| Title: | Companion to "Learning Statistics with R" |
|---|---|
| Description: | A collection of tools intended to make introductory statistics easier to teach, including wrappers for common hypothesis tests and basic data manipulation. It accompanies Navarro, D. J. (2015). Learning Statistics with R: A Tutorial for Psychology Students and Other Beginners, Version 0.6. |
| Authors: | Danielle Navarro [aut, cre] |
| Maintainer: | Danielle Navarro <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 0.5.2 |
| Built: | 2024-10-24 05:14:02 UTC |
| Source: | https://github.com/djnavarro/lsr |
Calculates the mean absolute deviation from the sample mean
aad(x, na.rm = FALSE)aad(x, na.rm = FALSE)
x |
A vector containing the observations. |
na.rm |
A logical value indicating whether or not missing values should be removed. Defaults to |
The aad function calculates the average (i.e. mean)
absolute deviation from the mean value of x, removing NA
values if requested by the user. It exists primarily to simplify the
discussion of descriptive statistics during an introductory stats class.
Numeric
# basic usage X <- c(1, 3, 6) # data aad(X) # returns a value of 1.777 # removing missing data X <- c(1, 3, NA, 6) # data aad(X) # returns NA aad(X, na.rm = TRUE) # returns 1.777# basic usage X <- c(1, 3, 6) # data aad(X) # returns a value of 1.777 # removing missing data X <- c(1, 3, NA, 6) # data aad(X) # returns NA aad(X, na.rm = TRUE) # returns 1.777
Convenience function that runs a chi-square test of association/independence. This is a wrapper function intended to be used for pedagogical purposes only.
associationTest(formula, data = NULL)associationTest(formula, data = NULL)
formula |
One-sided formula specifying the two variables (required). |
data |
Optional data frame containing the variables. |
The associationTest function runs the chi-square test
of association on the variables specified in the formula argument.
The formula must be a one-sided formula of the form
~variable1 + variable2, and both variables must be factors.
An object of class 'assocTest'. When printed, the output is organised into six short sections. The first section lists the name of the test and the variables included. The second lists the null and alternative hypotheses for the test. The third shows the observed contingency table, and the fourth shows the expected contingency table under the null. The fifth prints out the test results, and the sixth reports an estimate of effect size.
df <- data.frame( gender=factor(c("male","male","male","male","female","female","female")), answer=factor(c("heads","heads","heads","heads","tails","tails","heads")) ) associationTest( ~ gender + answer, df )df <- data.frame( gender=factor(c("male","male","male","male","female","female","female")), answer=factor(c("heads","heads","heads","heads","tails","tails","heads")) ) associationTest( ~ gender + answer, df )
Grouped bar plots with error bars
bars( formula, data = NULL, heightFun = mean, errorFun = ciMean, yLabel = NULL, xLabels = NULL, main = "", ylim = NULL, barFillColour = NULL, barLineWidth = 2, barLineColour = "black", barSpaceSmall = 0.2, barSpaceBig = 1, legendLabels = NULL, legendDownShift = 0, legendLeftShift = 0, errorBarLineWidth = 1, errorBarLineColour = "grey40", errorBarWhiskerWidth = 0.2 )bars( formula, data = NULL, heightFun = mean, errorFun = ciMean, yLabel = NULL, xLabels = NULL, main = "", ylim = NULL, barFillColour = NULL, barLineWidth = 2, barLineColour = "black", barSpaceSmall = 0.2, barSpaceBig = 1, legendLabels = NULL, legendDownShift = 0, legendLeftShift = 0, errorBarLineWidth = 1, errorBarLineColour = "grey40", errorBarWhiskerWidth = 0.2 )
formula |
A two-sided formula specifying the response variable and the grouping factors |
data |
An optional data frame containing the variables |
heightFun |
The function used to calculate the bar height for a group (default=mean) |
errorFun |
The function used to calculate the error bar for a group (default=ciMean). No bars drawn if |
yLabel |
The y-axis label (defaults to the name of the response variable) |
xLabels |
The x-axis bar labels (defaults to factor labels of the appropriate grouping variable) |
main |
The plot title |
ylim |
The y-axis limit: lower bound defaults to 0, default upper bound estimated |
barFillColour |
The colours to fill the bars (defaults to a rainbow palette with saturation .3) |
barLineWidth |
The width of the bar border lines (default=2) |
barLineColour |
The colour of the bar border lines (default="black") |
barSpaceSmall |
The size of the gap between bars within a cluster, as a proportion of bar width (default=.2) |
barSpaceBig |
The size of the gap separating clusters of bars, as a proportion of bar width (default=1) |
legendLabels |
The text for the legend (defaults to factor labels of the appropriate grouping variable). No legends drawn if |
legendDownShift |
How far below the top is the legend, as proportion of plot height? (default=0) |
legendLeftShift |
How far away from the right edge is the legend, as proportion of plot? (default=0) |
errorBarLineWidth |
The line width for the error bars (default=1) |
errorBarLineColour |
The colour of the error bars (default="grey40") |
errorBarWhiskerWidth |
The width of error bar whiskers, as proportion of bar width (default=.2) |
Plots group means (or other function, if specified) broken down by
one or two grouping factors. Confidence intervals (or other function) are
plotted. User specifies a two sided formula of the form
response ~ group1 + group2, where response must be numeric
and group1 and group2 are factors. The group1 variable
defines the primary separation on the x-axis, and the x-axis labels by
default print out the levels of this factor. The group2 variable
defines the finer grain separation, and the legend labels correspond to
the levels of this factor. Note that group2 is optional.
Invisibly returns a data frame containing the factor levels, group means and confidence intervals. Note that this function is usually called for its side effects.
Calculates confidence intervals for the mean of a normally-distributed variable.
ciMean(x, conf = 0.95, na.rm = FALSE)ciMean(x, conf = 0.95, na.rm = FALSE)
x |
A numeric vector, data frame or matrix containing the observations. |
conf |
The level of confidence desired. Defaults to a 95% confidence interval |
na.rm |
Logical value indicating whether missing values are to be removed. Defaults to |
This function calculates the confidence interval for the mean of
a variable (or set of variables in a data frame or matrix), under the
standard assumption that the data are normally distributed. By default it
returns a 95% confidence interval (conf = 0.95) and does not
remove missing values (na.rm = FALSE).
The output is a matrix containing the lower and upper ends of the confidence interval for each variable. If a data frame is specified as input and contains non-numeric variables, the corresponding rows in the output matrix have NA values.
X <- c(1, 3, 6) # data ciMean(X) # 95 percent confidence interval ciMean(X, conf = .8) # 80 percent confidence interval confint( lm(X ~ 1) ) # for comparison purposes X <- c(1, 3, NA, 6) # data with missing values ciMean(X, na.rm = TRUE) # remove missing valuesX <- c(1, 3, 6) # data ciMean(X) # 95 percent confidence interval ciMean(X, conf = .8) # 80 percent confidence interval confint( lm(X ~ 1) ) # for comparison purposes X <- c(1, 3, NA, 6) # data with missing values ciMean(X, na.rm = TRUE) # remove missing values
Calculates the Cohen's d measure of effect size.
cohensD( x = NULL, y = NULL, data = NULL, method = "pooled", mu = 0, formula = NULL )cohensD( x = NULL, y = NULL, data = NULL, method = "pooled", mu = 0, formula = NULL )
x |
A numeric variable containing the data for group 1, or possibly a formula of the form |
y |
If |
data |
If |
method |
Which version of the d statistic should we calculate? Possible values are |
mu |
The "null" value against which the effect size should be measured. This is almost always 0 (the default), so this argument is rarely specified. |
formula |
An alias for |
The cohensD function calculates the Cohen's d measure of
effect size in one of several different formats. The function is intended
to be called in one of two different ways, mirroring the t.test
function. That is, the first input argument x is a formula, then a
command of the form cohensD(x = outcome~group, data = data.frame)
is expected, whereas if x is a numeric variable, then a command of
the form cohensD(x = group1, y = group2) is expected.
