Package ‘questionr’

November 30, 2020

Maintainer Julien Barnier <[email protected]>
Version 0.7.4
Date 2020-11-30
License GPL (>= 2)
Encoding UTF-8
Title Functions to Make Surveys Processing Easier
Description Set of functions to make the processing and analysis of
surveys easier : interactive shiny apps and addins for data recoding,
contingency tables, dataset metadata handling, and several convenience
functions.
Depends R (>= 3.5.0)
Imports shiny (>= 1.0.5), miniUI, rstudioapi, highr, styler, classInt,
htmltools, graphics, stats, utils, labelled (>= 2.6.0)
Suggests testthat, roxygen2, dplyr, ggplot2, tidyr, janitor, forcats,
knitr, rmarkdown, survey, Hmisc
SystemRequirements xclip (Linux)
VignetteBuilder knitr

URL https://juba.github.io/questionr/

BugReports https://github.com/juba/questionr/issues
RoxygenNote 7.1.1
NeedsCompilation no
Author Julien Barnier [aut, cre],
François Briatte [aut],
Joseph Larmarange [aut]
Repository CRAN
Date/Publication 2020-11-30 14:10:02 UTC

1
2 R topics documented:

R topics documented:
addNAstr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
children . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
chisq.residuals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
clipcopy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
cprop . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
cramer.v . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
cross.multi.table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
describe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
duplicated2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
enfants . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
escape_regex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
fecondite . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
femmes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
fertility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
first_non_null . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
format.proptab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
freq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
freq.na . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
ggsurvey . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
happy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
hdv2003 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
households . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
icut . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
ifunc_get_css . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
ifunc_run_as_addin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
ifunc_show_alert . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
iorder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
irec . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
ltabs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
menages . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
multi.split . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
multi.table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
na.rm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
odds.ratio . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
print.proptab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
prop . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
qload . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
qscan . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
quant.cut . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
recode.na . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
rename.variable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
rm.unused.levels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
rp2012 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
rp99 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
rprop . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
tabs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
addNAstr 3

women . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
wtd.mean . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
wtd.table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

Index 44

addNAstr Transform missing values of a factor to an extra level

Description
This function modifies a factor by turning NA into an extra level (so that NA values are counted in
tables, for instance). This version of addNA extends the same function provided in R by allowing to
specify a string name for the extra level (see examples).

Usage
addNAstr(x, value = "NA", ...)

Arguments
x a vector of data, usually taking a small number of distinct values.
value string to use for the extra level name. If NULL, the extra level is created as NA,
and the result is the same as the one of the addNA function.
... arguments passed to addNA.

Value
an object of class "factor", original missing values being coded as an extra level named NA if
as.string=FALSE, "NA" if as.string=TRUE, as specified by as.string if as.string is a string.

Source
Adapted from James (https://stackoverflow.com/a/5817181) by Joseph Larmarange <[email protected]>

See Also
addNA (base).

Examples
f <- as.factor(c("a","b",NA,"a","b"))
f
addNAstr(f)
addNAstr(f, value="missing")
addNAstr(f, value=NULL)
4 chisq.residuals

children A fertility survey - "children" table

Description

Some fictive results from a fecondity survey.

Format

a data frame containing one record for each child of the surveyed women in the fertility survey.

chisq.residuals Return the chi-squared residuals of a two-way frequency table.

Description

Return the raw, standardized or Pearson’s residuals (the default) of a chi-squared test on a two-way
frequency table.

Usage

chisq.residuals(tab, digits = 2, std = FALSE, raw = FALSE)

Arguments

tab frequency table

digits number of digits to display
std if TRUE, returns the standardized residuals. Otherwise, returns the Pearson resid-
uals. Incompatible with raw.
raw if TRUE, returns the raw (observed -expected) residuals. Otherwise, returns
the Pearson residuals. Incompatible with std.

Details

This function is just a wrapper around the chisq.test base R function. See this function’s help
page for details on the computation.

See Also

chisq.test
clipcopy 5

Examples
## Sample table
data(Titanic)
tab <- apply(Titanic, c(1,4), sum)
## Pearson residuals
chisq.residuals(tab)
## Standardized residuals
chisq.residuals(tab, std = TRUE)
## Raw residuals
chisq.residuals(tab, raw = TRUE)

clipcopy Transform an object into HTML and copy it for export

Description
This function transforms its argument to HTML with knitr::kable and then copy it to the clipboard
or to a file for later use in an external application.

Usage
clipcopy(obj, ...)

## Default S3 method:
clipcopy(
obj,
append = FALSE,
file = FALSE,
filename = "temp.html",
clipboard.size = 4096,
...
)

## S3 method for class 'proptab'

clipcopy(obj, percent = NULL, digits = NULL, justify = "right", ...)

Arguments
obj object to be copied
... arguments passed to knitr::kable
append if TRUE, append to the file instead of replacing it
file if TRUE, export to a file instead of the clipboard
filename name of the file to export to
clipboard.size under Windows, size of the clipboard in kB
percent whether to add a percent sign in each cell
digits number of digits to display
justify justification
6 cprop

Details
Under Linux, this function requires that xclip is installed on the system to copy to the clipboard.

Value
NULL
NULL

See Also
kable, format.proptab
clipcopy, format.proptab

Examples
data(iris)
tab <- table(cut(iris$Sepal.Length,8),cut(iris$Sepal.Width,4))
## Not run: copie(tab)
ptab <- rprop(tab, percent=TRUE)
## Not run: clipcopy(ptab)

cprop Column percentages of a two-way frequency table.

