Spell Checker for R…qdap::check_spelling

I often have had requests for a spell checker for R character vectors. The utils::aspell function can be used to check spelling but many Windows users have reported difficulty with the function.

I came across an article on spelling in R entitled “Watch Your Spelling!” by Kurt Hornik and Duncan Murdoch. The paper walks us through definitions of spell checking, history, and a suggested spell checker implementation for R. A terrific read. Hornik & Murdoch (2010) end with the following call:

Clearly, more work will be needed: modern statistics needs better lexical resources, and a dictionary based on the most frequent spell check false alarms can only be a start. We hope that this article will foster community interest in contributing to the development of such resources, and that refined domain specific dictionaries can be made available and used for improved text analysis with R in the near future (p. 28).

I answered a question on stackoverflow.com a few months back that lead to creating a suite of spell checking functions. The original functions used an agrep approach that was slow and inaccurate. I discovered Mark van der Loo’s terrific stringdist package to do the heavy lifting. It calculates string distances very quickly with various methods.

The rest of this blog post is meant as a minimal introduction to qdap‘s spell checking functions. A video will lead you through most of the process and accompanying scripts are provided.

Primitive Spell Checking Function

The which_misspelled function is a low level function that basically determines if each word of a single string is in a dictionary. It optionally gives suggested corrections.

x <- "Robots are evl creatres and deserv exterimanitation."
which_misspelled(x, suggest=FALSE)
which_misspelled(x, suggest=TRUE)

Interactive Spell Checking

Typically a user will want to use the interactive spell checker (spell_checker_interactive) as it is more flexible and accurate.

dat <- DATA$state
dat[1] <- "Jasperita I likedd the cokie icekream"
##  [1] "Jasperita I likedd the cokie icekream"
##  [2] "No it's not, it's dumb."              
##  [3] "What should we do?"                   
##  [4] "You liar, it stinks!"                 
##  [5] "I am telling the truth!"              
##  [6] "How can we be certain?"               
##  [7] "There is no way."                     
##  [8] "I distrust you."                      
##  [9] "What are you talking about?"          
## [10] "Shall we move on?  Good then."        
## [11] "I'm hungry.  Let's eat.  You already?"
(o <- check_spelling_interactive(dat))
fixit <- attributes(o)$correct

A More Realistic Usage

m <- check_spelling_interactive(mraja1spl$dialogue[1:75])
fixit <- attributes(m)$correct


Hornik, K., & Murdoch, D. (2010). Watch Your Spelling!. The R Journal, 3(2), 22-28.

Posted in qdap, Uncategorized | Tagged , , , , , , | Leave a comment

Hijacking R Functions: Changing Default Arguments

I am working on a package to collect common regular expressions into a canned collection that users can easily use without having to know regexes. The package, qdapRegex, has a bunch of functions in the form of rm_xxx. The only difference between each function is one default parameter, the regular expression pattern is different. I had a default template function so what I really needed was to copy that template many times and change one parameter. It seems wasteful of code and electronic space to cut and paste the body of the template function over and over again…I needed to hijack the template.

Come on admit it you’ve all wished you could hijack a function before. Who hasn’t wished the default to data.frame was stringsAsFactors = FALSE? Or sum was na.rm = TRUE (OK maybe the latter is just me). So for the task of efficiently hijacking a function and changing the defaults in a manageable modular way my mind immediately went to Hadley’s pryr package (Wickham (2014)). I remember him hijacking functions in his Advanced R book as seen HERE with the partial function.

It worked except I couldn’t then change the newly set defaults back. In my case for package writing this was not a good thing (maybe there was a way and I missed it).

A Function Worth Hijacking

Here’s an example where we attempt to hijack data.frame.

dat <- data.frame(x1 = 1:3, x2 = c("a", "b", "c"))
str(dat)  # yuck a string as a factor
## 'data.frame':    3 obs. of  2 variables:
##  $ x1: int  1 2 3
##  $ x2: Factor w/ 3 levels "a","b","c": 1 2 3

Typically we’d do something like:

.data.frame <- function(..., row.names = NULL, check.rows = FALSE, check.names = TRUE,
    stringsAsFactors = FALSE) {

    data.frame(..., row.names = row.names, check.rows = check.rows,
        check.names = check.names, stringsAsFactors = stringsAsFactors)


dat <- .data.frame(x1 = 1:3, x2 = c("a", "b", "c"))
str(dat)  # yay!  strings are character
## 'data.frame':    3 obs. of  2 variables:
##  $ x1: int  1 2 3
##  $ x2: chr  "a" "b" "c"

But for my qdapRegex needs this required a ton of cut and paste. That means lots of extra code in the .R files.

The First Attempt to Hijack a Function

pryr to the rescue


## The hijack
.data.frame <- pryr::partial(data.frame, stringsAsFactors = FALSE)

dat <- .data.frame(x1 = 1:3, x2 = c("a", "b", "c"))
str(dat)  # yay! strings are character
## 'data.frame':    3 obs. of  2 variables:
##  $ x1: int  1 2 3
##  $ x2: chr  "a" "b" "c"

But I can’t change the default back…

.data.frame(x1 = 1:3, x2 = c("a", "b", "c"), stringsAsFactors = TRUE)
## Error: formal argument "stringsAsFactors" matched by multiple actual
## arguments

Hijacking In Style (formals)


After tinkering with many not so reasonable solutions I asked on stackoverflow.com. In a short time MrFlick responded most helpfully (as he often does) with a response that used formals to change the formals of a function. I should have thought of it myself as I’d seen its use in Advanced R as well.

