John Miyamoto - University of Washington



John Miyamoto

Useful R Commands (Top); Useful R Information Sources (Bottom)

Contents (Cntrl-left click on a link to jump to the corresponding section)

|Section |Topic |

|1RefTo: s1 |Useful R Functions |

|2RefTo: s0001 |Notes re plot and lines |

|3RefTo: s1b |Regular expressions in R |

|4RefTo: s6 |Special characters like "\n" |

|5RefTo: s2 |Useful Links and Documents (Bookmarks: 's2', 'Links', 'Docs') |

|6RefTo: s5 |Notes re the Built-In R Editor |

|7RefTo: s3 |Possible Editors for R Programming |

|8RefTo: s4 |Notes on R-Code/Computing (see also 'e:\r\notes' and 'e:\r\docs') |

1s1. Useful R Functions

|Function |Purpose |

|"imputation" |See packages 'cat', 'norm', and 'mix' for various imputation functions. See, also, the |

| |'transcan' function in the 'Hmisc' package. See, also, |

| |. |

|%in% |If X and Y are vectors, X %in% Y is a vector. length(X %in% Y) = length(X). The i-th element |

|match |of X %in% Y equals TRUE if X[i] is an element of Y and is FALSE otherwise. The match function |

| |serves similar purposes but is more easily modified. |

|.libPaths |.libPaths gets/sets the library trees within which packages are looked for. '.libPaths(new)' |

| |where 'new' is a character vector with the locations of R library trees. |

|.Platform |.Platform is a list with some details of the platform under which R was built. This provides |

|R.version |means to write OS portable R code. E.g., '.Platform$Os.type' gives the operating system that |

|() |the current version was written for. See also 'R.version' and '()'. |

| |The operators cause a search to made through the environment for an existing |

| |definition of the variable being assigned. If such a variable is found then its value is |

| |redefined, otherwise assignment takes place globally. Note that their semantics differ from that|

| |in the S language, but is useful in conjunction with the scoping rules of R. |

|all.equal |all.equal(x,y) is a utility to compare R objects x and y testing ``near equality''. If they are |

| |different, comparison is still made to some extent, and a report of the differences is returned.|

| |Don't use 'all.equal' directly in if expressions—either use 'identical' or combine the two, as |

| |shown in the documentation for 'identical'. See also 'identical' and '=='. |

|AnalyzeFMRI |Package for analyzing fMRI images. |

|arrows |Draw arrows between pairs of points. Also useful for creating error bars (set 'angle' to 90). |

|barplot |Makes bar plots. Note that 'x.loc gl(3,4) |

| |[1] 1 1 1 1 2 2 2 2 3 3 3 3 |

| |Levels: 1 2 3 |

|glm( ..., family = binomial) |Logistic regression. Note that the summary function gives results in the log odds ratio form. |

| |You need to transform back to odds ratios. |

|head |Returns the first or last parts of a vector, matrix, data frame or function. Useful for viewing|

| |or extracting a small subset of cases. |

|head |Returns the first few rows of a dataframe or matrix (or vector). |

|help.search |Searches the R help system for documentation matching a given character string in the (file) |

| |name, alias, title, concept or keyword entries (or any combination thereof), using either fuzzy |

| |matching or regular expression matching. Names and titles of the matched help entries are |

| |displayed nicely. See also 'RSiteSearch'. |

|identical |The safe and reliable way to test two objects for being exactly equal. It returns TRUE in this |

| |case, FALSE in every other case. See also 'all.equal' and '=='. |

|ifelse(test, yes, no) |'ifelse' returns a value with the same shape as test which is filled with elements selected from|

| |either 'yes' or 'no' depending on whether the element of 'test' is TRUE or FALSE. |

|image |Creates a grid of colored or gray-scale rectangles with colors corresponding to the values in z.|

| |This can be used to display three-dimensional or spatial data aka images. |

|image |Creates a grid of colored or gray-scale rectangles with colors corresponding to the values in z.|

| |This can be used to display three-dimensional or spatial data aka “images”. This is a generic |