The method argument allows the user to select one of several
different variants of Cohen's d. Assuming that the original t-test for
which an effect size is desired was an independent samples t-test (i.e.,
not one sample or paired samples t-test), then there are several
possibilities for how the normalising term (i.e., the standard deviation
estimate) in Cohen's d should be calculated. The most commonly used
method is to use the same pooled standard deviation estimate that is
used in a Student t-test (method = "pooled", the default). If
method = "raw" is used, then the same pooled standard deviation
estimate is used, except that the sample standard deviation is used
(divide by N) rather than the unbiased estimate of the population
standard deviation (divide by N-2). Alternatively, there may be reasons
to use only one of the two groups to estimate the standard deviation. To
do so, use method = "x.sd" to select the x variable, or
the first group listed in the grouping factor; and method = "y.sd"
to normalise by y, or the second group listed in the grouping
factor. The last of the "Student t-test" based measures is the unbiased
estimator of d (method = "corrected"), which multiplies the "pooled"
version by (N-3)/(N-2.25).
For other versions of the t-test, there are two possibilities implemented.
If the original t-test did not make a homogeneity of variance assumption,
as per the Welch test, the normalising term should mirror the Welch test
(method = "unequal"). Or, if the original t-test was a paired samples
t-test, and the effect size desired is intended to be based on the standard
deviation of the differences, then method = "paired" should be used.
The last argument to cohensD is mu, which represents the mean
against which one sample Cohen's d calculation should be assessed. Note that
this is a slightly narrower usage of mu than the t.test
function allows. cohensD does not currently support the use of a
non-zero mu value for a paired-samples calculation.
Numeric variable containing the effect size, d. Note that it does not show the direction of the effect, only the magnitude. That is, the value of d returned by the function is always positive or zero.
Cohen, J. (1988). Statistical power analysis for the behavioral sciences (2nd ed.). Hillsdale, NJ: Lawrence Erlbaum Associates.
# calculate Cohen's d for two independent samples: gradesA <- c(55, 65, 65, 68, 70) # 5 students with teacher A gradesB <- c(56, 60, 62, 66) # 4 students with teacher B cohensD(gradesA, gradesB) # calculate Cohen's d for the same data, described differently: grade <- c(55, 65, 65, 68, 70, 56, 60, 62, 66) # grades for all students teacher <- c("A", "A", "A", "A", "A", "B", "B", "B", "B") # teacher for each student cohensD(grade ~ teacher) # calculate Cohen's d for two paired samples: pre <- c(100, 122, 97, 25, 274) # a pre-treatment measure for 5 cases post <- c(104, 125, 99, 29, 277) # the post-treatment measure for the same 5 cases cohensD(pre, post, method = "paired") # ... explicitly indicate that it's paired, or else cohensD(post - pre) # ... do a "single-sample" calculation on the difference # support for data frames: exams <- data.frame(grade, teacher) cohensD(exams$grade ~ exams$teacher) # using $ cohensD(grade ~ teacher, data = exams) # using the 'data' argument# calculate Cohen's d for two independent samples: gradesA <- c(55, 65, 65, 68, 70) # 5 students with teacher A gradesB <- c(56, 60, 62, 66) # 4 students with teacher B cohensD(gradesA, gradesB) # calculate Cohen's d for the same data, described differently: grade <- c(55, 65, 65, 68, 70, 56, 60, 62, 66) # grades for all students teacher <- c("A", "A", "A", "A", "A", "B", "B", "B", "B") # teacher for each student cohensD(grade ~ teacher) # calculate Cohen's d for two paired samples: pre <- c(100, 122, 97, 25, 274) # a pre-treatment measure for 5 cases post <- c(104, 125, 99, 29, 277) # the post-treatment measure for the same 5 cases cohensD(pre, post, method = "paired") # ... explicitly indicate that it's paired, or else cohensD(post - pre) # ... do a "single-sample" calculation on the difference # support for data frames: exams <- data.frame(grade, teacher) cohensD(exams$grade ~ exams$teacher) # using $ cohensD(grade ~ teacher, data = exams) # using the 'data' argument
Copies a vector into a matrix
colCopy(x, times, dimnames = NULL) rowCopy(x, times, dimnames = NULL)colCopy(x, times, dimnames = NULL) rowCopy(x, times, dimnames = NULL)
x |
The vector to be copied |
times |
Number of copies of the vector to bind together |
dimnames |
List specifying row and column names |
This is a convenience function for binding together multiple copies
of the same vector. The intended usage is for situations where one might
ordinarily use rbind or cbind, but the work is done by the
matrix function. Instead of needing to input multiple copies of the
input vector x (as one would for rbind), one only needs to
specify the number of times that the vector should be copied.
For rowCopy, the output is a matrix with times rows
and length(x) columns, in which each row contains the vector x.
For colCopy, each column corresponds to the vector x.
#Example 1: basic usage data <- c(3,1,4,1,5) rowCopy( data, 4 ) colCopy( data, 4 ) #Example 2: attach dimension names dnames <- list( rows = c("r1","r2","r3"), cols = c("c1","c2","c3","c4","c5") ) rowCopy( data,3,dnames )#Example 1: basic usage data <- c(3,1,4,1,5) rowCopy( data, 4 ) colCopy( data, 4 ) #Example 2: attach dimension names dnames <- list( rows = c("r1","r2","r3"), cols = c("c1","c2","c3","c4","c5") ) rowCopy( data,3,dnames )
Computes a correlation matrix and runs hypothesis tests with corrections for multiple comparisons
correlate( x, y = NULL, test = FALSE, corr.method = "pearson", p.adjust.method = "holm" )correlate( x, y = NULL, test = FALSE, corr.method = "pearson", p.adjust.method = "holm" )
x |
Matrix or data frame containing variables to be correlated |
y |
Optionally, a second set of variables to be correlated with those in |
test |
Should hypothesis tests be displayed? (Default= |
corr.method |
What kind of correlations should be computed? Default is |
p.adjust.method |
What method should be used to correct for multiple comparisons. Default value is |
The correlate function calculates a correlation matrix
between all pairs of variables. Much like the cor function, if the
user inputs only one set of variables (x) then it computes all
pairwise correlations between the variables in x. If the user
specifies both x and y it correlates the variables in
x with the variables in y.
Unlike the cor function, correlate does not generate an
error if some of the variables are categorical (i.e., factors). Variables
that are not numeric (or integer) class are simply ignored. They appear in
the output, but no correlations are reported for those variables. The
decision to have the correlate function allow the user a little
leniency when the input contains non-numeric variables should be explained.
The motivation is pedagogical rather than statistical. It is sometimes the
case in psychology that students need to work with correlation matrices
before they are comfortable subsetting a data frame, so it is convenient
to allow them to type commands like correlate(data) even when
data contains variables for which Pearson/Spearman correlations
are not appropriate. (It is also useful to use the output of
correlate to illustrate the fact that Pearson correlations should
not be used for categorical variables).
A second difference between cor and correlate is that
correlate runs hypothesis tests for all correlations in the
correlation matrix (using the cor.test function to do the work).
The results of the tests are only displayed to the user if
test=TRUE. This is a pragmatic choice, given the (perhaps
unfortunate) fact that psychologists often want to see the results
of these tests: it is probably not coincidental that the corr.test
function in the psych package already provides this functionality
(though the output is difficult for novices to read).
The concern with running hypothesis tests for all elements of a correlation
matrix is inflated Type I error rates. To minimise this risk, reported
p-values are adjusted using the Holm method. The user can change this
setting by specifying p.adjust.method. See p.adjust
for details.
Missing data are handled using pairwise complete cases.
The printed output shows the correlation matrix, and if tests are
requested it also reports a matrix of p-values and sample sizes associated
with each correlation (these can vary if there are missing data). The
underlying data structure is an object of class correlate (an S3
class). It is effectively a list containing four elements:
correlation is the correlation matrix, p.value is the matrix
of p-values, sample.size is the matrix of sample sizes, and
args is a vector that stores information about what the user
requested.