Here I use the answer to make a hijack function. It does exactly what I want, take a function and reset its formal arguments as desired.

hijack <- function (FUN, ...) {
    .FUN <- FUN
    args <- list(...)
    invisible(lapply(seq_along(args), function(i) {
        formals(.FUN)[[names(args)[i]]] <<- args[[i]]

Let’s see it in action as it changes the defaults but allows the user to still set these arguments…

.data.frame <- hijack(data.frame, stringsAsFactors = FALSE)

dat <- .data.frame(x1 = 1:3, x2 = c("a", "b", "c"))
str(dat)  # yay! strings are character
## 'data.frame':    3 obs. of  2 variables:
##  $ x1: int  1 2 3
##  $ x2: chr  "a" "b" "c"
.data.frame(x1 = 1:3, x2 = c("a", "b", "c"), stringsAsFactors = TRUE)
##   x1 x2
## 1  1  a
## 2  2  b
## 3  3  c

Note that for some purposes Dason suggested an alternative solution that is similar to the first approach I describe above but requires less copying as it used ldots (ellipsis) to cover the parameters that we don’t want to change. This approach would look something like this:

.data.frame <- function(..., stringsAsFactors = FALSE) {

    data.frame(..., stringsAsFactors = stringsAsFactors)


dat <- .data.frame(x1 = 1:3, x2 = c("a", "b", "c"))
str(dat)  # yay!  strings are character
## 'data.frame':    3 obs. of  2 variables:
##  $ x1: int  1 2 3
##  $ x2: chr  "a" "b" "c"
.data.frame(x1 = 1:3, x2 = c("a", "b", "c"), stringsAsFactors = TRUE)
##   x1 x2
## 1  1  a
## 2  2  b
## 3  3  c

Less verbose than the first approach I had. This solution was not the best for me in that I wanted to document all of the arguments to the function for the package. I believe using this approach would limit me to the arguments …, stringsAsFactors in the documentation (though I didn’t try it with CRAN checks). Depending on the situation this approach may be ideal.


*Created using the reports package

Posted in package creation, Uncategorized | Tagged , , , , , , | 4 Comments

qdap 2.1.1 Released

We’re very pleased to announce the release of qdap 2.1.1

What is qdap?

qdap (Quantitative Discourse Analysis Package) is an R package designed to assist in quantitative discourse analysis. The package stands as a bridge between qualitative transcripts of dialogue and statistical analysis & visualization. qdap is designed for transcript analysis, however, many functions are applicable to other areas of Text Mining/Natural Language Processing.

qdap Version 2.1.1


This is the latest installment of the qdap package available at CRAN. Several important updates have occurred since we last blogged about the 1.3.1 release (demoing Version 1.3.1), most notable:

  1. Text checking that simplifies and standardizes (includes spell checking and a Cleaning Text & Debugging Vignette
  2. Added many plot methods including animated and network plotting
  3. Improved tm package compatibility
  4. The Introduction to qdap .Rmd vignette has been moved to an internal directory to save CRAN space and time checking the package source. The user may use the build_qdap_vignette function directly to build the vignette
  5. qdap officially begins utilizing the testthat package for unit testing
  6. qdapTools splits off of qdap with non-text specific tools
  7. New text analysis and processing functions



Changes up to qdap Version 2.1.1

A complete list of changes since Version 1.3.1 can be found in the NEWS.md found HERE

Future Focus

As the focus of my own research and dissertation has moved toward the graphical analysis of discourse, qdap will reflect this shift. We plan to demonstrate some of the features of qdap that have been added since our last blog article (demoing Version 1.3.1) via a series of small blog articles over the next month.

*Created using the reports package

Posted in qdap, Uncategorized | Tagged , , , , , , , | 5 Comments

What Would Cohen Have Titled “The Earth is Round (p < .05)" in 2014?

The area of bibliometrics is not my area of expertise but is still of interest as a researcher. I sometimes think about how Google has impacted the way we title articles. Gone are the days of witty, snappy titles. Title selection is an art form but of a different kind. Generally, researchers try to construct titles of the most searchable keywords. In trying to title an article today and came upon an Internet article entitled Heading for Success: Or How Not to Title Your Paper.

According to the article, to increase citation rates, a title should:

  1. Contain no ? or !
  2. May contain a :
  3. Should be between 31-40 character
  4. Avoid humor/pun

In seeing:

…some authors are tempted to spice them up with a touch of humour, which may be a pun, a play on words, or an amusing metaphor. This, however, is a risky strategy.

my mind went to the classic Jacob Cohen (1994) paper entitled The Earth is Round (p < .05). In 1994 the world was different; Google didn't exist yet. I ask, “What if Cohen had to title his classic title in 2014?” What would it look like?

Keywords: Mining “The Earth is Round (p < .05)”

I set to work by grabbing the paper's content and converting to plain text. Then I decided to tease out the most frequent terms after stemming and removing stopwords. Here's the script I used:

library(qdap); library(RCurl); library(wordcloud); library(ggplot2)

cohen_url <- "https://raw.githubusercontent.com/trinker/cohen_title/master/data/Cohen1994.txt"
cohen <- getURL(cohen_url, ssl.verifypeer = FALSE)

## remove reference section and title
cohen <- substring(strsplit(cohen, "REFERENCES")[[c(1, 1)]], 34)

## convert format so we can eliminate strange characters
cohen <- iconv(cohen, "", "ASCII", "byte")

## replacement parts
bads <- c("-", "<e2><80><9c>", "<e2><80><9d>", "<e2><80><98>", 
    "<e2><80><99>", "<e2><80><9b>", "<ef><bc><87>", "<e2><80><a6>", 
    "<e2><80><93>", "<e2><80><94>", "<c3><a1>", "<c3><a9>", 
    "<c2><bd>", "<ef><ac><81>", "<c2><a7>", "<ef><ac><82>", 
    "<ef><ac><81>", "<c2><a2>", "/j")

goods <- c(" ", " ", " ", "'", "'", "'", "'", "...", " ", 
    " ", "a", "e", "half", "fi", " | ", "ff", "ff", " ", "ff")

## sub the bad for the good
cohen <- mgsub(bads, goods, clean(cohen))

## Stem it
cohen_stem <- stemmer(cohen)

## Find top words
(cohen_top_20 <- freq_terms(cohen_stem, top = 20, stopwords = Top200Words))
##    WORD         FREQ
## 1  test           21
## 2  signiffc       19
## 3  research       18
## 4  probabl        17
## 5  size           17
## 6  data           15
## 7  h              15
## 8  effect         14
## 9  p              14
## 10 statist        14
## 11 given          13
## 12 hypothesi      13
## 13 analysi        11
## 14 articl         11
## 15 nhst           11
## 16 null           11
## 17 psycholog      11
## 18 conffdenc      10
## 19 correl         10
## 20 psychologist   10
## 21 result         10
## 22 theori         10

plot of chunk plot1

with(cohen_top_20, wordcloud(WORD, FREQ))
mtext("Content Cloud: The Earth is Round (p < .05)", col="blue")

plot of chunk plot2

What Would Cohen Have Titled “The Earth is Round (p < .05)”?