Description
Return the column percentages of a two-way frequency table with formatting and printing options.

Usage
cprop(tab, ...)

## S3 method for class 'table'

cprop(
tab,
digits = 1,
total = TRUE,
percent = FALSE,
drop = TRUE,
n = FALSE,
...
)

## S3 method for class 'data.frame'

cprop(
tab,
digits = 1,
cprop 7

total = TRUE,
percent = FALSE,
drop = TRUE,
n = FALSE,
...
)

## S3 method for class 'matrix'

cprop(
tab,
digits = 1,
total = TRUE,
percent = FALSE,
drop = TRUE,
n = FALSE,
...
)

## S3 method for class 'tabyl'

cprop(tab, digits = 1, total = TRUE, percent = FALSE, n = FALSE, ...)

Arguments
tab frequency table
... parameters passed to other methods.
digits number of digits to display
total if TRUE, add a row with the sum of percentages and a column with global per-
centages
percent if TRUE, add a percent sign after the values when printing
drop if TRUE, lines or columns with a sum of zero, which would generate NaN percent-
ages, are dropped.
n if TRUE, display number of observations per column.

Value
The result is an object of class table and proptab.

See Also
rprop, prop, table, prop.table

Examples
## Sample table
data(Titanic)
tab <- apply(Titanic, c(4,1), sum)
## Column percentages
cprop(tab)
8 cross.multi.table

## Column percentages with custom display

cprop(tab, digits=2, percent=TRUE, total=FALSE)

cramer.v Compute Cramer’s V of a two-way frequency table

Description
This function computes Cramer’s V for a two-way frequency table

Usage
cramer.v(tab)

Arguments
tab table on which to compute the statistic

Examples
data(Titanic)
tab <- apply(Titanic, c(4,1), sum)
#' print(tab)
cramer.v(tab)

cross.multi.table Two-way frequency table between a multiple choices question and a

factor

Description
This function allows to generate a two-way frequency table from a multiple choices question and a
factor. The question’s answers must be stored in a series of binary variables.

Usage
cross.multi.table(
df,
crossvar,
weights = NULL,
digits = 1,
freq = FALSE,
tfreq = "col",
n = FALSE,
na.rm = TRUE,
...
)
cross.multi.table 9

Arguments
df data frame with the binary variables
crossvar factor to cross the multiple choices question with
weights optional weighting vector
digits number of digits to keep in the output
freq display percentages
tfreq type of percentages to compute ("row" or "col")
n if TRUE, and freq is TRUE, display number of observations per row or column
na.rm Remove any NA values in crossvar
... arguments passed to multi.table

Details
See the multi.table help page for details on handling of the multiple choices question and corre-
sponding binary variables.
If freq is set to TRUE, the resulting table gives the columns percentages based on the contingency
table of crossvar in the respondants population.

Value
Object of class table.

See Also
multi.table, multi.split, table

Examples
## Sample data frame
set.seed(1337)
sex <- sample(c("Man","Woman"),100,replace=TRUE)
jazz <- sample(c(0,1),100,replace=TRUE)
rock <- sample(c(TRUE, FALSE),100,replace=TRUE)
electronic <- sample(c("Y","N"),100,replace=TRUE)
weights <- runif(100)*2
df <- data.frame(sex,jazz,rock,electronic,weights)
## Two-way frequency table on 'music' variables by sex
cross.multi.table(df[,c("jazz", "rock","electronic")], df$sex, true.codes=list("Y"))
## Column percentages based on respondants
cross.multi.table(df[,c("jazz", "rock","electronic")], df$sex, true.codes=list("Y"), freq=TRUE)
## Row percentages based on respondants
cross.multi.table(df[,c("jazz", "rock","electronic")],
df$sex, true.codes=list("Y"), freq=TRUE, tfreq="row", n=TRUE)
10 describe

describe Describe the variables of a data.frame

Description
This function describes the variables of a vector or a dataset that might include labels imported with
haven packages.

Usage
describe(x, ...)

## S3 method for class 'factor'

describe(x, n = 10, show.length = TRUE, freq.n.max = 10, ...)

## S3 method for class 'numeric'

describe(x, n = 10, show.length = TRUE, freq.n.max = 10, ...)

## S3 method for class 'character'

describe(x, n = 10, show.length = TRUE, freq.n.max = 10, ...)

## Default S3 method:
describe(x, n = 10, show.length = TRUE, freq.n.max = 10, ...)

## S3 method for class 'haven_labelled'

describe(x, n = 10, show.length = TRUE, freq.n.max = 10, ...)

## S3 method for class 'data.frame'

describe(x, ..., n = 10, freq.n.max = 0)

## S3 method for class 'description'

print(x, ...)

Arguments
x object to describe
... further arguments passed to or from other methods, see details
n number of first values to display
show.length display length of the vector?
freq.n.max display a frequency table if the number of unique values is less than this value,
0 to hide

Details
When describing a data.frame, you can provide variable names as character strings. Using the "*"
or "|" wildcards in a variable name will search for it using a regex match. The search will also take
into account variable labels, if any. See examples.
duplicated2 11

Value
an object of class description.

Author(s)
Joseph Larmarange <[email protected]>

See Also
lookfor

Examples
data(hdv2003)
describe(hdv2003$sexe)
describe(hdv2003$age)
describe(hdv2003)
describe(hdv2003, "cuisine", "heures.tv")
describe(hdv2003, "trav*")
describe(hdv2003, "trav|lecture")
describe(hdv2003, "trav", "lecture")

data(fertility)
describe(women$residency)
describe(women)
describe(women, "id")

duplicated2 Determine all duplicate elements

Description
The native duplicated function determines which elements of a vector or data frame are duplicates
of elements already observed in the vector or the data frame provided. Therefore, only the second
occurence (or third or nth) of an element is considered as a duplicate. duplicated2 is similar but
will also mark the first occurence as a duplicate (see examples).

