Histogram

Description

Abbreviation: hs

From the standard R function hist plots a frequency histogram with default colors, including background color and grid lines plus an option for a relative frequency and/or cumulative histogram, as well as summary statistics and a table that provides the bins, midpoints, counts, proportions, cumulative counts and cumulative proportions. Bins can be selected several different ways besides the default, including specifying just the bin width and/or the bin start. Also provides improved error diagnostics and feedback for the user on how to correct the problem when the bins do not contain all of the specified data.

If the provided object to analyze is a set of multiple variables, including an entire data frame, then each non-numeric variable in the data frame is analyzed and the results written to a pdf file in the current working directory. The name of each output pdf file that contains a bar chart and its path are specified in the output.

When output is assigned into an object, such as h in h <- hs(Y), the pieces of output can be accessed for later analysis. A primary such analysis is knitr for dynamic report generation from a generated R markdown file according to the Rmd option in which interpretative R output is embedded in documents. See value below.

Usage

Histogram(x=NULL, data=mydata, n.cat=getOption("n.cat"), Rmd=NULL,

         color.fill=getOption("color.fill.bar"), 
         color.stroke=getOption("color.stroke.bar"),
         color.bg=getOption("color.bg"),
         color.grid=getOption("color.grid"),
         color.box=getOption("color.box"),

         color.reg="snow2", over.grid=FALSE,
         cex.axis=0.75, color.axis="gray30",

         rotate.values=0, offset=0.5,

         breaks="Sturges", bin.start=NULL, bin.width=NULL, bin.end=NULL,

         prop=FALSE, cumul=c("off", "on", "both"), hist.counts=FALSE, 
         digits.d=NULL, xlab=NULL, ylab=NULL, main=NULL, sub=NULL,

         quiet=getOption("quiet"),
         pdf.file=NULL, pdf.width=5, pdf.height=5,
         fun.call=NULL, ...)

hs(...)

Arguments

Details

OVERVIEW
Results are based on the standard R hist function to calculate and plot a histogram, plus the additional provided color capabilities, a relative frequency histogram and summary statistics. However, a histogram with densities is not supported. The freq option from the standard R hist function has no effect as it is always set to FALSE in each internal call to hist. To plot densities, which correspond to setting freq to FALSE, use the lessR function Density.

DATA
The data may either be a vector from the global environment, the user's workspace, as illustrated in the examples below, or one or more variable's in a data frame, or a complete data frame. The default input data frame is mydata. Can specify the source data frame name with the data option. If multiple variables are specified, only the numerical variables in the list of variables are analyzed. The variables in the data frame are referenced directly by their names, that is, no need to invoke the standard R mechanisms of the mydata$name notation, the with function or the attach function. If the name of the vector in the global environment and of a variable in the input data frame are the same, the vector is analyzed.

To obtain a histogram of each numerical variable in the mydata data frame, use Histogram(). Or, for a data frame with a different name, insert the name between the parentheses. To analyze a subset of the variables in a data frame, specify the list with either a : or the c function, such as m01:m03 or c(m01,m02,m03).

COLORS
Individual colors in the plot can be manipulated with options such as color.bars for the color of the histogram bars. A color theme for all the colors can be chosen for a specific plot with the colors option with the lessR function theme. The default color theme is dodgerblue, but a gray scale is available with "gray", and other themes are available as explained in theme, such as "red" and "green". Use the option ghost=TRUE for a black background, no grid lines and partial transparency of plotted colors.

For the color options, such as color.grid, the value of "off" is the same as "transparent".

VARIABLE LABELS
If variable labels exist, then the corresponding variable label is by default listed as the label for the horizontal axis and on the text output. For more information, see Read.

ONLY VARIABLES ARE REFERENCED
The referenced variable in a lessR function can only be a variable name (or list of variable names). This referenced variable must exist in either the referenced data frame, such as the default mydata, or in the user's workspace, more formally called the global environment. That is, expressions cannot be directly evaluated. For example:

> Histogram(rnorm(50)) # does NOT work

Instead, do the following:

    > Y <- rnorm(50)   # create vector Y in user workspace
    > Histogram(Y)     # directly reference Y

ERROR DETECTION
A somewhat relatively common error by beginning users of the base R hist function may encounter is to manually specify a sequence of bins with the seq function that does not fully span the range of specified data values. The result is a rather cryptic error message and program termination. Here, Histogram detects this problem before attempting to generate the histogram with hist, and then informs the user of the problem with a more detailed and explanatory error message. Moreover, the entire range of bins need not be specified to customize the bins. Instead, just a bin width need be specified, bin.width, and/or a value that begins the first bin, bin.start. If a starting value is specified without a bin width, the default Sturges method provides the bin width.

PDF OUTPUT
Because of the customized graphic windowing system that maintains a unique graphic window for the Help function, the standard graphic output functions such as pdf do not work with the lessR graphics functions. Instead, to obtain pdf output, use the pdf.file option, perhaps with the optional pdf.width and pdf.height options. These files are written to the default working directory, which can be explicitly specified with the R setwd function.