| |function. The functions heat.colors, terrain.colors and topo.colors create heat-spectrum (red to|

| |white) and topographical color schemes suitable for displaying ordered data, with n giving the |

| |number of colors desired. |

|interaction.plot |Makes a line plot for a 2-way anova design with one factor on the X axis and the other factor |

| |with separate lines. |

|isoMDS (in MASS) |Alternative functions that perform nonmetric multidimensional scaling (mds). |

|sammon (in MASS) | |

|cmdscale (in mva) | |

|xgvis (in xgobi) | |

|layout |Used for making multiple graphs on a single screen (like mfrow or mfcol). Unlike mfrow or |

| |mfcol, row and column heights can be specified for individual rows or columns. |

|library('package name') |Loads 'package name'. |

|library(help = MASS) |Lists all objects in MASS along with short description. |

|ls(package:MASS) |Lists all objects in MASS if it is attached. |

|lines |Add lines and points to a plot. See Section 2RefTo: s0001 for more info. |

|list.files |This function produces a list containing the names of files in the named directory. dir is an |

| |alias. key = filenames |

|logtrans |MASS package: Find and optionally plot the marginal likelihood for alpha for a transformation |

| |model of the form log(y + alpha) ~ x1 + x2 + .... |

|make.names |Make syntactically valid names out of character vectors. |

|make.unique |Makes the elements of a character vector unique by appending sequence numbers to duplicates. |

| |Useful for creating unique names of variables or factor levels. |

|match.call |match.call returns a call in which all of the arguments are specified by their names. The most |

| |common use is to get the call of the current function, with all arguments named, i.e., use |

| |'match.call' if you want to return the current values of the parameters that were input to a |

| |function. |

|merge |Analogous to the SPSS command, JOIN MATCH / TABLE. |

| |Combines input dataframes on common values for columns with identical names or user-specified |

| |columns. |

|mvrnorm |MASS package: Generates multivariate normal random variables. |

|mvtnorm |'mvtnorm' package generate probabilities under a multivariate normal density function. Can be |

| |used to generate data with a given variance/covariance matrix (use 'rmvnorm'). Also, look at |

| |'mvrnorm' in the MASS package. |

|n.gt.1 |JM function that counts the number of cases in each condition (combination of factor levels) in |

| |a multifactor between subjects anova. The output is TRUE if the condition has more than 1 |

| |observation and FALSE if it has 0 or 1 observation. This function is useful in combination with|

| |'studres' in the MASS library because this function sometimes yields a value of 0 where it |

| |should be NA when a cell has only 1 observation. |

|na.omit |Omits cases from a dataframe if any variables have missing data. |

|onecode |JM function that creates a oneway anova factor from multiple input factors. 'onecode' is useful|

| |whenever it is easer to treat a multifactor between subects anova as a oneway anova. |

|oneway.test |Computes a oneway anova (between subjects). Default is to NOT assume homogeneity of variance. |

|optimize |The function optimize searches the interval from lower to upper for a minimum or maximum of the |

| |function f with respect to its first argument. |

|p.adjust |Multiple comparison procedure: Given a set of p values, returns p values adjusted using Holm |

| |method (default), Hochberg method, or Bonferroni method (in the base package). |

|'package functions' |These functions can be used to automatically compare the version numbers of installed packages |

|update.packages |with the newest available version on the repositories and update outdated packages on the fly. |

|available.packages | |

|old.packages | |

|new.packages | |

|download.packages | |

|install.packages | |

|contrib.url | |

|package.skeleton |'package.skeleton' automates some of the setup for a new source package. It creates directories,|

| |saves functions and data to appropriate places, and creates skeleton help files and ‘README’ |

| |files describing further steps in packaging. |

|pairs() |Produces all pairs of scatter plots. |

|pairwise.prop.test |Multiple comparison procedures for various tests (in the ctest package). |

|pairwise.t.test | |

|pairwise.table | |

|pairwise.wilcox.test | |

|par("mai") |A numerical vector of the form c(bottom, left, top, right) which gives the margin size specified|