So what would Cohen have titled “The Earth is Round (p < .05)” in 2014? Looking at the results… I don't know. It's fun to speculate. Maybe some could suggest in the comments but as for me I still like “The Earth is Round (p < .05)”.

Cohen, J. (1994). The earth is round (p < .05). American Psychologist, 49(12), 997-1003. doi:10.1037/0003-066X.49.12.997

Posted in qdap, text, Uncategorized | Tagged , , , , , | 2 Comments

Handling @S3method’s Death in roxygen2 Version 4.0.0

This is a quickie post and specific to package maintainers who use roxygen2.

Legal Disclaimer: This worked for me but make sure there’s not a corner case that would make it not work for you.  In other words back your stuff up, think it through, and tread lightly.

Welp I updated to the latest version of roxygen2, 4.0.0. Works well and some new niceties and handling. Anyway after you use it for the first time and if you have @S3method in your code it throws a warning along the lines of:

Warning messages:
@S3method is deprecated. Please use @export instead

Inconvenient to make the change if you have a small amount of functions in your package but a pain in the tush if you have tons. Obviously you’ll want to do this as @S3method is deprecated but it doesn’t make it hurt any less. It’s kinda like a a root canal, it’s for the good of the dental well being but it’s still painful. But then a thought occurred to me. Why not be lazy efficient? Read in the files, grepl to find the "#' @S3" and then replace with "#' @export". I tried it with the following code. You’ll have to supply your path to the location of the package’s R directory.

Now this may not be the best approach, hey it may even be wrong but I’ll rely on Cunningham’s Law to sort it out:

pth <- "C:/Users/trinker/qdap/R"

fls <- file.path(pth, dir(pth))

FUN <- function(x) {
    cont <- readLines(x)
    cont[grepl("#' @S3", cont)] <- "#' @export"
    cont[length(cont) + 1] <- ""
    cat(paste(cont, collapse="\n"), file=x)

lapply(fls, FUN)
Posted in package creation, qdap, Uncategorized | Tagged , , , , | 2 Comments

Shape File Selfies in ggplot2

In this post you will learn how to:

  1. Create your own quasi-shape file
  2. Plot your homemade quasi-shape file in ggplot2
  3. Add an external svg/ps graphic to a plot
  4. Change a grid grob's color and alpha

*Note get simple .md version here

Background (See just code if you don't care much about the process)

I started my journey wanting to replicate a graphic called a space manikin by McNeil (2005) and fill areas in that graphic like a choropleth. I won't share the image from McNeil's book as it's his intellectual property but know that the graphic is from a gesturing book that divides the body up into zones (p. 275). To get a sense of what the manikin looks like here is the ggplot2 version of it:

Figure 1: ggplot2 Version of McNeil’s (2005) Space Manikin

While this is a map of areas of a body you can see where this could be extended to any number of spatial tasks such as mapping the layout of a room.

1. Creating a Quasi-Shape File

So I figured “zones” that's about like states on a map. I have toyed with choropleth maps of the US in the past and figured I'd generalize this learning. The difference is I'd have to make the shape file myself as the maps package doesn't seem to have McNeil’s space manikin.

Let's look at what ggplot2 needs from the maps package:

library(maps); library(ggplot2)
##     long   lat group order  region subregion
## 1 -87.46 30.39     1     1 alabama      <NA>
## 2 -87.48 30.37     1     2 alabama      <NA>
## 3 -87.53 30.37     1     3 alabama      <NA>
## 4 -87.53 30.33     1     4 alabama      <NA>
## 5 -87.57 30.33     1     5 alabama      <NA>
## 6 -87.59 30.33     1     6 alabama      <NA>

Hmm coordinates, names of regions, and order to connect the coordinates. I figured I can handle that. I don't 100% know what a shape file is, mostly that it’s a file that makes shapes. What we're making may or may not technically be a shape file but know we're going to map shapes in ggplot2 (I use the quasi to avoid the wrath of those who do know precisely what a shape file is).

I needed to make the zones around an image of a person so I first grabbed a free png silhouette from: http://www.flaticon.com/free-icon/standing-frontal-man-silhouette_10633. I then knew I'd need to add some lines and figure out the coordinates of the outlines of each cell. So I read the raster image into R, plotted in ggplot2 and added lots of grid lines for good measure. Here's what I wound up with:

library(png); library(grid); library(qdap)
file.rename("eZ76jcu.png", "body.png")
img <- rasterGrob(readPNG("body.png"), 0, 0, 1, 1, just=c("left","bottom"))
ggplot(data.frame(x=c(0, 1), y=c(0, 1)), aes(x=x, y=y)) + 
    geom_point() +
    annotation_custom(img, 0, 1, 0, 1) + 
    scale_x_continuous(breaks=seq(0, 1, by=.05))+ 
    scale_y_continuous(breaks=seq(0, 1, by=.05)) + theme_bw() +
    theme(axis.text.x=element_text(angle = 90, hjust = 0, vjust=0))

plot of chunk unnamed-chunk-2

Figure 2: Silhouette from ggplot2 With Grid Lines

1b. Dirty Deeds Done Cheap

I needed to get reference lines on the plot so I could begin recording coordinates. Likely there's a better process but this is how I approached it and it worked. I exported the ggplot in Figure 2 into (GASP) Microsoft Word (I may have just lost a few die hard command line folks). I added lines there and and figured out the coordinates of the lines. It looked something like this:

