R commands/scripts and HTML outputs===
It's easy to save R scripts and commands that can be reused, shared and modified later or by others, as well as to create HTML or PDF files with R, Knitr, MiKTeX.

====Needed packages====
You may need to first install Knitr and Markdown (and/or MiKTeX/Pandoc). Open R or RStudio and install the packages:
# Install knitr
install.packages("knitr")
install.packages("markdown")

====Create a '''.Rmd''' File Containing Your Complete Protocol====
Open RStudio, click '''File''' --> '''New''' --> R Markdown, and enter meta-data (e.g., Author). Save as '''example.Rmd''' -- this generates an R Markdown document. A new markdown (.Rmd) file will be created that is populated with an example and contains the both ''R code'' and ''knitr'' code. Code between the sets of three apostrophes <code>```{r}</code> and <code>```</code> is pure R code. Code outside of these segments is knitr code (necessary for the export of entire protocol to HTML/PDF/etc). The R code tells R what to do and the Knitr code creates the output doc (e.g., HTML file). Below is an example of a fresh new Rmd file that is automatically generated as an example:

---
title: "SOCR Demo"
author: "SOCR Team"
date: "April 12, 2016"
output: html_document
---

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}
summary(cars)
```

You can also embed plots, for example:

```{r, echo=FALSE}
plot(cars)
```

Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.

<hr>
* SOCR Home page: http://www.socr.umich.edu

{{translate|pageName=http://wiki.socr.umich.edu/index.php?title=SMHS_Usage_Rfundamentals}}

← Older revision		Revision as of 18:38, 24 June 2016
Line 198:		Line 198:
	table(finalpred, test$\$$Dx)		table(finalpred, test$\$$Dx)
	```		```
		+
		+	===References===
		+	* [http://wiki.socr.umich.edu/images/0/08/RmarkdownReference.pdf R-markdown Reference Guide]

@@ Line 56: / Line 56: @@
   wiki <- read_html("http://wiki.socr.umich.edu/index.php/SOCR_Data_PD_BiomedBigMetadata")
   html_nodes(wiki, "#content")
-  pd <- html_table(html_nodes(wiki,"table")[[1]])
+  pd <- html_table(html_nodes(wiki,"table")$[[1]]$)
   ```

← Older revision		Revision as of 13:16, 12 April 2016
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−	==[[SMHS_Usage: SMHS EBook Usage]] - Some R Fundamentals==	+	==[[SMHS_Usage\| SMHS EBook Usage]] - Some R Fundamentals==

	===Command-line Help===		===Command-line Help===