Usage
duplicated2(x)

Arguments
x a vector, a data frame or a matrix

Value
A logical vector indicated wich elements are duplicated in x.
12 escape_regex

Source
http://forums.cirad.fr/logiciel-R/viewtopic.php?p=2968

See Also
duplicated

Examples
df <- data.frame(x=c("a","b","c","b","d","c"),y=c(1,2,3,2,4,3))
df
duplicated(df)
duplicated2(df)

enfants A fertility survey - "enfants" table

Description
Some fictive results from a fecondity survey.

Format
a data frame containing one record for each child of the surveyed women in the fecondite survey.

escape_regex Escape regex special chars Code directly taken from

Hmisc::escapeRegex

Description
Escape regex special chars Code directly taken from Hmisc::escapeRegex

Usage
escape_regex(s)

Arguments
s string to escape regex special chars from
fecondite 13

fecondite A fertility survey

Description
Some fictive results from a fecondity survey, with French labels.

Format
3 data frames with labelled data (as if data would have been imported from SPSS with haven):

• menages contains some information from the households selected for the survey;
• femmes contains the questionnaire administered to all 15-49 years old women living in the
selected households;
• enfants contains one record for each child of the surveyed women.

Data can be linked using the variables id_menage and id_femme.

See Also
fertility for an English version of this dataset.

Examples
data(fecondite)
describe(menages)
describe(femmes)
describe(enfants)

femmes A fertility survey - "femmes" table

Description
Some fictive results from a fecondity survey.

Format
a data frame containing the questionnaire administered to all 15-49 years old women living in the
selected households for the fecondite survey.
14 first_non_null

fertility A fertility survey

Description
Some fictive results from a fecondity survey, with English labels.

Format
3 data frames with labelled data (as if data would have been imported from SPSS with haven):

• households contains some information from the households selected for the survey;
• women contains the questionnaire administered to all 15-49 years old women living in the
selected households;
• children contains one record for each child of the surveyed women.

Data can be linked using the variables id_household and id_woman.

See Also
fecondite for an French version of this dataset.

Examples
data(fertility)
describe(households)
describe(women)
describe(children)

first_non_null Return first non-null of two values

Description
Return first non-null of two values

Usage
x %||% y

Arguments
x first object
y second object
format.proptab 15

format.proptab S3 format method for proptab objects.

Description

Format an object of class proptab for printing depending on its attributes.

Usage

## S3 method for class 'proptab'

format(x, digits = NULL, percent = NULL, justify = "right", ...)

Arguments

x object of class proptab

digits number of digits to display
percent if not NULL, add a percent sign after each value
justify justification of character vectors. Passed to format.default
... other arguments to pass to format.default

Details

This function is designed for internal use only.

See Also

format.default, print.proptab

freq Generate frequency tables.

Description

Generate and format frequency tables from a variable or a table, with percentages and formatting
options.
16 freq

Usage
freq(
x,
digits = 1,
cum = FALSE,
total = FALSE,
exclude = NULL,
sort = "",
valid = !(NA %in% exclude),
levels = c("prefixed", "labels", "values"),
na.last = TRUE
)

Arguments
x either a vector to be tabulated, or a table object
digits number of digits to keep for the percentages
cum if TRUE, display cumulative percentages
total if TRUE, add a final row with totals
exclude vector of values to exclude from the tabulation (if x is a vector)
sort if specified, allow to sort the table by increasing ("inc") or decreasing ("dec")
frequencies
valid if TRUE, display valid percentages
levels the desired levels for the factor in case of labelled vector (labelled package
must be installed): "labels" for value labels, "values" for values or "prefixed" for
labels prefixed with values
na.last if TRUE, NA values are always be last table row

Value
The result is an object of class data.frame.

See Also
table, prop, cprop, rprop

Examples
# factor
data(hdv2003)
freq(hdv2003$qualif)
freq(hdv2003$qualif, cum = TRUE, total = TRUE)
freq(hdv2003$qualif, cum = TRUE, total = TRUE, sort ="dec")

# labelled data
data(fecondite)
freq(femmes$region)
freq.na 17

freq(femmes$region, levels = "l")

freq(femmes$region, levels = "v")

freq.na Generate frequency table of missing values.

Description

Generate a frequency table of missing values as raw counts and percentages.

Usage

freq.na(data, ...)

Arguments

data either a vector or a data frame object

... if x is a data frame, the names of the variables to examine or keywords to search
for such variables. See lookfor for more details.

Value

The result is an object of class data.frame.

See Also

table, is.na

Examples

data(hdv2003)
## Examine a single vector.
freq.na(hdv2003$qualif)
## Examine a data frame.
freq.na(hdv2003)
## Examine several variables.
freq.na(hdv2003, "nivetud", "trav.satisf")
## To see only variables with the most number of missing values
head(freq.na(hdv2003))
18 ggsurvey

ggsurvey Easy ggplot2 with survey objects

Description

A function to facilitate ggplot2 graphs using a survey object. It will initiate a ggplot and map
survey weights to the corresponding aesthetic.

Usage

ggsurvey(design = NULL, mapping = NULL, ...)

Arguments

design A survey design object, usually created with survey::svydesign()

mapping Default list of aesthetic mappings to use for plot, to be created with ggplot2::aes().
... Other arguments passed on to methods. Not currently used.