Figure 3: Silhouette from ggplot2 with MS Word Augmented Border Lines

After that I began the tedious task of figuring out the corners of each of the shapes (“zones”) in the space manikin. Using Figure 3 and a list structure in R I mapped each of the corners, the approximate shape centers, and the order to plot the coordinates in for each shape. This is the code for corners:

dat <- list(
    `01`=data.frame(x=c(.4, .4, .6, .6), y=c(.67, .525, .525, .67)),
    `02`=data.frame(x=c(.35, .4, .6, .65), y=c(.75, .67, .67, .75)),
    `03`=data.frame(x=c(.6, .65, .65, .6), y=c(.525, .475, .75, .67)),
    `04`=data.frame(x=c(.4, .35, .65, .6), y=c(.525, .475, .475, .525)),
    `05`=data.frame(x=c(.35, .35, .4, .4), y=c(.75, .475, .525, .67)),
    `06`=data.frame(x=c(.4, .4, .6, .6), y=c(.87, .75, .75, .87)),
    `07`=data.frame(x=c(.6, .6, .65, .65, .73, .73), y=c(.87, .75, .75, .67, .67, .87)),
    `08`=data.frame(x=c(.65, .65, .73, .73), y=c(.67, .525, .525, .67)),
    `09`=data.frame(x=c(.6, .6, .73, .73, .65, .65), y=c(.475, .28, .28, .525, .525, .475)),
    `10`=data.frame(x=c(.4, .4, .6, .6), y=c(.475, .28, .28, .475)),
    `11`=data.frame(x=c(.27, .27, .4, .4, .35, .35), y=c(.525, .28, .28, .475, .475, .525)),
    `12`=data.frame(x=c(.27, .27, .35, .35), y=c(.67, .525, .525, .67)),
    `13`=data.frame(x=c(.27, .27, .35, .35, .4, .4), y=c(.87, .67, .67, .75, .75, .87)),
    `14`=data.frame(x=c(.35, .35, .65, .65), y=c(1, .87, .87, 1)),
    `15`=data.frame(x=c(.65, .65, .73, .73, 1, 1), y=c(1, .87, .87, .75, .75, 1)),
    `16`=data.frame(x=c(.73, .73, 1, 1), y=c(.75, .475, .475, .75)),
    `17`=data.frame(x=c(.65, .65, 1, 1, .73, .73), y=c(.28, 0, 0, .475, .475, .28)),
    `18`=data.frame(x=c(.35, .35, .65, .65), y=c(.28, 0, 0, .28)),
    `19`=data.frame(x=c(0, 0, .35, .35, .27, .27), y=c(.475, 0, 0, .28, .28, .475)),
    `20`=data.frame(x=c(0, 0, .27, .27), y=c(.75, .475, .475, .75)),
    `21`=data.frame(x=c(0, 0, .27, .27, .35, .35), y=c(1, .75, .75, .87, .87, 1))

dat <- lapply(dat, function(x) {
    x$order <- 1:nrow(x)

space.manikin.shape <- list_df2df(dat, "id")[, c(2, 3, 1, 4)]

And the code for the centers:

centers <- data.frame(
    id = unique(space.manikin.shape$id),
    center.x=c(.5, .5, .625, .5, .375, .5, .66, .69, .66, .5, .34, .31, 
        .34, .5, .79, .815, .79, .5, .16, .135, .16),
    center.y=c(.597, .71, .5975, .5, .5975, .82, .81, .5975, .39, .3775, .39, 
        .5975, .81, .935, .89, .6025, .19, .14, .19, .6025, .89)

There you have it folks your very own quasi-shape file. Celebrate the fruits of your labor by plotting that bad Oscar.

2. Plot Your Homemade Quasi-Shape File

 ggplot(centers) + annotation_custom(img,0,1,0,1) +
    geom_map(aes(map_id = id), map = space.manikin.shape, colour="black", fill=NA) +
    expand_limits(space.manikin.shape) +
    geom_text(data=centers, aes(center.x, center.y, label = id), color="grey60") 

plot of chunk unnamed-chunk-5

Figure 4: Plotting the Quasi-Shape File and a Raster Image

Then I said I may want to tone down the color of the silhouette a bit so I can plot geoms atop without distraction. Here's that attempt.

img[["raster"]][img[["raster"]] == "#0E0F0FFF"] <- "#E7E7E7"

ggplot(centers) + annotation_custom(img,0,1,0,1) +
    geom_map(aes(map_id = id), map = space.manikin.shape, colour="black", fill=NA) +
    expand_limits(space.manikin.shape) +
    geom_text(data=centers, aes(center.x, center.y, label = id), color="grey60") 

plot of chunk unnamed-chunk-6

Figure 5: Altered Raster Image Color

3. Add an External svg/ps

I realized quickly a raster was messy. I read up a bit on them in the R Journal (click here). In the process of reading and fooling around with Picasa I turned my original silhouette (body.png) blue and couldn't fix him. I headed back to http://www.flaticon.com/free-icon/standing-frontal-man-silhouette_10633 to download another. In this act I saw you could download a svg file of the silhouette. I thought maybe this will be less messier and easier to change colors. This led me to a google search and finding the grImport package after seeing this listserve post. And then I saw an article from Paul Murrell (2009) and figured I could turn the svg (I didn't realize what svg was until I opened it in Notepad++) into a ps file and read into R and convert to a flexible grid grob.

Probably there are numerous ways to convert an svg to a ps file but I chose a cloud convert service. After I read the file in with grImport per the Paul Murrell (2009) article. You're going to have to download the ps file HERE and get to your working directory.