# data frame with factors and missing values data <- data.frame( anxiety = c(1.31,2.72,3.18,4.21,5.55,NA), stress = c(2.01,3.45,1.99,3.25,4.27,6.80), depression = c(2.51,1.77,3.34,5.83,9.01,7.74), happiness = c(4.02,3.66,5.23,6.37,7.83,1.18), gender = factor( c("male","female","female","male","female","female") ), ssri = factor( c("no","no","no",NA,"yes","yes") ) ) # default output is just the (Pearson) correlation matrix correlate( data ) # other types of correlation: correlate( data, corr.method="spearman" ) # two meaningful subsets to be correlated: nervous <- data[,c("anxiety","stress")] happy <- data[,c("happiness","depression","ssri")] # default output for two matrix input correlate( nervous, happy ) # the same examples, with Holm-corrected p-values correlate( data, test=TRUE ) correlate( nervous, happy, test=TRUE )# data frame with factors and missing values data <- data.frame( anxiety = c(1.31,2.72,3.18,4.21,5.55,NA), stress = c(2.01,3.45,1.99,3.25,4.27,6.80), depression = c(2.51,1.77,3.34,5.83,9.01,7.74), happiness = c(4.02,3.66,5.23,6.37,7.83,1.18), gender = factor( c("male","female","female","male","female","female") ), ssri = factor( c("no","no","no",NA,"yes","yes") ) ) # default output is just the (Pearson) correlation matrix correlate( data ) # other types of correlation: correlate( data, corr.method="spearman" ) # two meaningful subsets to be correlated: nervous <- data[,c("anxiety","stress")] happy <- data[,c("happiness","depression","ssri")] # default output for two matrix input correlate( nervous, happy ) # the same examples, with Holm-corrected p-values correlate( data, test=TRUE ) correlate( nervous, happy, test=TRUE )
Calculate the Cramer's V measure of association
cramersV(...)cramersV(...)
... |
Arguments to be passed to the |
Calculates the Cramer's V measure of effect size for chi-square
tests of association and goodness of fit. The arguments to the
cramersV function are all passed straight to the chisq.test
function, and should have the same format.
A numeric variable with a single element corresponding to the value of V.
# Consider an experiment with two conditions, each with 100 # participants. Each participant chooses between one of three # options. Possible data for this experiment: condition1 <- c(30, 20, 50) condition2 <- c(35, 30, 35) X <- cbind( condition1, condition2 ) rownames(X) <- c( 'choice1', 'choice2', 'choice3' ) print(X) # To test the null hypothesis that the distribution of choices # is identical in the two conditions, we would run a chi-square # test: chisq.test(X) # To estimate the effect size we can use Cramer's V: cramersV( X ) # returns a value of 0.159# Consider an experiment with two conditions, each with 100 # participants. Each participant chooses between one of three # options. Possible data for this experiment: condition1 <- c(30, 20, 50) condition2 <- c(35, 30, 35) X <- cbind( condition1, condition2 ) rownames(X) <- c( 'choice1', 'choice2', 'choice3' ) print(X) # To test the null hypothesis that the distribution of choices # is identical in the two conditions, we would run a chi-square # test: chisq.test(X) # To estimate the effect size we can use Cramer's V: cramersV( X ) # returns a value of 0.159
Calculates eta-squared and partial eta-squared
etaSquared(x, type = 2, anova = FALSE)etaSquared(x, type = 2, anova = FALSE)
x |
An analysis of variance (aov) object. |
type |
What type of sum of squares to calculate? |
anova |
Should the full ANOVA table be printed out in addition to the effect sizes? |
Calculates the eta-squared and partial eta-squared measures of
effect size that are commonly used in analysis of variance. The input
x should be the analysis of variance object itself.
For unbalanced designs, the default in etaSquared is to compute
Type II sums of squares (type=2), in keeping with the Anova
function in the car package. It is possible to revert to the
Type I SS values (type=1) to be consistent with anova, but
this rarely tests hypotheses of interest. Type III SS values (type=3)
can also be computed.
If anova=FALSE, the output is an M x 2 matrix. Each of the
M rows corresponds to one of the terms in the ANOVA (e.g., main effect 1,
main effect 2, interaction, etc), and each of the columns corresponds to
a different measure of effect size. Column 1 contains the eta-squared
values, and column 2 contains partial eta-squared values. If
anova=TRUE, the output contains additional columns containing the
sums of squares, mean squares, degrees of freedom, F-statistics and p-values.
# Example 1: one-way ANOVA outcome <- c( 1.4,2.1,3.0,2.1,3.2,4.7,3.5,4.5,5.4 ) # data treatment1 <- factor( c( 1,1,1,2,2,2,3,3,3 )) # grouping variable anova1 <- aov( outcome ~ treatment1 ) # run the ANOVA summary( anova1 ) # print the ANOVA table etaSquared( anova1 ) # effect size # Example 2: two-way ANOVA treatment2 <- factor( c( 1,2,3,1,2,3,1,2,3 )) # second grouping variable anova2 <- aov( outcome ~ treatment1 + treatment2 ) # run the ANOVA summary( anova2 ) # print the ANOVA table etaSquared( anova2 ) # effect size# Example 1: one-way ANOVA outcome <- c( 1.4,2.1,3.0,2.1,3.2,4.7,3.5,4.5,5.4 ) # data treatment1 <- factor( c( 1,1,1,2,2,2,3,3,3 )) # grouping variable anova1 <- aov( outcome ~ treatment1 ) # run the ANOVA summary( anova1 ) # print the ANOVA table etaSquared( anova1 ) # effect size # Example 2: two-way ANOVA treatment2 <- factor( c( 1,2,3,1,2,3,1,2,3 )) # second grouping variable anova2 <- aov( outcome ~ treatment1 + treatment2 ) # run the ANOVA summary( anova2 ) # print the ANOVA table etaSquared( anova2 ) # effect size
Substitutes all factors in a data frame with the set of contrasts with which that factor is associated
expandFactors(data, ...)expandFactors(data, ...)
data |
A data frame. |
... |
Additional arguments to be passed to model.matrix |
The expandFactors function replaces all of the factors
in a data frame with the set of contrasts output by the contrasts
function or model.matrix. It may be useful for teaching purposes
when explaining relationship between ANOVA and regression.
A data frame.
grading <- data.frame( teacher = factor( c("Amy","Amy","Ben","Ben","Cat") ), gender = factor( c("male","female","female","male","male") ), grade = c(75,80,45,50,65) ) # expand factors using the default contrasts (usually treatment contrasts) expandFactors( grading ) # specify the contrasts using the contrasts.arg argument to model.matrix my.contrasts <- list( teacher = "contr.helmert", gender = "contr.treatment" ) expandFactors( grading, contrasts.arg = my.contrasts )grading <- data.frame( teacher = factor( c("Amy","Amy","Ben","Ben","Cat") ), gender = factor( c("male","female","female","male","male") ), grade = c(75,80,45,50,65) ) # expand factors using the default contrasts (usually treatment contrasts) expandFactors( grading ) # specify the contrasts using the contrasts.arg argument to model.matrix my.contrasts <- list( teacher = "contr.helmert", gender = "contr.treatment" ) expandFactors( grading, contrasts.arg = my.contrasts )
Convenience function that runs a chi-square goodness of fit test against specified probabilities. This is a wrapper function intended to be used for pedagogical purposes only.
goodnessOfFitTest(x, p = NULL)goodnessOfFitTest(x, p = NULL)
x |
Factor variable containing the raw outcomes. |
p |
Numeric variable containing the null-hypothesis probabilities (default = all outcomes equally likely) |
The goodnessOfFitTest function runs the chi-square
goodness of fit test of the hypothesis that the outcomes in the factor
x were generated according to the probabilities in the vector
p. The probability vector p must be a numeric variable
of length nlevels(x). If no probabilities are specified, all
outcomes are assumed to be equally likely.