Details

Graphs will be correct as long as only weights are required to compute the graph. However, statis-
tic or geometry requiring correct variance computation (like ggplot2::geom_smooth()) will be
statistically incorrect.

Examples
if (require(survey) & require(ggplot2)) {
data(api)
dstrat <- svydesign(
id = ~1, strata = ~stype,
weights = ~pw, data = apistrat,
fpc = ~fpc
)
ggsurvey(dstrat) +
aes(x = cnum, y = dnum) +
geom_count()

d <- as.data.frame(Titanic)
dw <- svydesign(ids = ~1, weights = ~Freq, data = d)
ggsurvey(dw) +
aes(x = Class, fill = Survived) +
geom_bar(position = "fill")
}
happy 19

happy Data related to happiness from the General Social Survey, 1972-2006.

Description

This data extract is taken from Hadley Wickham’s productplots package. The original description
follows, with minor edits.
The data is a small sample of variables related to happiness from the General Social Survey (GSS).
The GSS is a yearly cross-sectional survey of Americans, run from 1972. We combine data for
25 years to yield 51,020 observations, and of the over 5,000 variables, we select nine related to
happiness:

Format

A data frame with 51020 rows and 10 variables

Details

• age. age in years: 18–89.

• degree. highest education: lt high school, high school, junior college, bachelor, graduate.
• finrela. relative financial status: far above, above average, average, below average, far below.
• happy. happiness: very happy, pretty happy, not too happy.
• health. health: excellent, good, fair, poor.
• marital. marital status: married, never married, divorced, widowed, separated.
• sex. sex: female, male.
• wtsall. probability weight. 0.43–6.43.

References

Smith, Tom W., Peter V. Marsden, Michael Hout, Jibum Kim. General Social Surveys, 1972-2006.
[machine-readable data file]. Principal Investigator, Tom W. Smith; Co-Principal Investigators,
Peter V. Marsden and Michael Hout, NORC ed. Chicago: National Opinion Research Center, pro-
ducer, 2005; Storrs, CT: The Roper Center for Public Opinion Research, University of Connecticut,
distributor. 1 data file (57,061 logical records) and 1 codebook (3,422 pp).
20 icut

hdv2003 Histoire de vie 2003

Description
Sample from 2000 people and 20 variables taken from the Histoire de Vie survey, produced in
France in 2003 by INSEE.

Format
A data frame with 2000 rows and 20 variables

Source
https://www.insee.fr/fr/statistiques/2532244

households A fertility survey - "households" table

Description
Some fictive results from a fecondity survey.

Format
a data frame containing some information from the households selected for the fertility survey.

icut Interactive conversion from numeric to factor

Description
This function launches a shiny app in a web browser in order to do interactive conversion of a
numeric variable into a categorical one.

Usage
icut(obj = NULL, var_name = NULL)

Arguments
obj vector to recode or data frame to operate on
var_name if obj is a data frame, name of the column to be recoded, as a character string
(possibly without quotes)
ifunc_get_css 21

Value

The function launches a shiny app in the system web browser. The recoding code is returned in the
console when the app is closed with the "Done" button.

Examples

## Not run:
data(hdv2003)
icut(hdv2003, "age")
irec(hdv2003, heures.tv)

## End(Not run)

ifunc_get_css Returns custom CSS content

Description

Returns custom CSS content

Usage

ifunc_get_css()

ifunc_run_as_addin Check if we are currently running as an rstudio addin

Description

Check if we are currently running as an rstudio addin

Usage

ifunc_run_as_addin()
22 iorder

ifunc_show_alert Display an alert, only on first launch for the current session

Description
Display an alert, only on first launch for the current session

Usage
ifunc_show_alert(run_as_addin)

Arguments
run_as_addin TRUE if the function is running as an rstudio addin

iorder Interactive reordering of factor levels

Description
This function launches a shiny app in a web browser in order to do interactive reordering of the
levels of a categorical variable (character or factor).

Usage
iorder(obj = NULL, var_name = NULL)

Arguments
obj vector to recode or data frame to operate on
var_name if obj is a data frame, name of the column to be recoded, as a character string
(possibly without quotes)

Details
The generated convert the variable into a factor, as only those allow for levels ordering.

Value
The function launches a shiny app in the system web browser. The reordering code is returned in
the console when the app is closed with the "Done" button.
irec 23

Examples
## Not run:
data(hdv2003)
iorder(hdv2003, "qualif")

## End(Not run)

irec Interactive recoding

Description

This function launches a shiny app in a web browser in order to do interactive recoding of a cate-
gorical variable (character or factor).

Usage

irec(obj = NULL, var_name = NULL)

Arguments

obj vector to recode or data frame to operate on

var_name if obj is a data frame, name of the column to be recoded, as a character string
(possibly without quotes)

Value

The function launches a shiny app in the system web browser. The recoding code is returned in the
console when the app is closed with the "Done" button.

Examples
## Not run:
data(hdv2003)
irec()
v <- sample(c("Red","Green","Blue"), 50, replace=TRUE)
irec(v)
irec(hdv2003, "qualif")
irec(hdv2003, sexe) ## this also works

## End(Not run)
24 ltabs

ltabs Cross tabulation with labelled variables

Description

This function is a wrapper around xtabs, adding automatically value labels for labelled vectors if
labelled package eis installed.