## Move that file from your downloads to your working directory.
## Sorry I don't know how to automate this.

## Convert to xml

## Read back in and convert to a grob
being_img <- pictureGrob(readPicture("being.ps.xml"))

## Plot it
ggplot(centers) + annotation_custom(being_img,0,1,0,1) +
    geom_map(aes(map_id = id), map = space.manikin.shape, 
        colour="black", fill=NA) +
    expand_limits(space.manikin.shape) +
    geom_text(data=centers, aes(center.x, center.y, 
        label = id), color="grey60") 

plot of chunk unnamed-chunk-7

Figure 6: Quasi-Shape File with Grob Image Rather than Raster

4. Change a grid Grob's Color and Alpha

Now we have a flexible grob we can mess around with colors and alpha until our heart's content.

str is our friend to figure out where and how to mess with the grob (str(being_img)). That leads me to the following changes to the image to adjust color and/or alpha (transparency).

being_img[["children"]][[1]][[c("gp", "fill")]] <- 
  being_img[["children"]][[2]][[c("gp", "fill")]] <- "black"

being_img[["children"]][[1]][[c("gp", "alpha")]] <- 
  being_img[["children"]][[2]][[c("gp", "alpha")]] <- .2

## Plot it
ggplot(centers) + annotation_custom(being_img,0,1,0,1) +
    geom_map(aes(map_id = id), map = space.manikin.shape, 
        colour="black", fill=NA) +
    expand_limits(space.manikin.shape) +
    geom_text(data=centers, aes(center.x, center.y, 
        label = id), color="grey60") 

plot of chunk unnamed-chunk-8

Figure 7: Quasi-Shape File with Grob Image Alpha = .2

Let's Have Some Fun

Let's make it into a choropleth and a density plot. We'll make some fake fill values to fill with.

centers[, "Frequency"] <- rnorm(nrow(centers))

being_img[["children"]][[1]][[c("gp", "alpha")]] <- 
  being_img[["children"]][[2]][[c("gp", "alpha")]] <- .25

ggplot(centers, aes(fill=Frequency)) +
    geom_map(aes(map_id = id), map = space.manikin.shape, 
        colour="black") +
    scale_fill_gradient2(high="red", low="blue") +
    expand_limits(space.manikin.shape) +
    geom_text(data=centers, aes(center.x, center.y, 
        label = id), color="black") + 

plot of chunk unnamed-chunk-9

Figure 8: Quasi-Shape File as a Choropleth

centers[, "Frequency2"] <- sample(seq(10, 150, by=20, ), nrow(centers), TRUE)

centers2 <- centers[rep(1:nrow(centers), centers[, "Frequency2"]), ]

ggplot(centers2) +
#       geom_map(aes(map_id = id), map = space.manikin.shape, 
#       colour="grey65", fill="white") +
    stat_density2d(data = centers2, 
        aes(x=center.x, y=center.y, alpha=..level.., 
        fill=..level..), size=2, bins=12, geom="polygon") + 
    scale_fill_gradient(low = "yellow", high = "red") +
    scale_alpha(range = c(0.00, 0.5), guide = FALSE) +
    expand_limits(space.manikin.shape) +
    geom_text(data=centers, aes(center.x, center.y, 
        label = id), color="black") + 
    annotation_custom(being_img,0,1,0,1) +
    geom_density2d(data = centers2, aes(x=center.x, 
        y=center.y), colour="black", bins=8, show_guide=FALSE) 

plot of chunk unnamed-chunk-10

Figure 9: Quasi-Shape File as a Density Plot

Good times were had by all.

Created using the reports (Rinker, 2013) package

Get the .Rmd file here


Posted in discourse analysis, ggplot2, Uncategorized, visualization | Tagged , , , , | 1 Comment

qdap 1.3.1 Release: Demoing Dispersion Plots, Sentiment Analysis, Easy Hash Lookups, Boolean Searches and More…

We’re very pleased to announce the release of qdap 1.3.1


This is the latest installment of the qdap package available at CRAN. Several important updates have occurred since the 1.1.0 release, most notable the addition of two vignettes and some generic view methods.

The new vignettes include:

  1. An Introduction to qdap
  2. qdap-tm Package Compatibility

The former is a detailed HTML based guide over viewing the intended use of qdap functions.  The second vignette is an explanation of how to move between qdap and tm package forms as qdap moves to be more compatible with this seminal R text mining package.

To install use:


Some of the changes in versions 1.2.0-1.3.1 include:

Generic Methods

  • scores generic method added to view scores from select qdap objects.
  • counts generic method added to view counts from select qdap objects.
  • proportions generic method added to view proportions from select qdap objects.
  • preprocessed generic method added to view preprocessed data from select qdap objects.

These methods allow the user to grab particular parts of qdap objects in a consistent fashion.  The majority of these methods also pick up a corresponding plot method as well.  This adds to the qdap philosophy that data results should be easy to grab and easy to visualize. For instance:

(x <- question_type(DATA.SPLIT$state, DATA.SPLIT$person))

## methods
truncdf(preprocessed(x), 15)

Demoing Some of the New Features

We’d like to take the time to highlight some of the development that has happened in qdap in the past several months:

Dispersion Plots

 wrds <- freq_terms(pres_debates2012$dialogue, stopwords = Top200Words)

## Add leading/trailing spaces if desired
wrds2 <- spaste(wrds)

## Use `~~` to maintain spaces
wrds2 <- c(" governor~~romney ", wrds2[-c(3, 12)])

## Plot
with(pres_debates2012 , dispersion_plot(dialogue, wrds2, rm.vars = time, 
    color="black", bg.color="white")) 

 with(rajSPLIT, dispersion_plot(dialogue, c("love", "night"),
    bg.color = "black", grouping.var = list(fam.aff, sex),
    color = "yellow", total.color = "white", horiz.color="grey20")) 

Word Correlation

oil_cor1 <- apply_as_df(crude, word_cor, word = "oil", r=.7)

 oil_cor2 <- apply_as_df(crude, word_cor, word = qcv(texas, oil, money), r=.7)
plot(oil_cor2, ncol=2)

Easy Hash Table

A Small Example

 lookup(1:5, data.frame(1:4, 11:14))

## [1] 11 12 13 14 NA

## Leave alone elements w/o a match
lookup(1:5, data.frame(1:4, 11:14), missing = NULL) 

## [1] 11 12 13 14  5

Scaled Up 3 Million Records

key <- data.frame(x=1:2, y=c("A", "B"))

##   x y
## 1 1 A
## 2 2 B

big.vec <- sample(1:2, 3000000, T)
out <- lookup(big.vec, key)

## On my system 3 million records in:
## Time difference of 24.5534 secs

Binary Operator Version

 codes <- list(
    A = c(1, 2, 4), 
    B = c(3, 5),
    C = 7,
    D = c(6, 8:10)

1:12 %l% codes

##  [1] "A" "A" "B" "A" "B" "D" "C" "D" "D" "D" NA  NA 

1:12 %l+% codes

##  [1] "A"  "A"  "B"  "A"  "B"  "D"  "C"  "D"  "D"  "D"  "11" "12" 

Simple-Quick Boolean Searches

We’ll be demoing this capability on the qdap data set DATA:

 ##        person                                 state
## 1         sam         Computer is fun. Not too fun.
## 2        greg               No it's not, it's dumb.
## 3     teacher                    What should we do?
## 4         sam                  You liar, it stinks!
## 5        greg               I am telling the truth!
## 6       sally                How can we be certain?
## 7        greg                      There is no way.
## 8         sam                       I distrust you.
## 9       sally           What are you talking about?
## 10 researcher         Shall we move on?  Good then.
## 11       greg I'm hungry.  Let's eat.  You already? 

