Publish PDF

Package ‘Publish’
December 1, 2020
Type Package
Title Format Output of Various Routines in a Suitable Way for Reports
and Publication
Description
A bunch of convenience functions that transform the results of some basic statistical analyses
into table format nearly ready for publication. This includes descriptive tables, tables of
logistic regression and Cox regression results as well as forest plots.
Version 2020.11.30
Maintainer Thomas A. Gerds <tag@biostat.ku.dk>
Depends prodlim (>= 1.5.4)
Imports survival (>= 2.38), data.table (>= 1.10.4), lava (>= 1.5.1),
multcomp (>= 1.4)
Suggests riskRegression (>= 2020.09.07), testthat, smcfcs (>= 1.4.1),
rms (>= 6.1.0), mitools (>= 2.4), nlme (>= 3.1-131)
License GPL (>= 2)
RoxygenNote 7.1.1
NeedsCompilation no
Author Thomas A. Gerds [aut, cre],
Christian Torp-Pedersen [ctb],
Klaus K Holst [ctb],
Brice Ozenne [aut]
Repository CRAN
Date/Publication 2020-12-01 17:40:06 UTC
R topics documented:
Publish-package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
acut . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
ci.mean . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
ci.mean.default . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
CiTable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
1
2 R topics documented:
coxphSeries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Diabetes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
fixRegressionTable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
followupTable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
formatCI . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
glmSeries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
labelUnits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
lazyDateCoding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
lazyFactorCoding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
org . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
parseInteractionTerms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
plot.ci . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
plot.regressionTable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
plot.subgroupAnalysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
plotConfidence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
print.ci . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
print.subgroupAnalysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
print.table2x2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
print.univariateTable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
pubformat . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
publish . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
publish.CauseSpecificCox . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
publish.ci . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
publish.coxph . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
publish.glm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
publish.htest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
publish.matrix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
publish.MIresult . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
publish.riskRegression . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
publish.Score . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
publish.summary.aov . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
publish.survdiff . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
regressionTable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
SpaceT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
spaghettiogram . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
specialFrame . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
splinePlot.lrm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
stripes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
subgroupAnalysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
summary.ci . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
summary.regressionTable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
summary.subgroupAnalysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
summary.univariateTable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
sutable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
table2x2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
trace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
traceR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Units . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
Publish-package 3
univariateTable . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
Index 79
Publish-package Publish package
Description
This package processes results of descriptive statistcs and regression analysis into final tables and
figures of a manuscript
acut Automatic selection and formatting of breaks in cut
Description
A version of cut that easily formats the labels and places breaks by default.
Usage
acut(
x,
n = 5,
type = "default",
format = NULL,
format.low = NULL,
format.high = NULL,
dig.lab = 3,
right = TRUE,
breaks,
labels = TRUE,
...
)
Arguments
x a numeric vector which is to be converted to a factor by cutting (passed directly
to cut).
n number of bins to create based on the empirical quantiles of x. This will be
overruled if breaks is supplied.
type a high-level formatting option. For now, the only other option than the default
setting is "age". See details and examples.
format string used to make labels. %l and %u identifies the lower and upper value of
the breaks respectively. See examples.
4 acut
format.low string used specifically on the lowest label.

format.high string used specifically on the highest label.
dig.lab integer which is used when labels are not given. It determines the number of
digits used in formatting the break numbers. (Passed directly to cut.)
right logical, indicating if the intervals should be closed on the right (and open on the
left) or vice versa (passed directly to cut).
breaks specify breaks manually as in cut.
labels logical, indicating whether or not to make labels or simply use ordered numbers.
If TRUE, the labels are constructed as discribed above.
... further arguments passed to cut.
Details
The formats are supplied by specifiyng the text around the lower (%l) and upper (%l) value (see
examples). If user specified breaks are supplied, the default labels from cut are used. If automatic
breaks are used, the default labels are a slight modification at the end point of the default from cut
All this can of course be adjusted manually through the format functionality (see below).
By default, 5 breaks are constructed according to the quantiles with of the input x. The number of
breaks can be adjusted, and default specifying breaks (as in cut) can be supplied instead.
If type is changed from "default" to another option, a different formatting template is used. For
now the only other option is "age", which is designed to be well suited to easily group age variables.
When type="age" only the breaks argument is used, and it behaves different from otherwise. If
a single number is supplied, intervals of length breaks will automatically be constructed (starting
from 0). If a vector is supplied, the intervals are used as in cut but formatted differently, see
examples.
Value
same as for cut. A vector of ’factors’ is created, unless ’labels=FALSE’.
Author(s)
Anders Munch
Examples
data(Diabetes) # load dataset
## The default uses format similar to cut

chol.groups <- acut(Diabetes$chol)
table(chol.groups)
## The formatting can easily be changed

chol.groups <- acut(Diabetes$chol,format="%l-%u",n=5)
table(chol.groups)
## The default is to automatic place the breaks, so the number of this can easily be changed.
chol.groups <- acut(Diabetes$chol,n=7)
acut 5
table(chol.groups)
## Manually setting format and breaks

age.groups <- acut(Diabetes$age,format="%l-%u",breaks=seq(0,100,by=10))
table(age.groups)
## Other variations
age.groups <- acut(Diabetes$age,
format="%l-%u",
format.low="below %u",
format.high="above %l",
breaks=c(0, seq(20,80,by=10), Inf))
table(age.groups)
BMI.groups <- acut(Diabetes$BMI,

format="BMI between %l and %u",
format.low="BMI below %u",
format.high="BMI above %l")
table(BMI.groups)
org(as.data.frame(table(BMI=BMI.groups)))
## Instead of using the quantiles, we can specify equally spaced breaks,

## but still get the same formatting
BMI.grouping <-
seq(min(Diabetes$BMI,na.rm=TRUE), max(Diabetes$BMI,na.rm=TRUE), length.out=6)
BMI.grouping[1] <- -Inf # To get all included
BMI.groups <- acut(Diabetes$BMI,
breaks=BMI.grouping,
format="BMI between %l and %u",
format.low="BMI below %u",
format.high="BMI above %l")
table(BMI.groups)
org(as.data.frame(table(BMI=BMI.groups)))
## Using type="age"
## When using type="age", categories of 10 years are constructed by default.
## The are formatted to be easier to read when the values are ages.
table(acut(Diabetes$age, type="age"))
## This can be changes with the breaks argument.

## Note that this is diffent from cut when breaks is a single number.
table(acut(Diabetes$age, type="age", breaks=20))
## Of course We can also supply the breaks manually.

## The formatting depends on whether or not all the values fall within the breaks:
## All values within the breaks
table(acut(Diabetes$age, type="age", breaks=c(0, 30, 50, 80, 100)))
## Some values below and above the breaks
table(acut(Diabetes$age, type="age", breaks=c(30, 50, 80)))
6 ci.mean.default
ci.mean Compute mean values with confidence intervals
Description
Compute mean values with confidence intervals
Usage
ci.mean(x, ...)
Arguments
x object passed to methods
... passed to methods
Details
Normal approximation
Value
a list with mean values and confidence limits
ci.mean.default Compute mean values with confidence intervals
Description
Compute mean values with confidence intervals
Usage
## Default S3 method:
ci.mean(
x,
alpha = 0.05,
normal = TRUE,
na.rm = TRUE,
statistic = "arithmetic",
...
)
CiTable 7
Arguments
x numeric vector
alpha level of significance
normal If TRUE use quantile of t-distribution else use normal approximation and quantile
of normal approximation. Do you think this is confusing?
na.rm If TRUE remove missing values from x.
statistic Decide which mean to compute: either "arithmetic" or "geometric"
... not used
Details
Normal approximation
Value
a list with mean values and confidence limits
Author(s)
Thomas Gerds
CiTable CiTable data
Description
These data are used for testing Publish package functionality.
Format
A data frame with 27 observations on the following 9 variables.
Drug
Time
Drug.Time
Dose
Mean
SD
n
HazardRatio
lower
upper
p
8 coxphSeries
Examples
data(CiTable)
labellist <- split(CiTable[,c("Dose","Mean","SD","n")],CiTable[,"Drug"])
labellist
plotConfidence(x=CiTable[,c("HazardRatio","lower","upper")], labels=labellist)
coxphSeries Run a series of Cox regression models
Description
Run a series of Cox regression analyses for a list of predictor variables and summarize the results
in a table. The Cox models can be adjusted for a fixed set of covariates
This function runs on coxph from the survival package.
Usage
coxphSeries(formula, data, vars, ...)
Arguments
formula The fixed part of the regression formula. For univariate analyses this is sim-
ply Surv(time,status)~1 where Surv(time,status) is the outcome vari-
able. When the aim is to control the effect of vars in each element of the
series by a fixed set of variables it is Surv(time,status)~x1+x2 where again
Surv(time,status) is the outcome and x1 and x2 are confounders.
data A data.frame in which the formula gets evaluated.
vars A list of variable names, the changing part of the regression formula.
... passed to publish.coxph
Value
matrix with results
Author(s)
Thomas Alexander Gerds