An object of class 'gofTest'. When printed, the output is organised into four short sections. The first section lists the name of the test and the variables included. The second lists the null and alternative hypotheses for the test. The third shows the observed frequency table, the expected frequency table under the null hypothesis, and the probabilities specified by the null. The fourth prints out the test results.
chisq.test,
associationTest,
cramersV
# raw data gender <- factor( c( "male","male","male","male","female","female", "female","male","male","male" )) # goodness of fit test against the hypothesis that males and # females occur with equal frequency goodnessOfFitTest( gender ) # goodness of fit test against the hypothesis that males appear # with probability .6 and females with probability .4. goodnessOfFitTest( gender, p=c(.4,.6) ) goodnessOfFitTest( gender, p=c(female=.4,male=.6) ) goodnessOfFitTest( gender, p=c(male=.6,female=.4) )# raw data gender <- factor( c( "male","male","male","male","female","female", "female","male","male","male" )) # goodness of fit test against the hypothesis that males and # females occur with equal frequency goodnessOfFitTest( gender ) # goodness of fit test against the hypothesis that males appear # with probability .6 and females with probability .4. goodnessOfFitTest( gender, p=c(.4,.6) ) goodnessOfFitTest( gender, p=c(female=.4,male=.6) ) goodnessOfFitTest( gender, p=c(male=.6,female=.4) )
Creates variables in the workspace corresponding to the elements of a list
importList(x, ask = TRUE)importList(x, ask = TRUE)
x |
List to be imported |
ask |
Should R ask the user to confirm the new variables before creating them? (default is |
The importList function creates variables in the parent
environment (generally the global workspace) corresponding to each of the
elements of the list object x. If the names of these elements do
not correspond to legitimate variables names they are converted using
the make.names functions to valid variables names.
Invisibly returns 0 if the user chooses not to import the
variables, otherwise invisibly returns 1.
# data set organised into two groups data <- c(1,2,3,4,5) group <- c("group A","group A","group B","group B","group B") # the split function creates a list with two elements # named "group A" and "group B", each containing the # data for the respective groups data.list <- split( data, group ) # The data.list variable looks like this: # $`group A` # [1] 1 2 # # $`group B` # [1] 3 4 5 # importing the list with the default value of ask = TRUE will # cause R to wait on the user's approval. Typing this: # importList( data.list ) # would produce the following output: # Names of variables to be created: # [1] "group.A" "group.B" # Create these variables? [y/n] # If the user then types y, the new variables are created. # this version will silently import the variables. importList( x = data.list, ask = FALSE )# data set organised into two groups data <- c(1,2,3,4,5) group <- c("group A","group A","group B","group B","group B") # the split function creates a list with two elements # named "group A" and "group B", each containing the # data for the respective groups data.list <- split( data, group ) # The data.list variable looks like this: # $`group A` # [1] 1 2 # # $`group B` # [1] 3 4 5 # importing the list with the default value of ask = TRUE will # cause R to wait on the user's approval. Typing this: # importList( data.list ) # would produce the following output: # Names of variables to be created: # [1] "group.A" "group.B" # Create these variables? [y/n] # If the user then types y, the new variables are created. # this version will silently import the variables. importList( x = data.list, ask = FALSE )
Convenience function that runs an independent samples t-test. This is a wrapper function intended to be used for pedagogical purposes only.
independentSamplesTTest( formula, data = NULL, var.equal = FALSE, one.sided = FALSE, conf.level = 0.95 )independentSamplesTTest( formula, data = NULL, var.equal = FALSE, one.sided = FALSE, conf.level = 0.95 )
formula |
Formula specifying the outcome and the groups (required). |
data |
Optional data frame containing the variables. |
var.equal |
Should the test assume equal variances (default = |
one.sided |
One sided or two sided hypothesis test (default = |
conf.level |
The confidence level for the confidence interval (default = .95). |
The independentSamplesTTest function runs an
independent-samples t-test and prints the results in a format that is
easier for novices to handle than the output of t.test. All the
actual calculations are done by the t.test and cohensD
functions. The formula argument must be a two-sided formula of
the form outcome ~ group. When var.equal=TRUE, a Student's
t-test is run and the estimate of Cohen's d uses a pooled estimate of
standard deviation. When var.equal=FALSE, the Welch test is used,
and the estimate of Cohen's d uses the "unequal" method.
As with the t.test function, the default test is two sided,
corresponding to a default value of one.sided = FALSE. To specify
a one sided test, the one.sided argument must specify the name of
the factor level that is hypothesised (under the alternative) to have
the larger mean. For instance, if the outcome for "group2" is expected
to be higher than for "group1", then the corresponding one sided test
is specified by one.sided = "group2".
An object of class 'TTest'. When printed, the output is organised into five short sections. The first section lists the name of the test and the variables included. The second provides means and standard deviations. The third states explicitly what the null and alternative hypotheses were. The fourth contains the test results: t-statistic, degrees of freedom and p-value. The final section includes the relevant confidence interval and an estimate of the effect size (i.e., Cohen's d)
t.test,
oneSampleTTest,
pairedSamplesTTest,
cohensD
df <- data.frame( rt = c(451, 562, 704, 324, 505, 600, 829), cond = factor( x=c(1,1,1,2,2,2,2), labels=c("group1","group2"))) # Welch t-test independentSamplesTTest( rt ~ cond, df ) # Student t-test independentSamplesTTest( rt ~ cond, df, var.equal=TRUE ) # one sided test independentSamplesTTest( rt ~ cond, df, one.sided="group1" ) # missing data df$rt[1] <- NA df$cond[7] <- NA independentSamplesTTest( rt ~ cond, df )df <- data.frame( rt = c(451, 562, 704, 324, 505, 600, 829), cond = factor( x=c(1,1,1,2,2,2,2), labels=c("group1","group2"))) # Welch t-test independentSamplesTTest( rt ~ cond, df ) # Student t-test independentSamplesTTest( rt ~ cond, df, var.equal=TRUE ) # one sided test independentSamplesTTest( rt ~ cond, df, one.sided="group1" ) # missing data df$rt[1] <- NA df$cond[7] <- NA independentSamplesTTest( rt ~ cond, df )
Reshape a data frame from long form to wide form
longToWide(data, formula, sep = "_")longToWide(data, formula, sep = "_")
data |
The data frame. |
formula |
A two-sided formula specifying measure variables and within-subject variables |
sep |
Separator string used in wide-form variable names |
The longToWide function is the companion function to
wideToLong. The data argument is a "long form" data frame,
in which each row corresponds to a single observation. The output is a
"wide form" data frame, in which each row corresponds to a single
experimental unit (e.g., a single subject).
The reshaping formula should list all of the measure variables on the
left hand side, and all of the within-subject variables on the right
hand side. All other variables are assumed to be between-subject variables.
For example, if the accuracy of a participant's performance is
measured at multiple time points, then the formula would be
accuracy ~ time.
Multiple variables are supported on both sides of the formula. For example,
suppose we measured the response time rt and accuracy of
participants, across three separate days, and across three separate
sessions within each day. In this case the formula would be
rt + accuracy ~ days + sessions.
The output is a "wide form" data frame in containing one row per
subject (or experimental unit, more generally), with each observation of
that subject corresponding to a separate variable. The naming scheme for
these variables places the name of the measured variable first, followed
by the levels of within-subjects variable(s), separated by the separator
string sep. In the example above where the reshaping formula was
accuracy ~ time, if the default separator of sep="_" was
used, and the levels of the time variable are t1, t2
and t3, then the output would include the variables
accuracy_t1, accuracy_t2 and accuracy_t3.