Value

The output can optionally be saved into an R object, otherwise it simply appears in the console. Redesigned in lessR version 3.3 to provide two different types of components: the pieces of readable output, and a variety of statistics. The readable output are character strings such as tables amenable for reading. The statistics are numerical values amenable for further analysis. The motivation of these types of output is to facilitate R markdown documents, as the name of each piece, preceded by the name of the saved object and a $, can be inserted into the R~Markdown document (see examples).

READABLE OUTPUT
codeout_ss: Summary statistics
codeout_freq: Frequency distribution
codeout_outliers: Outlier analysis
codeout_file: Name and location of optional Rmd file

STATISTICS
codebin_width: Bin width
coden_bins: Number of bins
codebreaks: Breaks of the bins
codemids: Bin midpoints
codecounts: Bin counts
codeprop: Bin proportion
codecounts_cumul: Bin cumulative counts
codeprop_cumul: Bin cumulative proportion

Although not typically needed, if the output is assigned to an object named, for example, h, then the contents of the object can be viewed directly with the unclass function, here as unclass(h).

Author(s)

David W. Gerbing (Portland State University; gerbing@pdx.edu)

See Also

hist, plot, par, theme.

Examples

# generate 50 random normal data values with three decimal digits
y <- round(rnorm(50),3)


# --------------------
# different histograms
# --------------------

# histogram with all defaults
Histogram(y)
# short form
hs(y)
# compare to standard R function hist
hist(y)

# output saved for later analysis into object h
h <- hs(y)
# view full text output
h
# view just the outlier analysis
h$out_outliers
# list the names of all the components
names(h)

# histogram with no borders for the bars
Histogram(y, color.stroke="off")

# save the histogram to a pdf file
Histogram(y, pdf.file="MyHistogram.pdf")

# histogram with no grid, red bars, black background, and black border
Histogram(y, color.grid="off", color.bg="black",
          color.fill="red", color.stroke="black")
# or set this color scheme for all subsequent analyses
set("red", color.grid="off", color.bg="black", color.stroke.bar="black")
Histogram(y)

# histogram with orange color theme, transparent orange bars, no grid lines
theme(colors="orange", ghost=TRUE)
Histogram(y)
# back to default of "blue" color theme
theme(colors="blue")

# histogram with specified bin width
# can also use bin.start
Histogram(y, bin.width=.25)

# histogram with rotated axis values, offset more from axis
# suppress text output
Histogram(y, rotate.values=45, offset=1, quiet=TRUE)

# histogram with specified bins and grid lines displayed over the histogram
Histogram(y, breaks=seq(-5,5,.25), xlab="My Variable", over.grid=TRUE)

# histogram with bins calculated with the Scott method and values displayed
Histogram(y, breaks="Scott", hist.counts=TRUE, quiet=TRUE)

# histogram with the number of suggested bins, with proportions
Histogram(y, breaks=15, prop=TRUE)

# histogram with specified colors, overriding defaults
# color.bg and color.grid are defined in histogram
# all other parameters are defined in hist, par and plot functions
# generates caution messages that can be ignored regarding density and angle
#Histogram(y, color.fill="darkblue", color.stroke="lightsteelblue4", color.bg="ivory",
#  color.grid="darkgray", density=25, angle=-45, cex.lab=.8, cex.axis=.8,
#  col.lab="sienna3", main="My Title", col.main="gray40", xlim=c(-5,5), lwd=2,
#  xlab="My Favorite Variable")

# ---------------------
# cumulative histograms
# ---------------------

# cumulative histogram with superimposed regular histogram, all defaults
Histogram(y, cumul="both")

# cumulative histogram plus regular histogram
# present with proportions on vertical axis, override other defaults
Histogram(y, cumul="both", breaks=seq(-4,4,.25), prop=TRUE, 
  color.reg="mistyrose")


# -------------------------------------------------
# histograms for data frames and multiple variables
# -------------------------------------------------

# create data frame, mydata, to mimic reading data with Read function
# mydata contains both numeric and non-numeric data
mydata <- data.frame(rnorm(50), rnorm(50), rnorm(50), rep(c("A","B"),25))
names(mydata) <- c("X","Y","Z","C")

# although data not attached, access the variable directly by its name
Histogram(X)

# histograms for all numeric variables in data frame called mydata
#  except for numeric variables with unique values < n.cat
# mydata is the default name, so does not need to be specified with data
Histogram()

# variable of interest is in a data frame which is not the default mydata
# access the breaks variable in the R provided warpbreaks data set
# although data not attached, access the variable directly by its name
Histogram(breaks, data=warpbreaks)

# all histograms with specified options, including red axis labels
Histogram(color.fill="palegreen1", color.bg="ivory", hist.counts=TRUE, col.lab="red")

# histograms for all specified numeric variables
# use the combine or c function to specify a list of variables
Histogram(c(X,Y))

Results