Diabetes 9
Examples
library(survival)
data(pbc)
## collect hazard ratios from three univariate Cox regression analyses
pbc$edema <- factor(pbc$edema,levels=c("0","0.5","1"),labels=c("0","0.5","1"))
uni.hr <- coxphSeries(Surv(time,status==2)~1,vars=c("edema","bili","protime"),data=pbc)
uni.hr
## control the logistic regression analyses for age and gender

## but collect only information on the variables in `vars'.
controlled.hr <- coxphSeries(Surv(time,status==2)~age+sex,vars=c("edema","bili","protime"),data=pbc)
controlled.hr
Diabetes Diabetes data of Dr John Schorling
Description
These data are courtesy of Dr John Schorling, Department of Medicine, University of Virginia
School of Medicine. The data consist of 19 variables on 403 subjects from 1046 subjects who were
interviewed in a study to understand the prevalence of obesity, diabetes, and other cardiovascular
risk factors in central Virginia for African Americans. According to Dr John Hong, Diabetes Melli-
tus Type II (adult onset diabetes) is associated most strongly with obesity. The waist/hip ratio may
be a predictor in diabetes and heart disease. DM II is also agssociated with hypertension - they
may both be part of "Syndrome X". The 403 subjects were the ones who were actually screened for
diabetes. Glycosolated hemoglobin > 7.0 is usually taken as a positive diagnosis of diabetes.
Format
id subject id
chol Total Cholesterol
stab.glu Stabilized Glucose
hdl High Density Lipoprotein
ratio Cholesterol/HDL Ratio
glyhb Glycosolated Hemoglobin
location a factor with levels (Buckingham,Louisa)
age age (years)
gender male or female
height height (inches)
height.europe height (cm)
weight weight (pounds)
10 fixRegressionTable
weight.europe weight (kg)

frame a factor with levels (small,medium,large)
bp.1s First Systolic Blood Pressure
bp.1d First Diastolic Blood Pressure
bp.2s Second Diastolic Blood Pressure
bp.2d Second Diastolic Blood Pressure
waist waist in inches
hip hip in inches
time.ppn Postprandial Time when Labs were Drawn in minutes
AgeGroups Categorized age
BMI Categorized BMI
Source
http://192.38.117.59/~tag/Teaching/share/data/Diabetes.html
References
Willems JP, Saunders JT, DE Hunt, JB Schorling: Prevalence of coronary heart disease risk fac-
tors among rural blacks: A community-based study. Southern Medical Journal 90:814-820; 1997
Schorling JB, Roach J, Siegel M, Baturka N, Hunt DE, Guterbock TM, Stewart HL: A trial of
church-based smoking cessation interventions for rural African Americans. Preventive Medicine
26:92-101; 1997.
Examples
data(Diabetes)
fixRegressionTable Expand regression coefficient table
Description
Expand regression coefficient table
Usage
fixRegressionTable(
x,
varnames,
reference.value,
reference.style = NULL,
factorlevels,
followupTable 11
scale = NULL,
nmiss,
intercept
)
Arguments
x object resulting from lm, glm or coxph.
varnames Names of variables
reference.value
Reference value for reference categories
reference.style
Style for showing results for categorical variables. If "extraline" show an
additional line for the reference category.
factorlevels Levels of the categorical variables.
scale Scale for some or all of the variables
nmiss Number of missing values
intercept Intercept
Details
This function expands results from "regressionTable" with extralines and columns
For factor variables the reference group is shown. For continuous variables the units are shown and
for transformed continuous variables also the scale. For all variables the numbers of missing values
are added.
Value
a table with regression coefficients
Author(s)
Thomas Alexander Gerds <tag@biostat.ku.dk>
followupTable Summary tables for a given followup time point.
Description
Summarize baseline variables in groups defined by outcome at a given followup time point
Usage
followupTable(formula, data, followup.time, compare.groups, ...)
12 formatCI
Arguments
formula Formula A formula whose left hand side is a Hist object. In some special cases
it can also be a Surv response object. The right hand side is as in utable.
data A data.frame in which all the variables of formula can be interpreted.
followup.time Time point at which to evaluate outcome status.
compare.groups Method for comparing groups.
... Passed to utable. All arguments of utable can be controlled in this way except
for compare.groups which is set to "Cox". See details.
Details
If compare.groups!=FALSE, p-values are obtained from stopped Cox regression, i.e., all events
are censored at follow-up time. A univariate Cox regression model is fitted to assess the effect of
each variable on the right hand side of the formula on the event hazard and shown is the p-value of
anova(fit), see anova.coxph.
Value
Summary table.
Author(s)
Thomas A. Gerds <tag@biostat.ku.dk>
See Also
univariateTable
Examples
library(survival)
data(pbc)
pbc$sex <- factor(pbc$sex,levels=c("m","f"),labels=c("m","f"))
followupTable(Hist(time,status)~age+edema+sex,data=pbc,followup.time=1000)
formatCI Formatting confidence intervals
Description
Format confidence intervals
formatCI 13
Usage
formatCI(
x,
lower,
upper,
show.x = FALSE,
handler = "sprintf",
format = "[l;u]",
degenerated = "asis",
digits = 2,
nsmall = digits,
sep = "",
reference.pos,
reference.label = "",
...
)
Arguments
x not used (for compatibility with format)
lower Numeric vector of lower limits
upper Numeric vector of upper limits
show.x Logical. If TRUE show value of x in front of confidence interval.
handler Function to format numeric values. Default is sprintf, also supported are
format and prettyNum
format Character string in which l will be replaced by the value of the lower limit
(argument lower) and u by the value of the upper upper limit. For example,
(l,u) yields confidence intervals in round parenthesis in which the upper and
lower limits are comma separated. Default is [l;u].
degenerated String to show when lower==upper. Default is ’–’
digits If handler format or prettyNum used format numeric vectors.
nsmall If handler format or prettyNum used format numeric vectors.
sep Field separator
reference.pos Position of factor reference
reference.label
Label for factor reference
... passed to handler
Details
The default format for confidence intervals is [lower; upper].
Value
String vector with confidence intervals
14 glmSeries
Author(s)
See Also
plot.ci ci.mean
Examples
x=ci.mean(rnorm(10))
formatCI(lower=x[3],upper=x[4])
formatCI(lower=c(0.001,-2.8413),upper=c(1,3.0008884))
# change format
formatCI(lower=c(0.001,-2.8413),upper=c(1,3.0008884),format="(l, u)")
# show x
formatCI(x=x$mean,lower=x$lower,upper=x$upper,format="(l, u)",show.x=TRUE)
# change of handler function