First a brief explanation from the documentation:

terms – A character string(s) to search for. The terms are arranged in a single string with AND (use AND or && to connect terms together) and OR (use OR or || to allow for searches of either set of terms. Spaces may be used to control what is searched for. For example using ” I ” on c(“I’m”, “I want”, “in”) will result in FALSE TRUE FALSE whereas “I” will match all three (if case is ignored).

Let’s see how it works. We’ll start with ” I ORliar&&stinks”. This will find sentences that contain ” I “ or that contain “liar” and the word “stinks”.

 boolean_search(DATA$state, " I ORliar&&stinks")

## The following elements meet the criteria:
## [1] 4 5 8

boolean_search(DATA$state, " I &&.", values=TRUE)

## The following elements meet the criteria:
## [1] "I distrust you."

boolean_search(DATA$state, " I OR.", values=TRUE)

## The following elements meet the criteria:
## [1] "Computer is fun. Not too fun."        
## [2] "No it's not, it's dumb."              
## [3] "I am telling the truth!"              
## [4] "There is no way."                     
## [5] "I distrust you."                      
## [6] "Shall we move on?  Good then."        
## [7] "I'm hungry.  Let's eat.  You already?"

boolean_search(DATA$state, " I &&.")

## The following elements meet the criteria:
## [1] 8 

Exclusion as Well

boolean_search(DATA$state, " I ||.", values=TRUE)

## The following elements meet the criteria:
## [1] "Computer is fun. Not too fun."        
## [2] "No it's not, it's dumb."              
## [3] "I am telling the truth!"              
## [4] "There is no way."                     
## [5] "I distrust you."                      
## [6] "Shall we move on?  Good then."        
## [7] "I'm hungry.  Let's eat.  You already?"

boolean_search(DATA$state, " I ||.", exclude = c("way", "truth"), values=TRUE)

## The following elements meet the criteria:
## [1] "Computer is fun. Not too fun."        
## [2] "No it's not, it's dumb."              
## [3] "I distrust you."                      
## [4] "Shall we move on?  Good then."        
## [5] "I'm hungry.  Let's eat.  You already?"  

Binary Operator Version

 dat <- data.frame(x = c("Doggy", "Hello", "Hi Dog", "Zebra"), y = 1:4)

##        x y
## 1  Doggy 1
## 2  Hello 2
## 3 Hi Dog 3
## 4  Zebra 4

z <- data.frame(z =c("Hello", "Dog"))

##       z
## 1 Hello
## 2   Dog

dat[dat$x %bs% paste(z$z, collapse = "OR"), ]  

##        x y
## 1  Doggy 1
## 2  Hello 2
## 3 Hi Dog 3

Polarity (Sentiment)

The polarity function is an extension of the work originally done by Jeffrey Breen with some accompnaying plotting methods. For more information see the Introduction to qdap Vignette.

 poldat2 <- with(mraja1spl, polarity(dialogue,
    list(sex, fam.aff, died)))
colsplit2df(scores(poldat2))[, 1:7] 
    sex fam.aff  died total.sentences total.words ave.polarity sd.polarity
1     f     cap FALSE             158        1810  0.076422846   0.2620359
2     f     cap  TRUE              24         221  0.042477906   0.2087159
3     f    mont  TRUE               4          29  0.079056942   0.3979112
4     m     cap FALSE              73         717  0.026496626   0.2558656
5     m     cap  TRUE              17         185 -0.159815603   0.3133931
6     m   escal FALSE               9         195 -0.152764808   0.3131176
7     m   escal  TRUE              27         646 -0.069421082   0.2556493
8     m    mont FALSE              70         952 -0.043809741   0.3837170
9     m    mont  TRUE             114        1273 -0.003653114   0.4090405
10    m    none FALSE               7          78  0.062243180   0.1067989
11 none    none FALSE               5          18 -0.281649658   0.4387579

The Accompanying Plotting Methods



Question Type

 dat <- c("Kate's got no appetite doesn't she?",
    "Wanna tell Daddy what you did today?",
    "You helped getting out a book?", "umm hum?",
    "Do you know what it is?", "What do you want?",
    "Who's there?", "Whose?", "Why do you want it?",
    "Want some?", "Where did it go?", "Was it fun?")

left_just(preprocessed(question_type(dat))[, c(2, 6)])  
   raw.text                             q.type             
1  Kate's got no appetite doesn't she?  doesnt             
2  Wanna tell Daddy what you did today? what               
3  You helped getting out a book?       implied_do/does/did
4  Umm hum?                             unknown            
5  Do you know what it is?              do                 
6  What do you want?                    what               
7  Who's there?                         who                
8  Whose?                               whose              
9  Why do you want it?                  why                
10 Want some?                           unknown            
11 Where did it go?                     where              
12 Was it fun?                          was                
 x <- question_type(DATA.SPLIT$state, DATA.SPLIT$person)

      person tot.quest    what    how   shall implied_do/does/did
1       greg         1       0      0       0             1(100%)
2 researcher         1       0      0 1(100%)                   0
3      sally         2  1(50%) 1(50%)       0                   0
4    teacher         1 1(100%)      0       0                   0
5        sam         0       0      0       0                   0
plot(scores(x), high="orange")


These are a few of the more recent developments in qdap. We would encourage readers to dig into the new vignettes and start using qdap for various Natural Language Processing tasks. If you have suggestions or find a bug you are welcome to:

  • submit suggestions and bug-reports at: https://github.com/trinker/qdap/issues
  • send a pull request on: https://github.com/trinker/qdap

  • For a complete list of changes see qdap’s NEWS.md

    Development Version

    Posted in analysis, discourse analysis, qdap, text | Tagged , , , , , , , , , , , | 3 Comments

    qdap 1.1.0 Released on CRAN

    We’re very pleased to announce the release of qdap 1.1.0


    This is the fourth installment of the qdap package available at CRAN. Major development has taken place since the last CRAN update.