| |in inches. (Use 'mai' or 'mar' but not both.) |

|par("mar") |A numerical vector of the form 'c(bottom, left, top, right)' which gives the number of lines of |

| |margin to be specified on the four sides of the plot. The default is 'c(5, 4, 4, 2) + 0.1'. |

|par("mex") |'mex' is a character size expansion factor which is used to describe coordinates in the margins |

| |of plots. Note that this does not change the font size, rather specifies the size of font used |

| |to convert between 'mar' and 'mai', and between 'oma' and 'omi'. (Note that JM has been |

| |misusing this parameter until 8/21/2005.) |

|par("usr") |Gives the min and max on the x and y axis for the current plot. |

|par("xpd") |Logical. If FALSE, all plotting is clipped to the plot region, if TRUE, all plotting is clipped|

| |to the figure region, and if NA, all plotting is clipped to the device region. Can be used to |

| |put legend (or any other text) outside of the plotting region. |

|permn |In 'combinat' package. Generates all permutations of the elements of x, in a minimal- change |

| |order. If x is a positive integer, returns all permutations of the elements of seq(x). If |

| |argument "fun" is not null, applies a function given by the argument to each point. "..." are |

| |passed unchanged to the function given by argument fun, if any. |

|plot |Create plots. See Section 2RefTo: s0001 for more info. |

|power.prop.test |Computes power of test for equality of proportions, or determines parameters to obtain target |

| |power. |

|power.t.test |Compute power of test, or determine parameters to obtain target power. |

|proc.time |proc.time determines how much time (in seconds) the currently running R process already |

| |consumed. Value: A numeric vector of length 5, containing the user, system, and total elapsed |

| |times for the currently running R process, and the cumulative sum of user and system times of |

| |any child processes spawned by it. See also 'system.time' and 'gc'. |

|ptukey |Functions for the studentized range distribution. |

|qtukey | |

|qr |qr computes the QR decomposition of a matrix. The QR decomposition plays an important role in |

| |many statistical techniques. In particular it can be used to solve the equation Ax = b for given|

| |matrix A, and vector b. It is useful for computing regression coefficients and in applying the |

| |Newton-Raphson algorithm. The functions qr.coef, qr.resid, and qr.fitted return the |

| |coefficients, residuals and fitted values obtained when fitting y to the matrix with QR |

| |decomposition qr. qr.qy and qr.qty return Q %*% y and t(Q) %*% y, where Q is the Q matrix. |

|range |range usually returns the min and max of a vector, but see the following example for an |

| |illustration of how range deals with missing and infinite elements: |

| |x none, I can't get just one "\" where I need it. See example code |

|> below. I am using R 2.1.0, but plan to upgrade soon. Thanks in |

|> advance to anyone who can help. |

|> Roger |

|> |

|> rankPath rankDate rankFile rankFile |

|> [1] "R:New RanksSMCSMC20050819.xls" |

|> |

|> rankPath rankDate rankFile rankFile |

|> [1] "R:\\New Ranks\\SMC\\SMC20050819.xls" |

| |

|This is perfect, "\" is *printed* escaped, hence for file access you can perfectly use this character vector. |

|Uwe Ligges |

|... and you can see that the "\\" is correct by cat(rankFile) instead of print(rankFile), which is what entering the variable at the prompt |

|actually does. |

|-- Bert Gunter |

|**JM: The '\\' is printed in the second example, but it denotes the correct path and file as far as R is concerned. |

|'update packages' |

|Problem: Has anyone written a script to inspect a previous installation, then get & install the same packages into the new installation? |

|# Solution from Uwe Ligges. |

|x foo as.vector(foo[is.na(foo[, "Priority"]), 1]) |

| |

|will give you a character vector which you can feed to install.packages(), |

|so it's not complex to do manually. |

|'Type I sum of squares', 'Type II sum of squares', 'Type III sum of squares' |

|The 'base' function 'anova' computes Type I SS's. The 'car' function 'Anova' computes Type II and Type III SS's. |

Keywords followed by Note

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[1] From R. Ripley's R course, , see her "R Programming 2010-11".

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