l <- c(-0.0890139,0.0084736,144.898333,0.000000001)
u <- c(0.03911392,0.3784706,3338944.8821221,0.00001)
cbind(format=formatCI(lower=l,upper=u,format="[l;u)",digits=2,nsmall=2,handler="format"),
prettyNum=formatCI(lower=l,upper=u,format="[l;u)",digits=2,nsmall=2,handler="prettyNum"),
sprintf=formatCI(lower=l,upper=u,format="[l;u)",digits=2,nsmall=2,handler="sprintf"))
glmSeries Run a series of generalized linear regression analyses
Description
Run a series of generalized linear regression analyses for a list of predictor variables and summarize
the results in a table. The regression models can be adjusted for a fixed set of covariates.
Usage
glmSeries(formula, data, vars, ...)
Arguments
formula The fixed part of the regression formula. For univariate analyses this is simply
y~1 where y is the outcome variable. When the aim is to control the effect of
vars in each element of the series by a fixed set of variables it is y~x1+x2 where
again y is the outcome and x1 and x2 are confounders.
data A data.frame in which we evaluate the formula.
vars A list of variable names, the changing part of the regression formula.
... passed to glm
labelUnits 15
Value
Matrix with regression coefficients, one for each element of vars.
Author(s)
Examples
data(Diabetes)
Diabetes$hyper1 <- factor(1*(Diabetes$bp.1s>140))
## collect odds ratios from three univariate logistic regression analyses
uni.odds <- glmSeries(hyper1~1,vars=c("chol","hdl","location"),data=Diabetes,family=binomial)
uni.odds
## control the logistic regression analyses for age and gender
## but collect only information on the variables in `vars'.
controlled.odds <- glmSeries(hyper1~age+gender,
vars=c("chol","hdl","location"),
data=Diabetes, family=binomial)
controlled.odds
labelUnits labelUnits
Description
Label output tables
Usage
labelUnits(x, ...)
Arguments
x A matrix obtained with univariateTable.
... not used
Details
Modify labels and values of variables in summary tables
Value
The re-labeled matrix
Author(s)
16 lazyDateCoding
See Also
univariateTable
Examples
data(Diabetes)
tab <- summary(univariateTable(gender~AgeGroups+chol+waist,data=Diabetes))
publish(tab)
ltab <- labelUnits(tab,"chol"="Cholesterol (mg/dL)","<40"="younger than 40")
publish(ltab)
## pass labels immediately to utable

utable(gender~AgeGroups+chol+waist,data=Diabetes,
"chol"="Cholesterol (mg/dL)","<40"="younger than 40")
## sometimes useful to state explicitly which variables value

## should be re-labelled
utable(gender~AgeGroups+chol+waist,data=Diabetes,
"chol"="Cholesterol (mg/dL)","AgeGroups.<40"="younger than 40")
lazyDateCoding Efficient coding of date variables
Description
This function eases the process of generating date variables. All variables in a data.frame which
match a regular expression are included
Usage
lazyDateCoding(data, format, pattern, varnames, testlength = 10)
Arguments
data Data frame in which to search for date variables.
format passed to as.Date
pattern match date variables
varnames variable names
testlength how many rows of data should be evaluated to guess the format.
Details
The code needs to be copy-and-pasted from the R-output buffer into the R-code buffer. This can be
customized for the really efficiently working people, e.g., in emacs.
lazyFactorCoding 17
Value
R-code one line for each variable.
Author(s)
Examples
d <- data.frame(x0="190101",x1=c("12/8/2019"),x2="12-8-2019",x3="20190812",stringsAsFactors=FALSE)
lazyDateCoding(d,pattern="x")
lazyDateCoding(d,pattern="3")
lazyFactorCoding Efficient coding of factor levels
Description
This function eases the process of generating factor variables with relevant labels. All variables in
a data.frame with less than a user set number of levels result in a line which suggests levels and
labels. The result can then be modified for use.
Usage
lazyFactorCoding(data, max.levels = 10)
Arguments
data Data frame in which to search for categorical variables.
max.levels Treat non-factor variables only if the number of unique values less than max.levels.
Defaults to 10.
Details
The code needs to be copy-and-pasted from the R-output buffer into the R-code buffer. This can be
customized for the really efficiently working people e.g. in emacs.
Value
R-code one line for each variable.
Author(s)
18 parseInteractionTerms
Examples
data(Diabetes)
lazyFactorCoding(Diabetes)
org Wrapper function for publish with output format org
Description
Wrapper for publish(...,org=TRUE)
Usage
org(x, ...)
Arguments
x object to format as org

... passed to publish
Value
See publish
Author(s)
parseInteractionTerms Parse interaction terms
Description
Parse interaction terms for regression tables

parseInteractionTerms 19
Usage
parseInteractionTerms(
terms,
xlevels,
units,
format.factor,
format.contrast,
format.scale,
format.scale.unit,
sep = ": ",
...
)
Arguments
terms Terms of a formula

xlevels Factor levels corresponding to the variables in terms
units named list with unit labels. names should match variable names in formula.
format.factor For categorical variables. A string which specifies the print format for factor
labels. The string has to contain the keywords "var" and "level" which will be
replaced by the name of the variable and the current level, respectively. Default
is "var(level)".
format.contrast
For categorical variables. A string which specifies the print format for constrast
statements. The string has to contain the keywords "var", "level" and "ref"
which will be replaced by the name of the variable, the current level and the
reference level, respectively.
format.scale A string which specifies the print format for continuous variables without units.
The string has to contain the keyword "var" which will be replaced by the name
of the variable and the unit, respectively. Default is "var".
format.scale.unit
A string which specifies the print format for continuous variables with units. The
string has to contain the keywords "var" and "unit" which will be replaced by
the name of the variable and the unit, respectively. Default is "var(unit)".
sep a character string to separate the terms. Default is ": ".
... Not yet used
Details
Prepare a list of contrasts which combines regression coefficients to describe statistical interactions.
Value
List of contrasts which can be passed to lava::estimate.

20 plot.ci
Author(s)
See Also
lava::estimate
Examples
tt <- terms(formula(SBP~age+sex*BMI))
xlev <- list(sex=c("male","female"),BMI=c("normal","overweight","obese"))
parseInteractionTerms(terms=tt,xlevels=xlev)
parseInteractionTerms(terms=tt,xlevels=xlev,format.factor="var level")
parseInteractionTerms(terms=tt,xlevels=xlev,format.contrast="var(level:ref)")
tt2 <- terms(formula(SBP~age*factor(sex)+BMI))

xlev2 <- list("factor(sex)"=c("male","female"))
parseInteractionTerms(terms=tt2,xlevels=xlev2)
parseInteractionTerms(terms=tt2,xlevels=xlev2,units=list(age="yrs"))
data(Diabetes)
fit <- glm(bp.2s~age*factor(gender)+BMI,data=Diabetes)
parseInteractionTerms(terms=terms(fit$formula),xlevels=fit$xlevels,
format.scale="var -- level:ref",units=list("age"='years'))
parseInteractionTerms(terms=terms(fit$formula),xlevels=fit$xlevels,
format.scale.unit="var [unit]",units=list("age"='years'))
it <- parseInteractionTerms(terms=terms(fit$formula),xlevels=fit$xlevels)
ivars <- unlist(lapply(it,function(x)attr(x,"variables")))
lava::estimate(fit,function(p)lapply(unlist(it),eval,envir=sys.parent(-1)))
plot.ci Plot confidence intervals
Description
Function to plot confidence intervals
Usage
## S3 method for class 'ci'