In the second example listed above, where the reshaping formula was
rt + accuracy ~ days + sessions, the output variables would refer
to levels of both within-subjects variables. For instance,
rt_day1_session1, and accuracy_day2_session1 might be the
names of two of the variables in the wide form data frame.
long <- data.frame( id = c(1, 2, 3, 1, 2, 3, 1, 2, 3), time = c("t1", "t1", "t1", "t2", "t2", "t2", "t3", "t3", "t3"), accuracy = c(.50, .03, .72, .94, .63, .49, .78, .71, .16) ) longToWide(long, accuracy ~ time)long <- data.frame( id = c(1, 2, 3, 1, 2, 3, 1, 2, 3), time = c("t1", "t1", "t1", "t2", "t2", "t2", "t3", "t3", "t3"), accuracy = c(.50, .03, .72, .94, .63, .49, .78, .71, .16) ) longToWide(long, accuracy ~ time)
Calculate the mode of a sample: both modal value(s) and the corresponding frequency
maxFreq(x, na.rm = TRUE) modeOf(x, na.rm = TRUE)maxFreq(x, na.rm = TRUE) modeOf(x, na.rm = TRUE)
x |
A vector containing the observations. |
na.rm |
Logical value indicating whether NA values should be removed. |
These two functions can be used to calculate the mode (most
frequently observed value) of a sample, and the actual frequency of the
modal value. The only complication is in respect to missing data. If
na.rm = FALSE, then there are multiple possibilities for how to
calculate the mode. One possibility is to treat NA as another
possible value for the elements of x, and therefore if NA
is more frequent than any other value, then NA is the mode; and
the modal frequency is equal to the number of missing values. This is
the version that is currently implemented.
Another possibility is to treat NA as meaning "true value unknown",
and to the mode of x is itself known only if the number of missing
values is small enough that – regardless of what value they have – they
cannot alter the sample mode. For instance, if x were
c(1,1,1,1,2,2,NA), we know that the mode of x is 1
regardless of what the true value is for the one missing datum; and we
know that the modal frequency is between 4 and 5. This is also a valid
interpretation, depending on what precisely it is the user wants, but
is not currently implemented.
Because of the ambiguity of how na.rm = FALSE should be interpreted,
the default value has been set to na.rm = TRUE, which differs from
the default value used elsewhere in the package.
The modeOf function returns the mode of x. If there
are ties, it returns a vector containing all values of x that have
the modal frequency. The maxFreq function returns the modal
frequency as a numeric value.
# simple example eyes <- c("green","green","brown","brown","blue") modeOf(eyes) maxFreq(eyes) # vector with missing data eyes <- c("green","green","brown","brown","blue",NA,NA,NA) # returns NA as the modal value. modeOf(eyes, na.rm = FALSE) maxFreq(eyes, na.rm = FALSE) # returns c("green", "brown") as the modes, as before modeOf(eyes, na.rm = TRUE) maxFreq(eyes, na.rm = TRUE)# simple example eyes <- c("green","green","brown","brown","blue") modeOf(eyes) maxFreq(eyes) # vector with missing data eyes <- c("green","green","brown","brown","blue",NA,NA,NA) # returns NA as the modal value. modeOf(eyes, na.rm = FALSE) maxFreq(eyes, na.rm = FALSE) # returns c("green", "brown") as the modes, as before modeOf(eyes, na.rm = TRUE) maxFreq(eyes, na.rm = TRUE)
Convenience function that runs a one sample t-test. This is a wrapper function intended to be used for pedagogical purposes only.
oneSampleTTest(x, mu, one.sided = FALSE, conf.level = 0.95)oneSampleTTest(x, mu, one.sided = FALSE, conf.level = 0.95)
x |
The variable to be tested (required). |
mu |
The value against which the mean should be tested (required). |
one.sided |
One sided or two sided hypothesis test (default = |
conf.level |
The confidence level for the confidence interval (default = .95). |
The oneSampleTTest function runs a one-sample t-test on
the data in x, and prints the results in a format that is easier
for novices to handle than the output of t.test. All the actual
calculations are done by the t.test and cohensD functions.
As with the t.test function, the default test is two sided,
corresponding to a default value of one.sided = FALSE. To specify
a one sided test in which the alternative hypothesis is that x is
larger than mu, the input must be one.sided = "greater".
Similarly, if one.sided="less", then the alternative hypothesis
is that the mean of x is smaller than mu.
An object of class 'TTest'. When printed, the output is organised into five short sections. The first section lists the name of the test and the variables included. The second provides means and standard deviations. The third states explicitly what the null and alternative hypotheses were. The fourth contains the test results: t-statistic, degrees of freedom and p-value. The final section includes the relevant confidence interval and an estimate of the effect size (i.e., Cohen's d).
t.test,
pairedSamplesTTest,
independentSamplesTTest,
cohensD
likert <- c(3,1,4,1,4,6,7,2,6,6,7) oneSampleTTest( x = likert, mu = 4 ) oneSampleTTest( x = likert, mu = 4, one.sided = "greater" ) oneSampleTTest( x = likert, mu = 4, conf.level=.99 ) likert <- c(3,NA,4,NA,4,6,7,NA,6,6,7) oneSampleTTest( x = likert, mu = 4 )likert <- c(3,1,4,1,4,6,7,2,6,6,7) oneSampleTTest( x = likert, mu = 4 ) oneSampleTTest( x = likert, mu = 4, one.sided = "greater" ) oneSampleTTest( x = likert, mu = 4, conf.level=.99 ) likert <- c(3,NA,4,NA,4,6,7,NA,6,6,7) oneSampleTTest( x = likert, mu = 4 )
Convenience function that runs a paired samples t-test. This is a wrapper function intended to be used for pedagogical purposes only.
pairedSamplesTTest( formula, data = NULL, id = NULL, one.sided = FALSE, conf.level = 0.95 )pairedSamplesTTest( formula, data = NULL, id = NULL, one.sided = FALSE, conf.level = 0.95 )
formula |
Formula specifying the outcome and the groups (required). |
data |
Optional data frame containing the variables. |
id |
The name of the id variable (must be a character string). |
one.sided |
One sided or two sided hypothesis test (default = |
conf.level |
The confidence level for the confidence interval (default = .95). |
The pairedSamplesTTest function runs a paired-sample t-test,
and prints the results in a format that is easier for novices to handle than
the output of t.test. All the actual calculations are done by the
t.test and cohensD functions.
There are two different ways of specifying the formula, depending on whether
the data are in wide form or long form. If the data are in wide form, then
the input should be a one-sided formula of the form
~ variable1 + variable2. The id variable is not required: the
first element of variable1 is paired with the first element of
variable2 and so on. Both variable1 and variable2 must
be numeric.
If the data are in long form, a two sided formula is required. The simplest
way to specify the test is to input a formula of the form
outcome ~ group + (id). The term in parentheses is assumed to be
the id variable, and must be a factor. The group variable
must be a factor with two levels (if there are more than two levels but
only two are used in the data, a warning is given). The outcome
variable must be numeric.
The reason for using the outcome ~ group + (id) format is that it is
broadly consistent with the way repeated measures analyses are specified
in the lme4 package. However, this format may not appeal to some
people for teaching purposes. Given this, the pairedSamplesTTest
also supports a simpler formula of the form outcome ~ group, so
long as the user specifies the id argument: this must be a
character vector specifying the name of the id variable
As with the t.test function, the default test is two sided,
corresponding to a default value of one.sided = FALSE. To specify
a one sided test, the one.sided argument must specify the name of
the factor level (long form data) or variable (wide form data) that is
hypothesised (under the alternative) to have the larger mean. For instance,
if the outcome at "time2" is expected to be higher than at "time1", then
the corresponding one sided test is specified by one.sided = "time2".