Usage

ltabs(
formula,
data,
levels = c("prefixed", "labels", "values"),
variable_label = TRUE,
...
)

Arguments

formula a formula object (see xtabs)

data a data frame
levels the desired levels in case of labelled vector: "labels" for value labels, "values"
for values or "prefixed" for labels prefixed with values
variable_label display variable label if available?
... additional arguments passed to xtabs

See Also

xtabs.

Examples
data(fecondite)
ltabs(~radio, femmes)
ltabs(~radio+tv, femmes)
ltabs(~radio+tv, femmes, "l")
ltabs(~radio+tv, femmes, "v")
ltabs(~radio+tv+journal, femmes)
ltabs(~radio+tv, femmes, variable_label = FALSE)
menages 25

menages A fertility survey - "menages" table

Description
Some fictive results from a fecondity survey.

Format
a data frame containing some information from the households selected for the fecondite survey.

multi.split Split a multiple choices variable in a series of binary variables

Description
Split a multiple choices variable in a series of binary variables

Usage
multi.split(var, split.char = "/", mnames = NULL)

Arguments
var variable to split
split.char character to split at
mnames names to give to the produced variabels. If NULL, the name are computed from
the original variable name and the answers.

Details
This function takes as input a multiple choices variable where choices are recorded as a string and
separated with a fixed character. For example, if the question is about the favourite colors, answers
could be "red/blue", "red/green/yellow", etc. This function splits the variable into as many variables
as the number of different choices. Each of these variables as a 1 or 0 value corresponding to the
choice of this answer. They are returned as a data frame.

Value
Returns a data frame.

See Also
multi.table
26 multi.table

Examples
v <- c("red/blue","green","red/green","blue/red")
multi.split(v)
## One-way frequency table of the result
multi.table(multi.split(v))

multi.table One-way frequency table for multiple choices question

Description
This function allows to generate a frequency table from a multiple choices question. The question’s
answers must be stored in a series of binary variables.

Usage
multi.table(df, true.codes = NULL, weights = NULL, digits = 1, freq = TRUE)

Arguments
df data frame with the binary variables
true.codes optional list of values considered as ’true’ for the tabulation
weights optional weighting vector
digits number of digits to keep in the output
freq add a percentage column

Details
The function is applied to a series of binary variables, each one corresponding to a choice of the
question. For example, if the question is about seen movies among a movies list, each binary
variable would correspond to a movie of the list and be true or false depending of the choice of the
answer.
By default, only ’1’ and ’TRUE’ as considered as ’true’ values fro the binary variables, and counted
in the frequency table. It is possible to specify other values to be counted with the true.codes
argument. Note than ’1’ and ’TRUE’ are always considered as true values even if true.codes is
provided.
If freq is set to TRUE, a percentage column is added to the resulting table. This percentage is com-
puted by dividing the number of TRUE answers for each value by the total number of (potentially
weighted) observations. Thus, these percentages sum can be greater than 100.

Value
Object of class table.
na.rm 27

See Also
cross.multi.table, multi.split, table

Examples
## Sample data frame
set.seed(1337)
sex <- sample(c("Man","Woman"),100,replace=TRUE)
jazz <- sample(c(0,1),100,replace=TRUE)
rock <- sample(c(TRUE, FALSE),100,replace=TRUE)
electronic <- sample(c("Y","N"),100,replace=TRUE)
weights <- runif(100)*2
df <- data.frame(sex,jazz,rock,electronic,weights)
## Frequency table on 'music' variables
multi.table(df[,c("jazz", "rock","electronic")], true.codes=list("Y"))
## Weighted frequency table on 'music' variables
multi.table(df[,c("jazz", "rock","electronic")], true.codes=list("Y"), weights=df$weights)
## No percentages
multi.table(df[,c("jazz", "rock","electronic")], true.codes=list("Y"), freq=FALSE)

na.rm Remove observations with missing values

Description
na.rm is similar to na.omit but allows to specify a list of variables to take into account.

Usage
na.rm(x, v = NULL)

Arguments
x a data frame
v a list of variables

Details
If v is not specified, the result of na.rm will be the same as na.omit. If a list of variables is specified
through v, only observations with a missing value (NA) for one of the specified variables will be
removed from x. See examples.

Author(s)
Joseph Larmarange <[email protected]>

See Also
na.omit
28 odds.ratio

Examples
df <- data.frame(x = c(1, 2, 3), y = c(0, 10, NA), z= c("a",NA,"b"))
df
na.omit(df)
na.rm(df)
na.rm(df, c("x","y"))
na.rm(df, "z")

odds.ratio Odds Ratio

Description
S3 method for odds ratio

Usage
odds.ratio(x, ...)

## S3 method for class 'glm'

odds.ratio(x, level = 0.95, ...)

## S3 method for class 'multinom'

odds.ratio(x, level = 0.95, ...)

## S3 method for class 'factor'

odds.ratio(x, fac, level = 0.95, ...)

## S3 method for class 'table'

odds.ratio(x, level = 0.95, ...)

## S3 method for class 'matrix'

odds.ratio(x, level = 0.95, ...)

## S3 method for class 'numeric'

odds.ratio(x, y, level = 0.95, ...)

## S3 method for class 'odds.ratio'

print(x, signif.stars = TRUE, ...)

Arguments
x object from whom odds ratio will be computed
... further arguments passed to or from other methods
level the confidence level required
fac a second factor object
y a second numeric object
signif.stars logical; if TRUE, p-values are encoded visually as ’significance stars’
print.proptab 29

Details
For models calculated with glm, x should have been calculated with family=binomial. p-value are
the same as summary(x)$coefficients[,4]. Odds ratio could also be obtained with exp(coef(x))
and confidence intervals with exp(confint(x)).
For models calculated with multinom (nnet), p-value are calculated according to https://stats.
idre.ucla.edu/r/dae/multinomial-logistic-regression/.
For 2x2 table, factor or matrix, odds.ratio uses fisher.test to compute the odds ratio.