plot(x, xlim, xlab = "", labels, ...)
plot.ci 21
Arguments
x List, data.frame or other object of this form containing point estimates (first ele-
ment) and the corresponding confidence intervals as elements lower and upper.
xlim Limit of the x-axis
xlab Label for the y-axis
labels labels
... Used to transport arguments to plotConfidence.
Details
Function to plot means and other point estimates with confidence intervals
Author(s)
Examples
data(Diabetes)
x=ci.mean(bp.2s~AgeGroups,data=Diabetes)
plot(x,title.labels="Age groups",xratio=c(0.4,0.3))
x=ci.mean(bp.2s/500~AgeGroups+gender,data=Diabetes)
plot(x,xratio=c(0.4,0.2))
plot(x,xratio=c(0.4,0.2),
labels=split(x$labels[,"AgeGroups"],x$labels[,"gender"]),
title.labels="Age groups")
## Not run:
plot(x, leftmargin=0, rightmargin=0)
plotConfidence(x, leftmargin=0, rightmargin=0)
data(CiTable)
with(CiTable,plotConfidence(x=list(HazardRatio),
lower=lower,
upper=upper,
labels=CiTable[,2:6],
factor.reference.pos=c(1,10,19),
format="(u-l)",
points.col="blue",
digits=2))
with(CiTable,Publish::plot.ci(x=list(HazardRatio),
lower=lower,
upper=upper,
labels=CiTable[,2:6],
format="(u-l)",
points.col="blue",
digits=2,
leftmargin=-2,
22 plot.regressionTable
title.labels.cex=1.1,
labels.cex=0.8,values.cex=0.8))
## End(Not run)
plot.regressionTable Plotting regression coefficients with confidence limits
Description
Plotting regression coefficients with confidence limits
Usage
## S3 method for class 'regressionTable'
plot(x, xlim, xlab, style = 1, ...)
Arguments
x regression table obtained with regressionTable
xlim Limits for x-axis
xlab Label for x-axis
style Determines how to arrange variable names and their corresponding units
... passed to plotConfidence
Author(s)
See Also
regressionTable
Examples
## linear regression
data(Diabetes)
f <- glm(bp.1s~AgeGroups+chol+gender+location,data=Diabetes)
rtf <- regressionTable(f,factor.reference = "inline")
plot(rtf,cex=1.3)
## logistic regression
data(Diabetes)
f <- glm(I(BMI>25)~bp.1s+AgeGroups+chol+gender+location,data=Diabetes,family=binomial)
rtf <- regressionTable(f,factor.reference = "inline")
plot(rtf,cex=1.3)
## Poisson regression
plot.subgroupAnalysis 23
data(trace)
fit <- glm(dead ~ smoking+ sex+ age+Time+offset(log(ObsTime)), family = poisson,data=trace)
rtab <- regressionTable(fit,factor.reference = "inline")
plot(rtab,xlim=c(0.85,1.15),cex=1.8,xaxis.cex=1.5)
## Cox regression
library(survival)
data(pbc)
coxfit <- coxph(Surv(time,status!=0)~age+log(bili)+log(albumin)+factor(edema)+sex,data=pbc)
pubcox <- publish(coxfit)
plot(pubcox,cex=1.5,xratio=c(0.4,0.2))
plot.subgroupAnalysis plot.subgroupAnalysis
Description
This function operates on a "subgroupAnalysis" object to produce a formatted table and a forest
plot
Usage
## S3 method for class 'subgroupAnalysis'

plot(x, ...)
Arguments
x - a subgroupAnalysis object
... - passed on to plotConfidence
Details
This function produces a formatted table of a subgroupAnalysis object and adds a forest plot. If
further details needs attention before plotting is is advisable use adjust the table produced by the
summary function and then plotting with the plotConfidence function
Author(s)
Christian Torp-Pedersen
See Also
subgroupAnalysis, plotConfidence
24 plotConfidence
Examples
#load libraries
library(Publish)
library(survival)
library(data.table)
data(traceR) #get dataframe traceR
setDT(traceR)
traceR[,':='(wmi2=factor(wallMotionIndex<0.9,levels=c(TRUE,FALSE),
labels=c("bad","good")),
abd2=factor(abdominalCircumference<95, levels=c(TRUE,FALSE),
labels=c("slim","fat")),
sex=factor(sex))]
fit_cox <- coxph(Surv(observationTime,dead)~treatment,data=traceR)
# Selected subgroups - univariable analysis
sub_cox <- subgroupAnalysis(fit_cox,traceR,treatment="treatment",
subgroup=c("smoking","sex","wmi2","abd2")) # subgroups as character string
plot(sub_cox)
plotConfidence Plot confidence intervals
Description
Function to plot confidence intervals with their values and additional labels. One anticipated use of
this function involves first the generation of a regression object, then arrangement of a result table
with "regressionTable", further arrangment of table with with e.g. "fixRegressionTable" and various
user defined changes - and then finally table along with forest plot using the current function.
Usage
plotConfidence(
x,
y.at,
lower,
upper,
pch = 16,
cex = 1,
lwd = 1,
col = 4,
xlim,
xlab,
labels,
title.labels,
values,
title.values,
section.pos,
section.sep,
section.title = NULL,
plotConfidence 25
section.title.x,
section.title.offset,
order,
leftmargin = 0.025,
rightmargin = 0.025,
stripes,
factor.reference.pos,
factor.reference.label = "Reference",
factor.reference.pch = 16,
refline = 1,
title.line = TRUE,
xratio,
y.offset = 0,
y.title.offset,
digits = 2,
format,
extremearrows.length = 0.05,
extremearrows.angle = 30,
add = FALSE,
layout = TRUE,
xaxis = TRUE,
...
)
Arguments
x Either a vector containing the point estimates or a list whose first element con-
tains the point estimates. Further list elements can contain the confidence inter-
vals and labels. In this case the list needs to have names ’lower’ and ’upper’ to
indicate the values of the lower and the upper limits of the confidence intervals,
respectively, and may have an element ’labels’ which is a vector or matrix or list
with labels.
y.at Optional vector of y-position for the confidence intervals and corresponding val-
ues and labels.
lower Lower confidence limits. Used if object x is a vector and if x is a list lower
overwrites element x$lower.
upper Upper confidence limits. Used if object x is a vector and if x is a list upper
overwrites element x$upper.
pch Symbol for points.
cex Defaults size of all figures and plotting symbol. Single elements are controlled
separately. See ....
lwd Default width of all lines Single elements are controlled separately. See ....
col Default colour of confidence intervals.
xlim Plotting limits for the confidence intervals. See also xratio on how to control
the layout.
xlab Label for the x-axis.
26 plotConfidence
labels Vector or matrix or list with labels. Used if object x is a vector and if x is a list
it overwrites element x$labels. To avoid drawing of labels, set labels=FALSE.
title.labels Main title for the column which shows the labels. If labels is a matrix or list
title.labels should be a vector with as many elements as labels has columns
or elements.
values Either logical or vector, matrix or list with values. If values=TRUE values are
constructed according to format from lower and upper overwrites constructed
values. If values=FALSE do not draw values.
title.values Main title for the column values. If values is a matrix or list title.labels
should be a vector with as many elements as values has columns or elements.
section.pos Vector with y-axis posititions for section.titles.
section.sep Amount of space between paragraphs (applies only if labels is a named list)
section.title Intermediate section headings.
section.title.x
x-position for section.titles
section.title.offset
Y-offset for section.titles
order Order of the three columns: labels, confidence limits, values. See examples.
leftmargin Percentage of plotting region used for leftmargin. Default is 0.025. See also
Details.
rightmargin Percentage of plotting region used for rightmargin. Default is 0.025. See also
Details.
stripes Vector of up to three Logicals. If TRUE draw stripes into the background. The
first applies to the labels, the second to the graphical presentation of the confi-
dence intervals and the third to the values. Thus, stripes
factor.reference.pos
Position at which factors attain reference values.
factor.reference.label
Label to use at factor.reference.pos instead of values.
factor.reference.pch
Plotting symbol to use at factor.reference.pos
refline Position of a vertical line to indicate the null hypothesis. Default is 1 which
would work for odds ratios and hazard ratios.
title.line Position of a horizontal line to separate the title line from the plot
xratio One or two values between 0 and 1 which determine how to split the plot window
in horizontal x-direction. If there are two columns (labels, CI) or (CI, values)
only one value is used and the default is 0.618 (goldener schnitt) which gives
the graphical presentation of the confidence intervals 38.2 graph. The remaining
61.8 If there are three columns (labels, CI, values), xratio has two values which
default to fractions of 0.7 according to the relative widths of labels and values,
thus by default only 0.3 are used for the graphical presentation of the confidence
intervals. The remaining 30 confidence intervals. See examles.
plotConfidence 27
y.offset Either a single value or a vector determining the vertical offset of all rows. If it
is a single value all rows are shifted up (or down if negative) by this value. This
can be used to add a second set of confidence intervals to an existing graph or to
achieve a visual grouping of rows that belong together. See examples.
y.title.offset Numeric value by which to vertically shift the titles of the labels and values.
digits Number of digits, passed to pubformat and formatCI.
format Format for constructing values of confidence intervals. Defaults to ’(u;l)’ if there
are negative lower or upper values and to ’(u-l)’ otherwise.
extremearrows.length
Length of the arrows in case of confidence intervals that stretch beyond xlim.
extremearrows.angle
Angle of the arrows in case of confidence intervals that stretch beyond xlim.
add Logical. If TRUE do not draw labels or values and add confidence intervals to
existing plot.
layout Logical. If FALSE do not call layout. This is useful when several plotConfidence
results should be combined in one graph and hence layout is called externally.
xaxis Logical. If FALSE do not draw x-axis.
... Used to control arguments of the following subroutines: plot: Applies to plot-
ting frame of the graphical presentation of confidence intervals. Use arguments
of plot, e.g., plot.main="Odds ratio". points, arrows: Use arguments of
points and arrows, respectively. E.g., points.pch=8 and arrows.lwd=2.
refline: Use arguments of segments, e.g., refline.lwd=2. See segments.
labels, values, title.labels, title.values: Use arguments of text, e.g.,
labels.col="red" or title.values.cex=1.8. xaxis: Use arguments of axis,
e.g., xaxis.at=c(-0.3,0,0.3) xlab: Use arguments of mtext, e.g., xlab.line=2.
stripes: Use arguments of stripes. See examples. See examples for usage.
Details
Function to plot means and other point estimates with confidence intervals, their values and addi-
tional labels . Horizonal margins as determined by par()$mar are ignored. Instead layout is used to
divide the plotting region horizontally into two or three parts plus leftmargin and rightmargin.
When values is FALSE there are only two parts. The default order is labels on the left confidence
intervals on the right. When no labels are given or labels is FALSE there are only two parts. The
default order is confidence intervals on the left values on the right.
The default order of three parts from left to right is labels, confidence intervals, values. The order
can be changed as shown by the examples below. The relative widths of the two or three parts need
to be adapted to the actual size of the text of the labels. This depends on the plotting device and the
size of the font and figures and thus has to be adjusted manually.
Oma can be used to further control horizontal margins, e.g., par(oma=c(0,4,0,4)).
If confidence limits extend beyond the range determined by xlim, then arrows are drawn at the x-lim
borders to indicate that the confidence limits continue.
Value
List of dimensions and coordinates
28 plotConfidence
Author(s)
Examples
library(Publish)
data(CiTable)
## A first draft version of the plot is obtained as follows