An object of class 'TTest'. When printed, the output is organised into five short sections. The first section lists the name of the test and the variables included. The second provides means and standard deviations. The third states explicitly what the null and alternative hypotheses were. The fourth contains the test results: t-statistic, degrees of freedom and p-value. The final section includes the relevant confidence interval and an estimate of the effect size (i.e., Cohen's d)
t.test,
oneSampleTTest,
independentSamplesTTest,
cohensD
# long form data frame df <- data.frame( id = factor( x=c(1, 1, 2, 2, 3, 3, 4, 4), labels=c("alice","bob","chris","diana") ), time = factor( x=c(1,2,1,2,1,2,1,2), labels=c("time1","time2")), wm = c(3, 4, 6, 6, 9, 12,7,9) ) # wide form df2 <- longToWide( df, wm ~ time ) # basic test, run from long form or wide form data pairedSamplesTTest( formula= wm ~ time, data=df, id="id" ) pairedSamplesTTest( formula= wm ~ time + (id), data=df ) pairedSamplesTTest( formula= ~wm_time1 + wm_time2, data=df2 ) # one sided test pairedSamplesTTest( formula= wm~time, data=df, id="id", one.sided="time2" ) # missing data because of NA values df$wm[1] <- NA pairedSamplesTTest( formula= wm~time, data=df, id="id" ) # missing data because of missing cases from the long form data frame df <- df[-1,] pairedSamplesTTest( formula= wm~time, data=df, id="id" )# long form data frame df <- data.frame( id = factor( x=c(1, 1, 2, 2, 3, 3, 4, 4), labels=c("alice","bob","chris","diana") ), time = factor( x=c(1,2,1,2,1,2,1,2), labels=c("time1","time2")), wm = c(3, 4, 6, 6, 9, 12,7,9) ) # wide form df2 <- longToWide( df, wm ~ time ) # basic test, run from long form or wide form data pairedSamplesTTest( formula= wm ~ time, data=df, id="id" ) pairedSamplesTTest( formula= wm ~ time + (id), data=df ) pairedSamplesTTest( formula= ~wm_time1 + wm_time2, data=df2 ) # one sided test pairedSamplesTTest( formula= wm~time, data=df, id="id", one.sided="time2" ) # missing data because of NA values df$wm[1] <- NA pairedSamplesTTest( formula= wm~time, data=df, id="id" ) # missing data because of missing cases from the long form data frame df <- df[-1,] pairedSamplesTTest( formula= wm~time, data=df, id="id" )
Apply an arbitrary permutation to the ordering of levels within a factor
permuteLevels(x, perm, ordered = is.ordered(x), invert = FALSE)permuteLevels(x, perm, ordered = is.ordered(x), invert = FALSE)
x |
The factor to be permuted |
perm |
A vector specifying the permutation |
ordered |
Should the output be an ordered factor? |
invert |
Use the inverse of |
This is a convenience function used to shuffle the order in
which the levels of a factor are specified. It is similar in spirit to
the relevel function, but more general. The relevel
function only changes the first level of the factor, whereas
permuteLevels can apply an arbitrary permutation. This can be
useful for plotting data, because some plotting functions will display
the factor levels in the same order that they appear within the factor.
The perm argument is a vector of the same length as levels(x),
such that perm[k] is an integer that indicates which of the old
levels should be moved to position k. However, if invert=TRUE, the
inverse permutation is applied: that is, perm[k] is an integer
specifying where to move the k-th level of the original factor. See the
examples for more details.
Returns a factor with identical values, but with the ordering of the factor levels shuffled.
# original factor specifies the levels in order: a,b,c,d,e,f x <- factor( c(1,4,2,2,3,3,5,5,6,6), labels=letters[1:6] ) print(x) # apply permutation (5 3 2 1 4 6)... i.e., move 5th factor level (e) # into position 1, move 3rd factor level (c) into position 2, etc permuteLevels(x,perm = c(5,3,2,1,4,6)) # apply the inverse of permutation (5 3 2 1 4 6)... i.e., move 1st # level (a) into position 5, move 2nd level (b) into position 3, etc permuteLevels(x,perm = c(5,3,2,1,4,6),invert=TRUE)# original factor specifies the levels in order: a,b,c,d,e,f x <- factor( c(1,4,2,2,3,3,5,5,6,6), labels=letters[1:6] ) print(x) # apply permutation (5 3 2 1 4 6)... i.e., move 5th factor level (e) # into position 1, move 3rd factor level (c) into position 2, etc permuteLevels(x,perm = c(5,3,2,1,4,6)) # apply the inverse of permutation (5 3 2 1 4 6)... i.e., move 1st # level (a) into position 5, move 2nd level (b) into position 3, etc permuteLevels(x,perm = c(5,3,2,1,4,6),invert=TRUE)
Performs pairwise t-tests for an analysis of variance, making corrections for multiple comparisons.
posthocPairwiseT(x, ...)posthocPairwiseT(x, ...)
x |
An |
... |
Arguments to be passed to |
The intention behind this function is to allow users to use simple
tools for multiple corrections (e.g., Bonferroni, Holm) as post hoc
corrections in an ANOVA context, using the fitted model object (i.e., an
aov object) as the input. The reason for including this function is
that Tukey / Scheffe methods for constructing simultaneous confidence
intervals (as per TukeyHSD) are not often discussed in the
context of an introductory class, and the more powerful tools provided by
the multcomp package are not appropriate for students just beginning
to learn statistics.
This function is currently just a wrapper function for
pairwise.t.test, and it only works for one-way ANOVA, but
this may change in future versions.
As per pairwise.t.test
# create the data set to analyse: dataset <- data.frame( outcome = c( 1,2,3, 2,3,4, 5,6,7 ), group = factor(c( "a","a","a", "b","b","b","c","c","c")) ) # run the ANOVA and print out the ANOVA table: anova1 <- aov( outcome ~ group, data = dataset ) summary(anova1) # Currently, the following two commands are equivalent: posthocPairwiseT( anova1 ) pairwise.t.test( dataset$outcome, dataset$group )# create the data set to analyse: dataset <- data.frame( outcome = c( 1,2,3, 2,3,4, 5,6,7 ), group = factor(c( "a","a","a", "b","b","b","c","c","c")) ) # run the ANOVA and print out the ANOVA table: anova1 <- aov( outcome ~ group, data = dataset ) summary(anova1) # Currently, the following two commands are equivalent: posthocPairwiseT( anova1 ) pairwise.t.test( dataset$outcome, dataset$group )
Print method for lsr chi-square tests
## S3 method for class 'assocTest' print(x, ...)## S3 method for class 'assocTest' print(x, ...)
x |
An object of class 'assocTest' |
... |
For consistency with the generic (unused) |
Invisibly returns the original object
Print method for correlate objects
## S3 method for class 'correlate' print(x, ...)## S3 method for class 'correlate' print(x, ...)
x |
An object of class 'correlate' |
... |
For consistency with the generic (unused) |
Invisibly returns the original object
Print method for lsr goodness-of-fit tests
## S3 method for class 'gofTest' print(x, ...)## S3 method for class 'gofTest' print(x, ...)
x |
An object of class 'gofTest' |
... |
For consistency with the generic (unused) |
Invisibly returns the original object
Print method for lsr t-tests
## S3 method for class 'TTest' print(x, ...)## S3 method for class 'TTest' print(x, ...)
x |
An object of class 'TTest' |
... |
For consistency with the generic (unused) |
Invisibly returns the original object
Print method for whoList objects
## S3 method for class 'whoList' print(x, ...)## S3 method for class 'whoList' print(x, ...)
x |
An object of class 'whoList' |
... |
For consistency with the generic (unused) |
Invisibly returns the original object
Cuts a variable into equal sized categories
It is sometimes convenient (though not always wise) to split a
continuous numeric variable x into a set of n discrete
categories that contain an approximately equal number of cases. The
quantileCut function does exactly this. The actual categorisation
is done by the cut function. However, instead of selecting
ranges of equal sizes (the default behaviour in cut), the
quantileCut function uses the quantile function to
select unequal sized ranges so as to ensure that each of the categories
contains the same number of observations. The intended purpose of the
function is to assist in exploratory data analysis; it is not generally
a good idea to use the output of quantileCut function as a factor
in an analysis of variance, for instance, since the factor levels are not
interpretable and will almost certainly violate homogeneity of variance.
quantileCut(x, n, ...)quantileCut(x, n, ...)
x |
A vector containing the observations. |
n |
Number of categories |
... |
Additional arguments to cut |
A factor containing n levels. The factor levels are
determined in the same way as for the cut function, and can be
specified manually using the labels argument, which is passed to
the cut function.
