hsFrom 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.
Histogram(x=NULL, data=mydata, n.cat=getOption("n.cat"), Rmd=NULL, col.fill=getOption("col.fill.bar"),
col.stroke=getOption("col.stroke.bar"),
col.bg=getOption("col.bg"),
col.grid=getOption("col.grid"),
col.reg="snow2", over.grid=FALSE,
cex.axis=0.75, col.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(...)
cmydata.set or use rgb function directly.cumul="both".TRUE, plot the grid lines over the histogram.cex.axis.offset.bin.start value.FALSE.labels options, which has multiple
definitions in R. Specifies to display the count of each bin."on" displays the
cumulative histogram, with default of "off". The value of "both"
superimposes the regular histogram.TRUE, no text output. Can change system default with set function..pdf, the filetype is added to the name.knitr to pass the function call when
obtained from the abbreviated function call hs.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 col.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 set. The default color theme is dodgerblue, but a gray scale is available with "gray", and other themes are available as explained in set, such as "red" and "green". Use the option ghost=TRUE for a black background, no grid lines and partial transparency of plotted colors.
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.
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 $, can be inserted into the R~Markdown document (see examples).
READABLE OUTPUT
code{out_ss}: Summary statistics
code{out_freq}: Frequency distribution
code{out_outliers}: Outlier analysis
code{out_file}: Name and location of optional Rmd file
STATISTICS
code{bin_width}: Bin width
code{n_bins}: Number of bins
code{breaks}: Breaks of the bins
code{mids}: Bin midpoints
code{counts}: Bin counts
code{prop}: Bin proportion
code{counts_cumul}: Bin cumulative counts
code{prop_cumul}: Bin cumulative proportion
Although not typically needed, if the output is assigned to an object named, for example, h, then the contents of the object can be viewed directly with the unclass function, here as unclass(h).
[object Object],[object Object]
# -------------------- # different histograms # --------------------
# histogram with all defaults Histogram(y) # short form hs(y) # compare to standard R function hist hist(y)
# output saved for later analysis into object h h <- hs(y) # view full text output h # view just the outlier analysis h$out_outliers # list the names of all the components names(h)
# histogram with no borders for the bars Histogram(y, col.stroke="transparent")
# 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, col.grid="transparent", col.bg="black", col.fill="red", col.stroke="black") # or set this color scheme for all subsequent analyses set("red", col.grid="transparent", col.bg="black", col.stroke.bar="black") Histogram(y)
# histogram with orange color theme, transparent orange bars, no grid lines set(colors="orange", ghost=TRUE) Histogram(y) # back to default of "blue" color theme set(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 # col.bg and col.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, col.fill="darkblue", col.stroke="lightsteelblue4", col.bg="ivory", # col.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, col.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(col.fill="palegreen1", col.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))