    The qdap package automates many of the tasks associated with quantitative discourse analysis of transcripts containing discourse, including frequency counts of sentence types, words, sentence, turns of talk, syllable counts and other assorted analysis tasks. The package provides parsing tools for preparing transcript data but may be useful for many other natural language processing tasks. Many functions enable the user to aggregate data by any number of grouping variables providing analysis and seamless integration with other R packages that undertake higher level analysis and visualization of text.

    This version is a major overhaul of the qdap package. The word lists and dictionaries in qdap have been moved to qdapDictionaries. Additionally, many functions have been renamed with underscores instead of the former period separators. These changes break backward compatibility. Thus this is a major release (ver. 1.0.0). It is the general practice to deprecate functions within a package before removal, however, the number of necessary changes in light of qdap being relatively new to CRAN, made these changes sensible at this point.

    To install use:


    Some of the changes in version 1.1.0 include:


    qdap gains an HTML package vignette to better explain the intended workflow and function use for the package. This is not currently a part of the build but can be accessed via:



    qdap 1.1.0 attempts to gain compatability with the tm package. This enables data structures from tm to be utilized with qdap functions and conversely qdap data structures to be utilized with functions intended for tm data sets. Some of the following changes have been made to gain tm compatability:

    • tdm and dtm are now truly compatable with the tm package. tdm and dtm produce outputs of the class "TermDocumentMatrix" and "DocumentTermMatrix" respectively. This change (coupled with the renaming of stopwords to rm_stopwords) should make the two packages logical companions and further extend the qdap package to integrate with the many packages that already handle "TermDocumentMatrix" and "DocumentTermMatrix".
    • tm2qdap a function to convert "TermDocumentMatrix" and "DocumentTermMatrix" to a wfm added to allow easier integration with the tm package.
    • apply_as_tm a function to allow functions intended to be used on the tm package’s TermDocumentMatrix to be applied to a wfm object.
    • tm_corpus2df and df2tm_corpus added to convert a tm package corpus to a dataframe for use in qdap or vice versa.


    • hash_look (and %ha%) a counterpart to hash added to allow quick access to a hash table. Intended for use within functions or multiple uses of the same hash table, whereas lookup is intended for a single external (non-function) use which is more convenient though could be slower.
    • word_cor added to find words within grouping variables that are associated based on correlation.
    • dispersion_plot added to enable viewing of word dispersion through discourse.
    • word_proximity added to compliment dispersion_plot and word_cor functions. word_proximity gives the average distance between words in the unit of sentences.
    • boolean_search, a Boolean term search function, added to allow for indexed searches of Boolean terms.
    • wfm now uses mtabulate and is ~10x faster.


    Several Plotting Functions have been added to qdap. Many functions pick up a corresponding plotting method as well.

    This version of qdap has seen some exciting changes. We look forward to continued development. In the future we plan to:

    • Further develop the new_report function to better incorporate the reports package and smooth workflow.
    • Incorporate the dplyr package to gain speed boosts in some of qdap’s functions.

    For a complete list of changes see qdap’s NEWS.md

    Development Version

    Posted in qdap | Tagged , , , , , , , , , | 1 Comment

    Sochi Olympic Medals

    For those who are addicted to R and haven’t the time to click the mouse on a web browser you too can still be informed about the results of the 2014 Sochi Winter Olympics. I was inspired by a SO response around the London games a couple years back.

    Packages to Load

    packs <- c("knitr", "ggplot2", "XML", "reshape2", "rCharts")
    lapply(packs, require, character.only = TRUE)

    The Script

    olympics <- 
    function(theurl = "http://www.sochi2014.com/en/medal-standings", include.zero = FALSE) {
        invisible(lapply(c('ggplot2', 'XML', 'reshape2') , require, character.only=TRUE))
        ## Grab Data, Clean and Reshape
        raw <- readHTMLTable(theurl, header=FALSE, 
            colClasses = c(rep("factor", 2), rep("numeric", 4)))
        raw <- as.data.frame(raw)[, -1]
        colnames(raw) <- c("Country", "Gold", "Silver", "Bronze", "Total")
        raw <- with(raw, raw[order(Total, Gold, Silver, Bronze), ])
        if (!include.zero) {
            raw <- raw[raw[, "Total"] != 0, ]
        raw[, "Country"] <- factor(raw[, "Country"], levels = raw[, "Country"])
        rownames(raw) <- NULL
        mdat <- melt(raw, value.name = "Count", variable.name = "Place", id.var = "Country")
        mdat[, "Place"] <- factor(mdat[, "Place"], levels=c("Gold", "Silver", "Bronze", "Total"))  
        ## Plot the Data
        plot1 <- ggplot(mdat, aes(x = Count, y = Country, colour = Place)) +
          geom_point() +
          facet_grid(.~Place) + theme_bw()+
          scale_colour_manual(values=c("#CC6600", "#999999", "#FFCC33", "#000000")) 

    The Visual Results

    x <- olympics()


    As a Data Table

    dTable(x)$show('inline', include_assets = TRUE, cdn = TRUE)

    WordPress and Data Table don’t play well together so you’ll need to run the code to see it in action.


    I have chosen a dot plot to display the data because it’s easy to quickly get a sense of the data yet be able to compare relatively easily. Dot plots take advantage of the powerful pre-attentive attribute of distance (The most powerful way to visually convey quantitative information). Stephen Few gives his two cents about dot plots here.

    I’m lazy but this would be a fun Shiny app to build. [EDIT @Ty Henkaline answers the call for a Shiny app and provides the ui.R and server.R]

    Thanks to @Ramnath for help implementing the chart as a jQuery DataTable.