plotConfidence(x=CiTable[,c("HazardRatio","lower","upper","p")],
labels=CiTable[,c("Drug.Time","Dose","Mean","SD","n")])
## if argument labels is a named list the table is subdivided:

labellist <- split(CiTable[,c("Dose","Time","Mean","SD","n")],CiTable[,"Drug"])
labellist
## the data need to be ordered accordingly
CC= data.table::rbindlist(split(CiTable[,c("HazardRatio","lower","upper")],CiTable[,"Drug"]))
plotConfidence(x=CC, labels=labellist)
## The graph consist of at most three columns:

##
## column 1: labels
## column 2: printed values of the confidence intervals
## column 3: graphical presentation of the confidence intervals
##
## NOTE: column 3 appears always, the user decides if also
## column 1, 2 should appear
##
## The columns are arranged with the function layout
## and the default order is 1,3,2 such that the graphical
## display of the confidence intervals appears in the middle
##
## the order of appearance of the three columns can be changed as follows
plotConfidence(x=CiTable[,c("HazardRatio","lower","upper")],
labels=CiTable[,c("Drug.Time","Dose","Mean","SD","n")],
order=c(1,3,2))
order=c(2,3,1))
## if there are only two columns the order is 1, 2
values=FALSE,
order=c(2,1))
values=FALSE,
order=c(1,2))
plotConfidence 29
## The relative size of the columns needs to be controlled manually

## by using the argument xratio. If there are only two columns
xratio=c(0.4,0.15))
## The amount of space on the left and right margin can be controlled
## as follows:
xratio=c(0.4,0.15),
leftmargin=0.1,rightmargin=0.00)
## The actual size of the current graphics device determines

## the size of the figures and the space between them.
## The sizes and line widths are increased as follows:
xlab="Hazard ratio",
points.cex=3,
cex=2,
lwd=3,
xaxis.lwd=1.3,
xaxis.cex=1.3)
## Note that 'cex' of axis ticks is controlled via 'par' but
## cex of the label via argument 'cex' of 'mtext'.
## The sizes and line widths are decreased as follows:
cex=0.8,
lwd=0.8,
xaxis.lwd=0.8,
xaxis.cex=0.8)
## Another good news is that all figures can be controlled separately
## The size of the graphic device can be controlled in the usual way, e.g.:
## Not run:
pdf("~/tmp/testCI.pdf",width=8,height=8)
labels=CiTable[,c("Drug.Time","Dose","Mean","SD","n")])
dev.off()
## End(Not run)
## More control of the x-axis and confidence intervals that

## stretch outside the x-range end in an arrow.
## the argument xlab.line adjusts the distance of the x-axis
## label from the graph
xlab.line=1.8,
30 plotConfidence
xaxis.at=c(0.8,1,1.3),
xlim=c(0.8,1.3))
## log-scale
xlab.line=1.8,
xaxis.at=c(0.8,1,1.3),
xlim=c(0.8,1.3),plot.log="x")
## More pronounced arrows
## Coloured xlab expression
xlab=expression(HR[1](s)),
xlab.line=1.8,
xlab.col="darkred",
extremearrows.angle=50,
extremearrows.length=0.1,
xlim=c(0.8,1.3))
## Controlling the labels and their titles

## and the values and their titles
title.values=expression(bold(HR (CI[95]))),
title.labels=c("Drug/Time","Dose","Mean","St.dev.","N"),
factor.reference.pch=16,
cex=1.3,
xaxis.at=c(0.75,1,1.25,1.5,2))
## For factor reference groups, one may want to replace the

## confidence intervals by the word Reference, as in the previous example.
## To change the word 'Reference' we use the argument factor.reference.label:
## To change the plot symbol for the reference lines factor.reference.pch
## To remove the plot symbol in the reference lines use 'NA' as follows:
factor.reference.label="Ref",
title.values=expression(bold(HR (CI[95]))),
title.labels=c("Drug/Time","Dose","Mean","St.dev.","N"),
factor.reference.pch=NA,
cex=1.3,
xaxis.at=c(0.75,1,1.25,1.5,2))
## changing the style of the graphical confidence intervals

plotConfidence 31
points.pch=15,
points.col=rainbow(27),
points.cex=2,
arrows.col="darkblue",
cex=1.3,
order=c(1,3,2),
xaxis.at=c(0.75,1,1.25,1.5))
## the values column of the graph can have multiple columns as well
## to illustrate this we create the confidence intervals
## before calling the function and then cbind them
## to the pvalues
HR <- pubformat(CiTable[,6])
CI95 <- formatCI(lower=CiTable[,7],upper=CiTable[,8],format="(l-u)")
pval <- format.pval(CiTable[,9],digits=3,eps=10^{-3})
pval[pval=="NA"] <- ""
values=list("HR"=HR,"CI-95"=CI95,"P-value"=pval),
cex=1.2,
xratio=c(0.5,0.3))
## Finally, vertical columns can be delimited with background color