Value
Returns a data.frame of class odds.ratio with odds ratios, their confidence interval and p-values.
If x and y are proportions, odds.ratio simply returns the value of the odds ratio, with no confidence
interval.

Author(s)
Joseph Larmarange <[email protected]>

See Also
glm in the stats package.
multinom in the nnet package.
fisher.test in the stats package.
printCoefmat in the stats package.

Examples
data(hdv2003)
reg <- glm(cinema ~ sexe + age, data=hdv2003, family=binomial)
odds.ratio(reg)
odds.ratio(hdv2003$sport, hdv2003$cuisine)
odds.ratio(table(hdv2003$sport, hdv2003$cuisine))
M <- matrix(c(759, 360, 518, 363), ncol = 2)
odds.ratio(M)
odds.ratio(0.26, 0.42)

print.proptab S3 print method for proptab objects.

Description
Print an object of class proptab.

Usage
## S3 method for class 'proptab'
print(x, digits = NULL, percent = NULL, justify = "right", ...)
30 prop

Arguments
x object of class proptab
digits number of digits to display
percent if not NULL, add a percent sign after each value
justify justification of character vectors. Passed to format.default
... other arguments to pass to format.default

See Also
format.proptab

prop Global percentages of a two-way frequency table.

Description
Return the percentages of a two-way frequency table with formatting and printing options.

Usage
prop(tab, ...)

prop_table(
tab,
digits = 1,
total = TRUE,
percent = FALSE,
drop = TRUE,
n = FALSE,
...
)

## S3 method for class 'data.frame'

prop(
tab,
digits = 1,
total = TRUE,
percent = FALSE,
drop = TRUE,
n = FALSE,
...
)

## S3 method for class 'matrix'

prop(
prop 31

tab,
digits = 1,
total = TRUE,
percent = FALSE,
drop = TRUE,
n = FALSE,
...
)

## S3 method for class 'tabyl'

prop(tab, digits = 1, total = TRUE, percent = FALSE, n = FALSE, ...)

Arguments

tab frequency table

... parameters passed to other methods
digits number of digits to display
total if TRUE, add a column with the sum of percentages and a row with global per-
centages
percent if TRUE, add a percent sign after the values when printing
drop if TRUE, lines or columns with a sum of zero, which would generate NaN percent-
ages, are dropped.
n if TRUE, display number of observations per row and per column.

Value

The result is an object of class table and proptab.

See Also

rprop, cprop, table, prop.table

Examples

## Sample table
data(Titanic)
tab <- apply(Titanic, c(1,4), sum)
## Percentages
prop(tab)
## Percentages with custom display
prop(tab, digits=2, percent=TRUE, total=FALSE, n=TRUE)
32 qload

qload Load one or more packages, installing them first if necessary

Description

This function quickly loads one or more packages, installing them quietly if necessary.

Usage

qload(..., load = TRUE, silent = TRUE)

Arguments

... the packages to load/install. Packages are loaded with library and installed
first with install.packages if necessary.
load load the packages. Set to FALSE to just install any missing packages. Defaults
to TRUE.
silent keep output as silent as possible. Defaults to TRUE.

Details

The function probably requires R 3.0.0 or above to make use of the quiet argument when calling
install.packages. It is not clear what the argument previously achieved in older versions of R.

Value

The result is a list of packages cited in the scripts.

Author(s)

François Briatte <[email protected]>

See Also

qscan, install.packages, library

Examples
qload("questionr")
qload("questionr", silent = FALSE)
qscan 33

qscan Scan R scripts and load/install all detected packages

Description

This function scans one or more R scripts and tries to quick-load/install the packages mentioned by
library or require functions.

Usage

qscan(..., load = TRUE, detail = TRUE)

Arguments

... the scripts to scan. Defaults to all R scripts in the current working directory.
load quick-load/install the cited packages (see details). Defaults to TRUE.
detail show the list of packages found in each script. Defaults to TRUE.

Details

The function calls the qload function to quick-load/install the packages.

Value

The result is a list of packages cited in the scripts.

Author(s)

François Briatte <[email protected]>

See Also

qload, library

Examples

## Scan the working directory.

## Not run: qscan()
34 quant.cut

quant.cut Transform a quantitative variable into a qualitative variable

Description

This function transforms a quantitative variable into a qualitative one by breaking it into classes
with the same frequencies.

Usage

quant.cut(var, nbclass, include.lowest = TRUE, right = FALSE, dig.lab = 5, ...)

Arguments

var variable to transform

nbclass number of classes
include.lowest argument passed to the cut function
right argument passed to the cut function
dig.lab argument passed to the cut function
... arguments passed to the cut function

Details

This is just a simple wrapper around the cut and quantile functions.

Value

The result is a factor.

See Also

cut, quantile

Examples
data(iris)
sepal.width3cl <- quant.cut(iris$Sepal.Width,3)
table(sepal.width3cl)
recode.na 35

recode.na Recode values of a variable to missing values, using exact or regular

expression matching.

Description
This function recodes selected values of a quantitative or qualitative variable by matching its levels
to exact or regular expression matches.