    *Created using the reports package

    Posted in Uncategorized, data, reshape, ggplot2, visualization | Tagged , , , , | 19 Comments

    Sentence Drawing: Part II

    In a recent blog post I introduced Stefanie Posavec‘s Sentence Drawings. We created this ggplot2 rendition:

    We left off weighing the aesthetics of the Sentence Drawing with information of quality visualizations. I asked others to think of ways to display the information and also hinted that I’d use Yihui’s animation package to show the fluid nature of the conversation. Jim Vallandingham stepped up with a D3 rendering of the Sentence Drawing (though not implemented in R as we’ve grown accustomed to with rCharts) that gives a mouse over of the dialogue (GitHub here). I too followed up with the animation version as seen in the video outcome and accompanying script below.

    Click Here to view the html version.

    [https://www.youtube.com/watch?v=mA6VYCPVb8M?autoplay=0&w=640&h=360]Mp4 Video

    If you likes what you see then have a lookyloo at the code below.

    Getting Started

    Installing Packages from GitHub and Turn Function

    # install.packages("devtools")
    install_github(c('slidify', 'slidifyLibraries'), 'ramnathv', ref = 'dev')
    install_github("knitcitations", "cboettig")
    install_github(c("reports", "qdapDictionaries", "qdap"), "trinker")
    install_github("ggthemes", "jrnold")
    invisible(lapply(c("qdap", "ggplot2", "ggthemes", "scales", "grid"), 
        require, character.only = TRUE))
    turn_it <- function(dataframe, len.col, turn = -pi/2) {
        dat <- dataframe
        dat[, "turn"] <- rep(turn, nrow(dataframe))
        dat <- within(dat, { 
            facing <- pi/2 + cumsum(turn)
            move <- dat[, len.col] * exp(1i * facing)
            position <- cumsum(move)
            x2 <- Re(position)
            y2 <- Im(position)
            x1 <- c(0, head(x2, -1))
            y1 <- c(0, head(y2, -1))
        dat[, c("x1", "y1", "x2", "y2")] <- 
            lapply(dat[, c("x1", "y1", "x2", "y2")], round, digits=0)
        data.frame(dataframe, dat[, c("x1", "y1", "x2", "y2")])

    The Animation Code

    ## Prepping the data
    dat2b <- rajSPLIT
    dat2b$wc <- wc(rajSPLIT$dialogue)
    dat2b <- dat2b[!is.na(dat2b[, "wc"]), ]
    ## Reassign names to family affiliation
    dat2b[, "fam.aff"] <- factor(lookup(as.character(dat2b[, "fam.aff"]), 
        levels(dat2b[, "fam.aff"])[1:3], qcv(Escalus, Capulet, Montague), 
        missing = NULL))
    ## Make dataframe with the beginning coordinates of each act
    beg_act <- do.call(rbind, lapply(with(turn_it(dat2b, "wc"), 
        split(turn_it(dat2b, "wc"), act)), function(x) {
            x[1, qcv(act, x1, y1, x2, y2)]
    keys <- sapply(split(1:nrow(dat2b), dat2b[, "act"]), head, 1)
    ani_dat <- turn_it(dat2b, "wc")
    yl <- range(ani_dat[, c("y1", "y2")])
    xl <- range(ani_dat[, c("x1", "x2")])
    ## An animation base function
    ani_sent <- function(i){
        base <- ggplot(ani_dat[1:i, ], aes(x = x1, y = y1, xend = x2, yend = y2)) + 
            geom_segment(aes(color=fam.aff), lineend = "butt", size=1) +
            guides(colour = guide_legend(override.aes = list(alpha = 1))) + 
            theme_few() + 
            scale_colour_few(name="Family\nAffiliation", drop = FALSE) +
            theme(axis.ticks = element_blank(), 
                axis.text = element_blank(),  
                axis.title= element_blank(),
                legend.position = c(.1, .85),
                legend.title.align = .5) +
            ggtitle("Romeo and Juliet Family\nAffiliation: Sentence Drawing") 
        addon1 <- geom_text(data=beg_act[i >= keys,], 
            aes(x = x1, y=y1, label = paste("Act", act)), 
            colour = "grey25", hjust = -.1, size=5, fontface = "bold") 
        addon2 <- geom_point(data=beg_act[i >= keys,], 
            aes(x = x1, y=y1), size=2.3, colour = "grey25") 
        base2 <- base + addon1 + addon2
        info <- ani_dat[i, c("tot", "act")]
        base3 <- base2 +  geom_rect(aes(xmin = -173, xmax = -79, ymin = -160, ymax = -110), 
            fill="white", colour="grey75") + 
            annotate("text", x = -150, y=-125, label = "ACT", 
                colour="grey75", size=4, fontface = "bold") + 
            annotate("text", x = -105, y=-125, label = "T.O.T.", 
                colour="grey75", size=4, fontface = "bold") +
            annotate("text", x = -150, y=-145, label = as.character(info[2]), 
                colour="grey75", size=4, fontface = "bold") + 
            annotate("text", x = -105, y=-145, label = as.character(info[1]),  
                colour="grey75", size=4, fontface = "bold")  +
            xlim(xl) + ylim(yl)
    pp2 <- function(x=base, alph = .15){
        for(i in 1:nrow(ani_dat)){
    ## Plot it
    out <- file.path(getwd(), "sent3") ## Change this as needed
    saveVideo(pp2(), interval = 0.01, outdir = out, 
        ffmpeg = "C:/Program Files (x86)/ffmpeg-latest-win32-static/ffmpeg-20130306-git-28adecf-win32-static/bin/ffmpeg.exe")
    saveHTML(pp2(), autoplay = FALSE, loop = FALSE, verbose = FALSE, outdir = out,
        single.opts = "'controls': ['first', 'previous', 'play', 'next', 'last', 'loop', 'speed'], 'delayMin': 0")

    For more on intro to animations see, this blog post.

    *Blog post created using the reports package

    Posted in Uncategorized, text, ggplot2, qdap, visualization, discourse analysis, animation | Tagged , , , , , , | 1 Comment