# An example illustrating why care is needed dataset <- c( 0,1,2, 3,4,5, 7,10,15 ) # note the uneven spread of data x <- quantileCut( dataset, 3 ) # cut into 3 equally frequent bins table(x) # tabulate # For comparison purposes, here is the behaviour of the more standard cut # function when applied to the same data: y <- cut( dataset, 3 ) table(y)# An example illustrating why care is needed dataset <- c( 0,1,2, 3,4,5, 7,10,15 ) # note the uneven spread of data x <- quantileCut( dataset, 3 ) # cut into 3 equally frequent bins table(x) # tabulate # For comparison purposes, here is the behaviour of the more standard cut # function when applied to the same data: y <- cut( dataset, 3 ) table(y)
Removes all objects from the workspace
rmAll(ask = TRUE)rmAll(ask = TRUE)
ask |
Logical value indicating whether to ask user to confirm deletions. Default is |
The rmAll function provides a simple way of deleting all
objects from the workspace. It is almost equivalent to the usual
rm(list = objects()) command. The only difference that it requires
the user to confirm the deletions first if ask = TRUE, after
displaying a list of the current objects in the worspace. This can
occasionally be useful for teaching purposes.
Invisibly returns 0 if no deletions are made, 1 if at least one deletion is made.
Sorts a data frame using one or more variables.
sortFrame(x, ..., alphabetical = TRUE)sortFrame(x, ..., alphabetical = TRUE)
x |
Data frame to be sorted |
... |
A list of sort terms (see below) |
alphabetical |
Should character vectors be sorted alphabetically? |
The simplest use of this function is to sort a data frame x
in terms of one or more of the variables it contains. If for instance,
the data frame x contains two variables a and b, then
the command sortFrame(x,a,b) sorts by variable a, breaking
ties using variable b. Numeric variables are sorted in ascending
order: to sort in descending order of a and then ascending order
of b, use the command sortFrame(x,-a,b). Factors are treated
as numeric variables, and are sorted by the internal codes (i.e., the first
factor level equals 1, the second factor levels equals 2 and so on).
Character vectors are sorted in alphabetical order, which differs from the
ordering used by the sort function; to use the default 'ascii'
ordering, specify alphabetical=FALSE. Minus signs can be used in
conjunction with character vectors in order to sort in reverse alphabetical
order. If c represents a character variable, then sortFrame(x,c)
sorts in alphabetical order, whereas sortFrame(x,-c) sorts in reverse
alphabetical order.
It is also possible to specify more complicated sort terms by including
expressions using multiple variables within a single term, but care is
required. For instance, it is possible to sort the data frame by the sum of
two variables, using the command sortFrame(x, a+b). For numeric
variables expressions of this kind should work in the expected manner, but
this is not always the case for non-numeric variables: sortFrame uses
the xtfrm function to provide, for every variable referred to
in the list of sort terms (...) a numeric vector that sorts in the
same order as the original variable. This reliance is what makes reverse
alphabetical order (e.g., sortFrame(x,-c)) work. However, it also
means that it is possible to specify somewhat nonsensical sort terms for
character vectors by abusing the numerical coding (e.g.
sortFrame(x,(c-3)^2); see the examples section). It also means
that sorting in terms of string operation functions (e.g., nchar)
do not work as expected. See examples section. Future versions of
sortFrame will (hopefully) address this, possibly by allowing the
user to "switch off" the internal use of xtfrm, or else by allowing
AsIs expressions to be used in sort terms.
The sorted data frame
txt <- c("bob","Clare","clare","bob","eve","eve") num1 <- c(3,1,2,0,0,2) num2 <- c(1,1,3,0,3,2) etc <- c("not","used","as","a","sort","term") dataset <- data.frame( txt, num1, num2, etc, stringsAsFactors=FALSE ) sortFrame( dataset, num1 ) sortFrame( dataset, num1, num2 ) sortFrame( dataset, txt )txt <- c("bob","Clare","clare","bob","eve","eve") num1 <- c(3,1,2,0,0,2) num2 <- c(1,1,3,0,3,2) etc <- c("not","used","as","a","sort","term") dataset <- data.frame( txt, num1, num2, etc, stringsAsFactors=FALSE ) sortFrame( dataset, num1 ) sortFrame( dataset, num1, num2 ) sortFrame( dataset, txt )
Calculates the standardised regression coefficients for a linear model.
standardCoefs(x)standardCoefs(x)
x |
A linear model object (i.e. class |
Calculates the standardised regression coefficients (beta-weights), namely the values of the regression coefficients that would have been observed has all regressors and the outcome variable been scaled to have mean 0 and variance 1 before fitting the regression model. Standardised coefficients are sometimes useful in some applied contexts since there is a sense in which all beta values are "on the same scale", though this is not entirely unproblematic.
A matrix with the regressors as rows, and the two different regression coefficients (unstandardised and standardised) as the two columns. The columns are labeled b (unstandardised) and beta (standardised).
# Example 1: simple linear regression # data X1 <- c(0.69, 0.77, 0.92, 1.72, 1.79, 2.37, 2.64, 2.69, 2.84, 3.41) Y <- c(3.28, 4.23, 3.34, 3.73, 5.33, 6.02, 5.16, 6.49, 6.49, 6.05) model1 <- lm( Y ~ X1 ) # run a simple linear regression coefficients( model1 ) # extract the raw regression coefficients standardCoefs( model1 ) # extract standardised coefficients # Example 2: multiple linear regression X2 <- c(0.19, 0.22, 0.95, 0.43, 0.51, 0.04, 0.12, 0.44, 0.38, 0.33) model2 <- lm( Y ~ X1 + X2 ) # new model standardCoefs( model2 ) # standardised coefficients #Example 3: interaction terms model3 <- lm( Y ~ X1 * X2 ) coefficients( model3 ) standardCoefs( model3 ) # Note that these beta values are equivalent to standardising all # three regressors including the interaction term X1:X2, not merely # standardising the two predictors X1 and X2.# Example 1: simple linear regression # data X1 <- c(0.69, 0.77, 0.92, 1.72, 1.79, 2.37, 2.64, 2.69, 2.84, 3.41) Y <- c(3.28, 4.23, 3.34, 3.73, 5.33, 6.02, 5.16, 6.49, 6.49, 6.05) model1 <- lm( Y ~ X1 ) # run a simple linear regression coefficients( model1 ) # extract the raw regression coefficients standardCoefs( model1 ) # extract standardised coefficients # Example 2: multiple linear regression X2 <- c(0.19, 0.22, 0.95, 0.43, 0.51, 0.04, 0.12, 0.44, 0.38, 0.33) model2 <- lm( Y ~ X1 + X2 ) # new model standardCoefs( model2 ) # standardised coefficients #Example 3: interaction terms model3 <- lm( Y ~ X1 * X2 ) coefficients( model3 ) standardCoefs( model3 ) # Note that these beta values are equivalent to standardising all # three regressors including the interaction term X1:X2, not merely # standardising the two predictors X1 and X2.
Transposes a data frame, converting variables to cases and vice versa
tFrame(x)tFrame(x)
x |
The data frame to be transposed. |
The tFrame function is a convenience function that simply
transposes the input data frame and coerces the result back to a data frame.
Apart from a very small amount of exception handling, it is equivalent to
as.data.frame(t(x)). It exists simply because I sometimes find it
convenient when teaching statistics to discuss simple data handling before
going into details regarding coercion; similarly, since I generally have
students work with data frames before exposing them to matrices, it is
convenient to have a transpose function that returns a data frame as output.
Naturally, the tFrame function should only be used when it is
actually sensible to think of the cases of x as variables in their
own right. In real life I expect that this maps almost perfectly onto those
cases where x could be a matrix just as easily as a data frame, so
I don't believe that tFrame is useful in real world data analysis. It
is intended as a teaching tool.