## NOTE: this may slow things down and potentially create
## large figures (many bytes)
col1 <- rep(c(prodlim::dimColor("green",density=22),
prodlim::dimColor("green")),length.out=9)
col2 <- rep(c(prodlim::dimColor("orange",density=22),
prodlim::dimColor("orange")),length.out=9)
col3 <- rep(c(prodlim::dimColor("blue",density=22),
prodlim::dimColor("blue")),length.out=9)
stripes=c(1,0,1),
stripes.col=c(col1,col2,col3))
stripes=c(1,1,1),
stripes.col=c(col1,col2,col3))
threegreens <- c(prodlim::dimColor("green",density=55),

prodlim::dimColor("green",density=33),
prodlim::dimColor("green",density=22))
values=FALSE,
xlim=c(0.75,1.5),
stripes=c(1,1,1),
xratio=c(0.5,0.15),
stripes.horizontal=c(0,9,18,27)+0.5,
32 print.ci
stripes.col=threegreens)
# combining multiple plots into one

layout(t(matrix(1:5)))
labels=CiTable[,c("Mean","n")],
layout=FALSE)
layout=FALSE)
print.ci Print confidence intervals
Description
Print confidence intervals
Usage
print(x, se = FALSE, print = TRUE, ...)
Arguments
x Object containing point estimates and the corresponding confidence intervals
se If TRUE add the standard error.
print Logical: if FALSE do not actually print confidence intervals but just return them
invisibly.
... passed to summary.ci
Details
This format of the confidence intervals is user-manipulable.
Value
A string: the formatted confidence intervals
Author(s)
See Also
ci plot.ci formatCI summary.ci
print.subgroupAnalysis 33
Examples
library(lava)
m <- lvm(Y~X)
m <- categorical(m,Y~X,K=4)
set.seed(4)
d <- sim(m,24)
ci.mean(Y~X,data=d)
x <- ci.mean(Y~X,data=d)
print(x,format="(l,u)")
print.subgroupAnalysis
Printing univariate tables
Description
Print function for subgroupAnalysis
Usage
print(x, ...)
Arguments
x - An object obtained with subgroupAnalysis
... Passed to summary.subgroupAnalysis
Details
This function is simply calling summary.subgroupAnalysis
Value
The result of summary.subgroupAnalysis(x)
Author(s)
Christian Torp-Pedersen (ctp@heart.dk)
See Also
subgroupAnalysis
34 print.table2x2
print.table2x2 print results of 2x2 contingency table analysis
Description
print results of 2x2 contingency table analysis
Usage
## S3 method for class 'table2x2'

print(x, digits = 1, ...)
Arguments
x object obtained with table2x2

digits rounding digits
... not used
Value
invisible x
Author(s)
See Also
table2x2
Examples
table2x2(table("marker"=rbinom(100,1,0.4),"response"=rbinom(100,1,0.1)))
table2x2(matrix(c(71,18,38,8),ncol=2),stats="table")
table2x2(matrix(c(71,18,38,8),ncol=2),stats=c("rr","fisher"))
print.univariateTable 35
print.univariateTable Printing univariate tables
Description
Print function for univariate tables
Usage
## S3 method for class 'univariateTable'
print(x, ...)
Arguments
x An object obtained with univariateTable
... Passed to summary.univariateTable
Details
This function is simply calling summary.univariateTable
Value
The result of summary.univariateTable(x)
Author(s)
See Also
univariateTable
pubformat Format numbers for publication
Description
Format numbers according to a specified handler function. Currently supported are sprintf, format
and prettyNum.
Usage
pubformat(x, digits = 2, nsmall = digits, handler = "sprintf", ...)
36 publish
Arguments
x numeric vector
digits number of digits
nsmall see handler
handler String specififying the name of the function which should perform the format-
ting. See sprintf, format and prettyNum.
... Passed to handler function if applicable, i.e., not to sprintf.
Value
Formatted number
Author(s)
See Also
sprintf, format, prettyNum
Examples
pubformat(c(0.000143,12.8,1))
pubformat(c(0.000143,12.8,1),handler="format")
pubformat(c(0.000143,12.8,1),handler="format",trim=TRUE)
pubformat(c(0.000143,12.8,1),handler="prettyNum")
publish Publishing tables and figures
Description
Publish provides summary functions for data and results of statistical analysis in ready-for-publication
design
Usage
publish(object, ...)
Arguments
object object to be published
... Passed to method.
publish.CauseSpecificCox 37
Details
Some warnings are currently suppressed.
Value
Tables and figures
Author(s)
See Also
publish.CauseSpecificCox publish.ci publish.coxph publish.glm publish.riskRegression publish.survdiff
publish.CauseSpecificCox
Tabulizing cause-specific hazard ratio from all causes with confidence
limits and Wald test p-values.
Description
Publish cause-specific Cox models
Usage
## S3 method for class 'CauseSpecificCox'
publish(
object,
cause,
confint.method,
pvalue.method,
factor.reference = "extraline",
units = NULL,
print = TRUE,
...
)
Arguments
object Cause-specific hazard model obtained with CSC.
cause Show a table for this cause. If omitted, list all causes.
confint.method See regressionTable
pvalue.method See regressionTable
factor.reference
See regressionTable
38 publish.ci
units See regressionTable

print If TRUE print the table(s).
... passed on to control formatting of parameters, confidence intervals and p-values.
See summary.regressionTable.
Details
The cause-specific hazard ratio’s are combined into one table.
Value
Table with cause-specific hazard ratios, confidence limits and p-values.
Author(s)
Thomas Alexander Gerds <tab@biostat.ku.dk>
Examples
if (requireNamespace("riskRegression",quietly=TRUE)){
library(riskRegression)
library(prodlim)
library(survival)
data(Melanoma,package="riskRegression")
fit1 <- CSC(list(Hist(time,status)~sex,Hist(time,status)~invasion+epicel+age),
data=Melanoma)
publish(fit1)
publish(fit1,pvalue.stars=TRUE)
publish(fit1,factor.reference="inline",units=list("age"="years"))
# wide format (same variables in both Cox regression formula)

fit2 <- CSC(Hist(time,status)~invasion+epicel+age, data=Melanoma)
publish(fit2)
# with p-values
x <- publish(fit2,print=FALSE)
table <- cbind(x[[1]]$regressionTable,
x[[2]]$regressionTable[,-c(1,2)])
}
publish.ci Publish tables with confidence intervals
Description
Publish tables with confidence intervals
publish.coxph 39
Usage
publish(object, format = "[u;l]", se = FALSE, ...)
Arguments
object Object of class ci containing point estimates and the corresponding confidence
intervals
format A string which indicates the format used for confidence intervals. The string
is passed to formatCI with two arguments: the lower and the upper limit. For
example '(l;u)' yields confidence intervals with round parenthesis in which
the upper and the lower limits are separated by semicolon.
se If TRUE add standard error.
... passed to publish
Details
This function calls summary.ci with print=FALSE and then publish
Value
table with confidence intervals
Author(s)
See Also
summary.ci
Examples
data(Diabetes)
publish(ci.mean(chol~location+gender,data=Diabetes),org=TRUE)
publish.coxph Tabulize hazard ratios with confidence intervals and p-values.
Description
Tabulize the part of the result of a Cox regression analysis which is commonly shown in publica-
tions.
40 publish.coxph
Usage
## S3 method for class 'coxph'
publish(
object,
confint.method,
pvalue.method,
print = TRUE,
units = NULL,
probindex = FALSE,
...
)
Arguments
object A coxph object.
confint.method See regressionTable
pvalue.method See regressionTable
print If FALSE do not print results.
factor.reference
See regressionTable
units See regressionTable
probindex Logical. If TRUE show coefficients on probabilistic index scale instead of hazard
ratio scale.
... passed to summary.regressionTable and also to labelUnits.
Details
Transforms the log hazard ratios to hazard ratios and returns them with confidence limits and p-
values. If explanatory variables are log transformed or log2 transformed, a scaling factor is multi-
plied to both the log-hazard ratio and its standard-error.
Value
Table with hazard ratios, confidence intervals and p-values.
Author(s)
Examples
library(survival)
data(pbc)
pbc$edema <- factor(pbc$edema,
levels=c("0","0.5","1"), labels=c("0","0.5","1"))
fit = coxph(Surv(time,status!=0)~age+sex+edema+log(bili)+log(albumin),
publish.glm 41
data=na.omit(pbc))
publish(fit)
## forest plot
plot(publish(fit),cex=1.3)
publish(fit,ci.digits=2,pvalue.eps=0.01,pvalue.digits=2,pvalue.stars=TRUE)
publish(fit,ci.digits=2,ci.handler="prettyNum",pvalue.eps=0.01,
pvalue.digits=2,pvalue.stars=TRUE)
publish(fit, ci.digits=2, ci.handler="sprintf", pvalue.eps=0.01,
pvalue.digits=2,pvalue.stars=TRUE, ci.trim=FALSE)
fit2 = coxph(Surv(time,status!=0)~age+sex+edema+log(bili,base=2)+log(albumin)+log(protime),
data=na.omit(pbc))
publish(fit2)
# with cluster variable