Usage
recode.na(x, ..., verbose = FALSE, regex = TRUE, as.numeric = FALSE)

Arguments
x variable to recode. The variable is coerced to a factor if necessary.
... levels to recode as missing in the variable. The values are coerced to character
strings, meaning that you can pass numeric values to the function.
verbose print a table of missing levels before recoding them as missing. Defaults to
FALSE.
regex use regular expressions to match values that include the "*" or "|" wildcards.
Defaults to TRUE.
as.numeric coerce the recoded variable to numeric. The function recommends the option
when the recode returns only numeric values. Defaults to FALSE.

Value
The result is a factor with properly encoded missing values. If the recoded variable contains only
numeric values, it is converted to an object of class numeric.

Author(s)
François Briatte <[email protected]>

See Also
regex

Examples
data(hdv2003)
## With exact string matches.
hdv2003$nivetud = recode.na(hdv2003$nivetud, "Inconnu")
## With regular expressions.
hdv2003$relig = recode.na(hdv2003$relig, "[A|a]ppartenance", "Rejet|NSP")
## Showing missing values.
hdv2003$clso = recode.na(hdv2003$clso, "Ne sait pas", verbose = TRUE)
36 rm.unused.levels

## Test results with freq.

freq(recode.na(hdv2003$trav.satisf, "Equilibre"))
## Truncate a count variable (recommends numeric conversion).
freq(recode.na(hdv2003$freres.soeurs, 5:22))

rename.variable Rename a data frame column

Description
Rename a data frame column

Usage
rename.variable(df, old, new)

Arguments
df data frame
old old name
new new name

Value
A data frame with the column named "old" renamed as "new"

Examples
data(iris)
str(iris)
iris <- rename.variable(iris, "Species", "especes")
str(iris)

rm.unused.levels Remove unused levels

Description
This function removes unused levels of a factor or in a data.frame. See examples.

Usage
rm.unused.levels(x, v = NULL)
rp2012 37

Arguments

x a factor or a data frame

v a list of variables (optional, if x is a data frame)

Details

If x is a data frame, only factor variables of x will be impacted. If a list of variables is provided
through v, only the unused levels of the specified variables will be removed.

Author(s)

Joseph Larmarange <[email protected]>

Examples

df <- data.frame(v1=c("a","b","a","b"),v2=c("x","x","y","y"))
df$v1 <- factor(df$v1,c("a","b","c"))
df$v2 <- factor(df$v2,c("x","y","z"))
df
str(df)
str(rm.unused.levels(df))
str(rm.unused.levels(df,"v1"))

rp2012 2012 French Census - French cities of more than 2000 inhabitants

Description

Sample from the 2012 national french census. It contains results for every french city of more than
2000 inhabitants, and a small subset of variables, both in population counts and proportions.

Format

A data frame with 5170 rows and 60 variables

Source

https://www.insee.fr/fr/information/2008354
38 rprop

rp99 1999 French Census - Cities from the Rhône state

Description
Sample from the 1999 french census for the cities of the Rhône state.

Format
A data frame with 301 rows and 21 variables

Source
https://www.insee.fr/fr/information/2008354

rprop Row percentages of a two-way frequency table.

Description
Return the row percentages of a two-way frequency table with formatting and printing options.

Usage
rprop(tab, ...)

## S3 method for class 'table'

rprop(
tab,
digits = 1,
total = TRUE,
percent = FALSE,
drop = TRUE,
n = FALSE,
...
)

## S3 method for class 'data.frame'

rprop(
tab,
digits = 1,
total = TRUE,
percent = FALSE,
drop = TRUE,
n = FALSE,
rprop 39

...
)

## S3 method for class 'matrix'

rprop(
tab,
digits = 1,
total = TRUE,
percent = FALSE,
drop = TRUE,
n = FALSE,
...
)

## S3 method for class 'tabyl'

rprop(tab, digits = 1, total = TRUE, percent = FALSE, n = FALSE, ...)

Arguments
tab frequency table
... parameters passed to other methods.
digits number of digits to display
total if TRUE, add a column with the sum of percentages and a row with global per-
centages
percent if TRUE, add a percent sign after the values when printing
drop if TRUE, lines or columns with a sum of zero, which would generate NaN percent-
ages, are dropped.
n if TRUE, display number of observations per row.

Value
The result is an object of class table and proptab.

See Also
cprop, prop, table, prop.table

Examples
## Sample table
data(Titanic)
tab <- apply(Titanic, c(1,4), sum)
## Column percentages
rprop(tab)
## Column percentages with custom display
rprop(tab, digits=2, percent=TRUE, total=FALSE)
40 tabs

tabs Weighted Crossresult

Description
Generate table with multiple weighted crossresult (full sample is first column). kable(), which is
found in library(knitr), is recommended for use with RMarkdown.

Usage
tabs(
df,
x,
y,
type = "percent",
percent = FALSE,
weight = NULL,
normwt = FALSE,
na.rm = TRUE,
na.show = FALSE,
exclude = NULL,
digits = 1
)

Arguments
df A data.frame that contains x and (optionally) y and weight.
x variable name (found in df). tabs(my.data, x = ’q1’).
y one (or more) variable names. tabs(my.data, x = ’q1’, y = c(’sex’, ’job’)).
type ’percent’ (default ranges 0-100), ’proportion’, or ’counts’ (type of table re-
turned).
percent if TRUE, add a percent sign after the values when printing
weight variable name for weight (found in df).
normwt if TRUE, normalize weights so that the total weighted count is the same as the
unweighted one
na.rm if TRUE, remove NA values before computation
na.show if TRUE, show NA count in table output
exclude values to remove from x and y. To exclude NA, use na.rm argument.
digits Number of digits to display; ?format.proptab for formatting details.