The transposed data frame
# Create a data frame that could sensibly be transposed... Gf <- c(105, 119, 121, 98) # fluid intelligence for 4 people Gc <- c(110, 115, 119, 103) # crystallised intelligence Gs <- c(112, 102, 108, 99) # speed of processing dataset <- data.frame( Gf, Gc, Gs ) rownames(dataset) <- paste( "person", 1:4, sep="" ) print(dataset) # Now transpose it... tFrame( dataset )# Create a data frame that could sensibly be transposed... Gf <- c(105, 119, 121, 98) # fluid intelligence for 4 people Gc <- c(110, 115, 119, 103) # crystallised intelligence Gs <- c(112, 102, 108, 99) # speed of processing dataset <- data.frame( Gf, Gc, Gs ) rownames(dataset) <- paste( "person", 1:4, sep="" ) print(dataset) # Now transpose it... tFrame( dataset )
A wrapper function to detach that removes a package
from the search path, but takes a package name as input similar to library.
unlibrary(package)unlibrary(package)
package |
A package name, which may be specified with or without quotes. |
Unloads a package. This is just a wrapper for the detach
function. However, the package argument is just the name of the
package (rather than the longer string that is required by the detach
function), and – like the library function – can be specified
without quote marks. The unlibrary function does not unload dependencies,
only the named package.
The name "unlibrary" is a bit of an abuse of both R terminology (in which
one has a library of packages) and the English language, but I think it
helps convey that the goal of the unlibrary function is to do the
opposite of what the library function does.
Identical to detach.
Prints out a simple summary of all the objects in the workspace
who(expand = FALSE)who(expand = FALSE)
expand |
Should R "expand" data frames when listing variables? If
|
The who function prints out some basic information about
all variables in the workspace. Specifically, it lists the names of all
variables, what class they are, and how big they are (see below for
specifics). If the expand argument is TRUE it will also
print out the same information about variables within data frames. See
the examples below to see what the output looks like.
The purpose for the function is to show more information than the
objects function (especially as regards the names of variables
inside data frames), but not to show as much detail as the ls.str
function, which is generally too verbose for novice users.
The "size" of an object is only reported for some kinds of object:
specifically, only those objects whose mode is either
numeric, character, logical, complex or
list. Nothing is printed for any other kind of object. If the
object has explicit dimensions (e.g., data frames or matrices) then
who prints out the dimension sizes (e.g., "2 x 3" ). Otherwise
the length of the object is printed.
who returns an object of class whoList which is
just a data frame with a dedicated print method.
cats <- 4 mood <- "happy" who() dataset <- data.frame( hi = c( "hello","cruel","world" ), pi = c( 3,1,4 ) ) who() who(expand = TRUE)cats <- 4 mood <- "happy" who() dataset <- data.frame( hi = c( "hello","cruel","world" ), pi = c( 3,1,4 ) ) who() who(expand = TRUE)
Reshape a data frame from wide form to long form using the variable names
wideToLong(data, within = "within", sep = "_", split = TRUE)wideToLong(data, within = "within", sep = "_", split = TRUE)
data |
The data frame. |
within |
Name to give to the long-form within-subject factor(s) |
sep |
Separator string used in wide-form variable names |
split |
Should multiple within-subject factors be split into multiple variables? |
The wideToLong function is the companion function to longToWide.
The data argument is a "wide form" data frame, in which each row corresponds to
a single experimental unit (e.g., a single subject). The output is a "long form" data
frame, in which each row corresponds to a single observation.
The wideToLong function relies on the variable names to determine how the data
should be reshaped. The naming scheme for these variables places the name of the
measured variable first, followed by the levels of the within-subjects variable(s),
separated by the separator string sep (default is _) The separator
string cannot appear anywhere else in the variable names: variables without
the separator string are assumed to be between-subject variables.
If the experiment measured the accuracy of participants at some task
at two different points in time, then the wide form data frame would contain
variables of the form accuracy_t1 and accuracy_t2. After
reshaping, the long form data frame would contain one measured variable
called accuracy, and a within-subjects factor with levels t1
and t2. The name of the within-subjects factor is the within
argument.
The function supports experimental designs with multiple within-subjects
factors and multi-variable observations. For example, suppose each
experimental subject is tested in two conditions (cond1 and
cond2), on each of two days (day1 and day2),
yielding an experimental design in which four observations are made for
each subject. For each such observation, we record the mean response time
MRT for and proportion of correct responses PC for the
participant. The variable names needed for a design such as this one would
be MRT_cond1_day1, MRT_cond1_day2, PC_cond1_day1, etc.
The within argument should be a vector of names for the
within-subject factors: in this case, within = c("condition","day").
By default, if there are multiple within-subject factors implied by the
existence of multiple separators, the output will keep these as distinct
variables in the long form data frame (split=FALSE). If
split=TRUE, the within-subject factors will be collapsed into a
single variable.
A data frame containing the reshaped data
# Outcome measure is mean response time (MRT), measured in two conditions # with 4 participants. All participants participate in both conditions. wide <- data.frame( accuracy_t1 = c( .15,.50,.78,.55 ), # accuracy at time point 1 accuracy_t2 = c( .55,.32,.99,.60 ), # accuracy at time point 2 id = 1:4 ) # id variable # convert to long form wideToLong( wide, "time" ) # A more complex design with multiple within-subject factors. Again, we have only # four participants, but now we have two different outcome measures, mean response # time (MRT) and the proportion of correct responses (PC). Additionally, we have two # different repeated measures variables. As before, we have the experimental condition # (cond1, cond2), but this time each participant does both conditions on two different # days (day1, day2). Finally, we have multiple between-subject variables too, namely # id and gender. wide2 <- data.frame( id = 1:4, gender = factor( c("male","male","female","female") ), MRT_cond1_day1 = c( 415,500,478,550 ), MRT_cond2_day1 = c( 455,532,499,602 ), MRT_cond1_day2 = c( 400,490,468,502 ), MRT_cond2_day2 = c( 450,518,474,588 ), PC_cond1_day1 = c( 79,83,91,75 ), PC_cond2_day1 = c( 82,86,90,78 ), PC_cond1_day2 = c( 88,92,98,89 ), PC_cond2_day2 = c( 93,97,100,95 ) ) # conversion to long form: wideToLong( wide2 ) wideToLong( wide2, within = c("condition","day") ) # treat "condition x day" as a single repeated measures variable: wideToLong( wide2, split = FALSE)# Outcome measure is mean response time (MRT), measured in two conditions # with 4 participants. All participants participate in both conditions. wide <- data.frame( accuracy_t1 = c( .15,.50,.78,.55 ), # accuracy at time point 1 accuracy_t2 = c( .55,.32,.99,.60 ), # accuracy at time point 2 id = 1:4 ) # id variable # convert to long form wideToLong( wide, "time" ) # A more complex design with multiple within-subject factors. Again, we have only # four participants, but now we have two different outcome measures, mean response # time (MRT) and the proportion of correct responses (PC). Additionally, we have two # different repeated measures variables. As before, we have the experimental condition # (cond1, cond2), but this time each participant does both conditions on two different # days (day1, day2). Finally, we have multiple between-subject variables too, namely # id and gender. wide2 <- data.frame( id = 1:4, gender = factor( c("male","male","female","female") ), MRT_cond1_day1 = c( 415,500,478,550 ), MRT_cond2_day1 = c( 455,532,499,602 ), MRT_cond1_day2 = c( 400,490,468,502 ), MRT_cond2_day2 = c( 450,518,474,588 ), PC_cond1_day1 = c( 79,83,91,75 ), PC_cond2_day1 = c( 82,86,90,78 ), PC_cond1_day2 = c( 88,92,98,89 ), PC_cond2_day2 = c( 93,97,100,95 ) ) # conversion to long form: wideToLong( wide2 ) wideToLong( wide2, within = c("condition","day") ) # treat "condition x day" as a single repeated measures variable: wideToLong( wide2, split = FALSE)