fit3 = coxph(Surv(time,status!=0)~age+cluster(sex)+edema+log(bili,base=2)
+log(albumin)+log(protime),
data=na.omit(pbc))
publish(fit3)
# with strata and cluster variable

fit4 = coxph(Surv(time,status!=0)~age+cluster(sex)+strata(edema)+log(bili,base=2)
+log(albumin)+log(protime),
data=pbc)
publish(fit4)
publish.glm Tabulize regression coefficients with confidence intervals and p-values.
Description
Tabulate the results of a generalized linear regression analysis.
Usage
## S3 method for class 'glm'
publish(
object,
confint.method,
pvalue.method,
digits = c(2, 4),
print = TRUE,
intercept = ifelse((is.null(object$family) || object$family$family == "gaussian"),
1L, 0L),
units = NULL,
...
)
42 publish.glm
Arguments
object A glm object.
confint.method See regressionTable.
pvalue.method See regressionTable.
digits A vector of two integer values. These determine how to round numbers (first
value) and p-values (second value). E.g., c(1,3) would mean 1 digit for all num-
bers and 3 digits for p-values. The actual rounding is done by summary.regressionTable.
factor.reference
Style for showing results for categorical. See regressionTable.
intercept See regressionTable.
units See regressionTable.
... passed to summary.regressionTable and also to labelUnits.
reference Style for showing results for categorical variables. If "extraline" show an
additional line for the reference category.
Details
The table shows changes in mean for linear regression and odds ratios for logistic regression (family
= binomial).
Value
Table with regression coefficients, confidence intervals and p-values.
Author(s)
Examples
data(Diabetes)
## Linear regression
f = glm(bp.2s~frame+gender+age,data=Diabetes)
publish(f)
publish(f,factor.reference="inline")
publish(f,pvalue.stars=TRUE)
publish(f,ci.format="(l,u)")
### interaction
fit = glm(bp.2s~frame+gender*age,data=Diabetes)
summary(fit)
publish(fit)
Fit = glm(bp.2s~frame*gender+age,data=Diabetes)
publish(Fit)
publish.htest 43
## Logistic regression
Diabetes$hyper1 <- factor(1*(Diabetes$bp.1s>140))
lrfit <- glm(hyper1~frame+gender+age,data=Diabetes,family=binomial)
publish(lrfit)
### interaction
lrfit1 <- glm(hyper1~frame+gender*age,data=Diabetes,family=binomial)
publish(lrfit1)
lrfit2 <- glm(hyper1~frame*gender+age,data=Diabetes,family=binomial)

publish(lrfit2)
## Poisson regression
data(trace)
trace <- Units(trace,list("age"="years"))
fit <- glm(dead ~ smoking+sex+age+Time+offset(log(ObsTime)), family="poisson",data=trace)
rtf <- regressionTable(fit,factor.reference = "inline")
summary(rtf)
publish(fit)
## gls regression
if (requireNamespace("nlme",quietly=TRUE)){
requireNamespace("lava",quietly=TRUE)
library(lava)
library(nlme)
m <- lvm(Y ~ X1 + gender + group + Interaction)
distribution(m, ~gender) <- binomial.lvm()
distribution(m, ~group) <- binomial.lvm(size = 2)
constrain(m, Interaction ~ gender + group) <- function(x){x[,1]*x[,2]}
d <- sim(m, 1e2)
d$gender <- factor(d$gender, labels = letters[1:2])
d$group <- factor(d$group)
e.gls <- gls(Y ~ X1 + gender*group, data = d,

weights = varIdent(form = ~1|group))
publish(e.gls)
## lme
fm1 <- lme(distance ~ age*Sex,
random = ~1|Subject,
data = Orthodont)
res <- publish(fm1)
}
publish.htest Pretty printing of test results.
Description
Pretty printing of test results.
44 publish.matrix
Usage
## S3 method for class 'htest'
publish(object, title, ...)
Arguments
object Result of t.test or wilcox.test
title Decoration also used to name output
... Used to transport arguments ci.arg and pvalue.arg to subroutines format.pval
and formatCI. See also prodlim::SmartControl.
Author(s)
Examples
data(Diabetes)
publish(t.test(bp.2s~gender,data=Diabetes))
publish(wilcox.test(bp.2s~gender,data=Diabetes))
publish(with(Diabetes,t.test(bp.2s,bp.1s,paired=TRUE)))
publish(with(Diabetes,wilcox.test(bp.2s,bp.1s,paired=TRUE)))
publish.matrix Publishing a matrix in raw, org, latex, or muse format
Description
This is the heart of the Publish package
Usage
## S3 method for class 'matrix'
publish(
object,
title,
colnames = TRUE,
rownames = TRUE,
col1name = "",
digits = 4,
try.convert = TRUE,
sep = " ",
endhead,
endrow,
style,
inter.lines,
publish.matrix 45
latex = FALSE,
wiki = FALSE,
org = FALSE,
markdown = FALSE,
tabular = TRUE,
latex.table.format = NA,
latex.hline = 1,
latex.nodollar = FALSE,
...
)
Arguments
object Matrix to be published

title Title for table, only in wiki and muse format
colnames If TRUE show column names
rownames If TRUE show row names
col1name Name for first column
digits Numbers are rounded according to digits
try.convert Logical. If TRUE try to convert also non-numeric formats such as character to
numeric before rounding. Default is TRUE.
sep Field separator when style is "none"
endhead String to be pasted at the end of the first row (header)
endrow String to be pasted at the end of each row
style Table style for export to "latex", "org", "markdown", "wiki", "none". Over-
written by argments below.
inter.lines A named list which contains strings to be placed between the rows of the ta-
ble. An element with name "0" is used to place a line before the first column,
elements with name "r" are placed between line r and r+1.
latex If TRUE use latex table format
wiki If TRUE use mediawiki table format
org If TRUE use emacs orgmode table format
markdown If TRUE use markdown table format
tabular For style latex only: if TRUE enclose the table in begin/end tabular environe-
ment.
latex.table.format
For style latex only: format of the tabular environement.
latex.hline For style latex only: if TRUE add hline statements add the end of each line.
latex.nodollar For style latex only: if TRUE do not enclose numbers in dollars.
... Used to transport arguments. Currently supports wiki.class.
46 publish.MIresult
Examples
x <- matrix(1:12,ncol=3)
publish(x)
# rounding the numeric part of data mixtures

y <- cbind(matrix(letters[1:12],ncol=3),x,matrix(rnorm(12),ncol=3))
publish(y,digits=1)
publish(x,inter.lines=list("1"="text between line 1 and line 2",