Details
tabs calls wtd.table on ‘x‘ and, as applicable, each variable named by ‘y‘.
women 41

Author(s)
Pete Mohanty

Examples
data(hdv2003)
tabs(hdv2003, x = "relig", y = c("qualif", "trav.imp"), weight = "poids")
result <- tabs(hdv2003, x = "relig", y = c("qualif", "trav.imp"), type = "counts")
format(result, digits = 3)
# library(knitr)
# xt <- tabs(hdv2003, x = "relig", y = c("qualif", "trav.imp"), weight = "poids")
# kable(format(xt)) # to use with RMarkdown...

women A fertility survey - "women" table

Description
Some fictive results from a fecondity survey.

Format
a data frame containing the questionnaire administered to all 15-49 years old women living in the
selected households for the fertility survey.

wtd.mean Weighted mean and variance of a vector

Description
Compute the weighted mean or weighted variance of a vector. Exact copies of Hmisc functions.

Usage
wtd.mean(x, weights = NULL, na.rm = TRUE)

Arguments
x Numeric data vector
weights Numeric weights vector. Must be the same length as x
na.rm if TRUE, delete NA values.

Details
If weights is NULL, then an uniform weighting is applied.
42 wtd.table

Author(s)
These functions are exact copies of the wtd.mean and wtd.var function from the wtd.stats package.
They have been created by Frank Harrell, Department of Biostatistics, Vanderbilt University School
of Medicine, <[email protected]>.

See Also
mean,var, wtd.table and the survey package.

Examples
data(hdv2003)
mean(hdv2003$age)
wtd.mean(hdv2003$age, weights=hdv2003$poids)

wtd.table Weighted one-way and two-way frequency tables.

Description
Generate weighted frequency tables, both for one-way and two-way tables.

Usage
wtd.table(
x,
y = NULL,
weights = NULL,
digits = 3,
normwt = FALSE,
useNA = c("no", "ifany", "always"),
na.rm = TRUE,
na.show = FALSE,
exclude = NULL
)

Arguments
x a vector
y another optional vector for a two-way frequency table. Must be the same length
as x
weights vector of weights, must be the same length as x
digits Number of significant digits.
normwt if TRUE, normalize weights so that the total weighted count is the same as the
unweighted one
useNA wether to include NA values in the table
wtd.table 43

na.rm (deprecated) if TRUE, remove NA values before computation

na.show (deprecated) if TRUE, show NA count in table output
exclude values to remove from x and y. To exclude NA, use na.rm argument.

Details
If weights is not provided, an uniform weghting is used.

Value
If y is not provided, returns a weighted one-way frequency table of x. Otherwise, returns a weighted
two-way frequency table of x and y

See Also
wtd.table, table, and the survey package.

Examples
data(hdv2003)
wtd.table(hdv2003$sexe, weights=hdv2003$poids)
wtd.table(hdv2003$sexe, weights=hdv2003$poids, normwt=TRUE)
table(hdv2003$sexe, hdv2003$hard.rock)
wtd.table(hdv2003$sexe, hdv2003$hard.rock, weights=hdv2003$poids)
Index

∗ connection femmes, 13
clipcopy, 5 fertility, 4, 13, 14, 20, 41
∗ datasets first_non_null, 14
children, 4 fisher.test, 29
enfants, 12 format.default, 15
fecondite, 13 format.proptab, 6, 15, 30
femmes, 13 freq, 15
fertility, 14 freq.na, 17
happy, 19
hdv2003, 20 ggplot2::aes(), 18
households, 20 ggplot2::geom_smooth(), 18
menages, 25 ggsurvey, 18
rp2012, 37 glm, 29
rp99, 38
women, 41 happy, 19
∗ manip hdv2003, 20
rename.variable, 36 households, 20
∗ univar
icut, 20
cramer.v, 8
ifunc_get_css, 21
addNA, 3 ifunc_run_as_addin, 21
addNAstr, 3 ifunc_show_alert, 22
install.packages, 32
children, 4 iorder, 22
chisq.residuals, 4 irec, 23
chisq.test, 4 is.na, 17
clipcopy, 5, 6
copie (clipcopy), 5 kable, 6
cprop, 6, 16, 31, 39
cramer.v, 8 library, 32, 33
cross.multi.table, 8, 27 lookfor, 11, 17
cut, 34 lprop (rprop), 38
ltabs, 24
describe, 10
duplicated, 11, 12 mean, 42
duplicated2, 11 menages, 25
multi.split, 9, 25, 27
enfants, 12 multi.table, 9, 25, 26
escape_regex, 12 multinom, 29

fecondite, 12, 13, 13, 14, 25 na.omit, 27

44
INDEX 45

na.rm, 27
nnet, 29

odds.ratio, 28

print.description (describe), 10
print.odds.ratio (odds.ratio), 28
print.proptab, 15, 29
printCoefmat, 29
prop, 7, 16, 30, 39
prop.table, 7, 31, 39
prop_table (prop), 30

qload, 32, 33
qscan, 32, 33
quant.cut, 34
quantile, 34

recode.na, 35
regex, 35
rename.variable, 36
renomme.variable (rename.variable), 36
residus (chisq.residuals), 4
rm.unused.levels, 36
rp2012, 37
rp99, 38
rprop, 7, 16, 31, 38

stats, 29
survey::svydesign(), 18

table, 7, 9, 16, 17, 27, 31, 39, 43

tabs, 40

var, 42

women, 41
wtd.mean, 41
wtd.stats, 42
wtd.table, 42, 42, 43
wtd.var (wtd.mean), 41

xtabs, 24