"3"="text between line 3 and line 4"))
publish.MIresult Present logistic regression and Cox regression obtained with mi-
tools::MIcombine based on smcfcs::smcfcs multiple imputation anal-
ysis
Description
Regression tables after multiple imputations
Usage
## S3 method for class 'MIresult'
publish(
object,
confint.method,
pvalue.method,
digits = c(2, 4),
print = TRUE,
intercept,
units = NULL,
fit,
data,
...
)
Arguments
object Object obtained with mitools::MIcombine based on smcfcs::smcfcs multiple im-
putation analysis
confint.method No options here. Only Wald type confidence intervals.
pvalue.method No options here. Only Wald type tests.
digits Rounding digits for all numbers but the p-values.
publish.MIresult 47
print If FALSE suppress printing of the results

factor.reference
Style for showing results for categorical. See regressionTable.
intercept See regressionTable.
units See regressionTable.
fit One fitted model using the same formula as object. This can be the fit to the
complete case data or the fit to one of the completed data. It is used to get
xlevels, formula and terms. For usage see examples. is used to fit
data Original data set which includes the missing values
... passed to summary.regressionTable, labelUnits and publish.default.
Details
Show results of smcfcs based multiple imputations of missing covariates in publishable format
Author(s)
Examples
## Not run:
if (requireNamespace("riskRegression",quietly=TRUE)
& requireNamespace("mitools",quietly=TRUE)
& requireNamespace("smcfcs",quietly=TRUE)){
library(mitools)
library(smcfcs)
## continuous outcome: linear regression
# lava some data with missing values
set.seed(7)
d=sampleData(78)
## generate missing values
d[X1==1,X6:=NA]
d[X2==1,X3:=NA]
d=d[,.(X8,X4,X3,X6,X7)]
sapply(d,function(x)sum(is.na(x)))
# multiple imputation (should set m to a large value)
set.seed(17)
f= smcfcs(d,smtype="lm",
smformula=X8~X4+X3+X6+X7,
method=c("","","logreg","norm",""),m=3)
ccfit=lm(X8~X4+X3+X6+X7,data=d)
mifit=MIcombine(with(imputationList(f$impDatasets),
lm(X8~X4+X3+X6+X7)))
publish(mifit,fit=ccfit,data=d)
publish(ccfit)
48 publish.MIresult
## binary outcome
set.seed(7)
db=sampleData(78,outcome="binary")
db[X1==1,X6:=NA]
db[X2==1,X3:=NA]
db=db[,.(Y,X4,X3,X6,X7)]
sapply(db,function(x)sum(is.na(x)))
# multiple imputation (should set m to a large value)

set.seed(17)
fb= smcfcs(db,smtype="logistic",
smformula=Y~X4+X3+X6+X7,
method=c("","","logreg","norm",""),m=2)
ccfit=glm(Y~X4+X3+X6+X7,family="binomial",data=db)
mifit=MIcombine(with(imputationList(fb$impDatasets),
glm(Y~X4+X3+X6+X7,family="binomial")))
publish(mifit,fit=ccfit)
publish(ccfit)
## survival: Cox regression

library(survival)
set.seed(7)
ds=sampleData(78,outcome="survival")
ds[X5==1,X6:=NA]
ds[X2==1,X3:=NA]
ds=ds[,.(time,event,X4,X3,X6,X7)]
sapply(ds,function(x)sum(is.na(x)))
set.seed(17)
fs= smcfcs(ds,smtype="coxph",
smformula="Surv(time,event)~X4+X3+X6+X7",
method=c("","","","logreg","norm",""),m=2)
ccfit=coxph(Surv(time,event)~X4+X3+X6+X7,data=ds)
mifit=MIcombine(with(imputationList(fs$impDatasets),
coxph(Surv(time,event)~X4+X3+X6+X7)))
publish(mifit,fit=ccfit,data=ds)
publish(ccfit)
## competing risks: Cause-specific Cox regression

library(survival)
set.seed(7)
dcr=sampleData(78,outcome="competing.risks")
dcr[X5==1,X6:=NA]
dcr[X2==1,X3:=NA]
dcr=dcr[,.(time,event,X4,X3,X6,X7)]
sapply(dcr,function(x)sum(is.na(x)))
publish.riskRegression 49
set.seed(17)
fcr= smcfcs(dcr,smtype="compet",
smformula=c("Surv(time,event==1)~X4+X3+X6+X7",
"Surv(time,event==2)~X4+X3+X6+X7"),
method=c("","","","logreg","norm",""),m=2)
## cause 2
ccfit2=coxph(Surv(time,event==2)~X4+X3+X6+X7,data=dcr)
mifit2=MIcombine(with(imputationList(fcr$impDatasets),
coxph(Surv(time,event==2)~X4+X3+X6+X7)))
publish(mifit2,fit=ccfit2,data=dcr)
publish(ccfit2)
}
## End(Not run)
publish.riskRegression
Publishing results of riskRegression
Description
Preparing a publishable table from riskRegression results
Usage
## S3 method for class 'riskRegression'
publish(object, digits = c(2, 4), print = TRUE, ...)
Arguments
object object of class riskRegression as obtained with functions ARR and LRR.
digits Number of digits for regression coefficients
print If FALSE do not print the results
... passed to publish.matrix
Value
Table with regression coefficients, confidence intervals and p-values
Author(s)
See Also
ARR LRR
50 publish.Score
Examples
library(prodlim)
library(lava)
library(survival)
set.seed(20)
d <- SimCompRisk(20)
f <- ARR(Hist(time,event)~X1+X2,data=d,cause=1)
publish(f)
publish(f,digits=c(1,3))
}
publish.Score Publish predictive accuracy results
Description
Write output of riskRegression::Score in tables
Usage
## S3 method for class 'Score'
publish(object, metrics, score = TRUE, contrasts = TRUE, level = 3, ...)
Arguments
object Object obtained with riskRegression::Score
metrics Which metrics to put into tables. Defaults to object$metrics.
score Logical. If TRUE print the score elements, i.e., metric applied to the risk predic-
tion models.
contrasts Logical. If TRUE print the contrast elements (if any). These compare risk predic-
tion models according to metrics.
level Level of subsection headers, i.e., ** for level 2 and *** for level 3 (useful for
emacs org-users). Default is plain subsection headers no stars. A negative value
will suppress subjection headers.
... Passed to publish
Details
Collect prediction accuracy results in tables
Value
Results of Score in tabular form
publish.summary.aov 51
Author(s)
Examples
library(survival)
learn = sampleData(100)
val= sampleData(100)
f1=CSC(Hist(time,event)~X1+X8,data=learn)
f2=CSC(Hist(time,event)~X1+X5+X6+X8,learn)
xs=Score(list(f1,f2),data=val,formula=Hist(time,event)~1)
publish(xs)
}
publish.summary.aov Format summary table of aov results
Description
Format summary table of aov results
Usage
## S3 method for class 'summary.aov'
publish(
object,
print = TRUE,
handler = "sprintf",
digits = c(2, 4),
nsmall = digits,
...
)
Arguments
object glm object
print Logical. Decide about whether or not to print the results.
handler see pubformat
digits see pubformat
nsmall see pubformat
... used to transport further arguments
52 publish.survdiff
Examples
data(Diabetes)
f <- glm(bp.1s~age+chol+gender+location,data=Diabetes)
publish(summary(aov(f)),digits=c(1,2))
publish.survdiff Alternative summary of survdiff results
Description
Alternative summary of survdiff results
Usage
## S3 method for class 'survdiff'

publish(object, digits = c(2, 4), print = TRUE, ...)
Arguments
object Object obtained with survival::survdiff.

digits Vector with digits for rounding numbers: the second for pvalues, the first for all
other numbers.
... Not (yet) used.
Author(s)
Examples
library(survival)
data(pbc)
sd <- survdiff(Surv(time,status!=0)~sex,data=pbc)
publish(sd)
publish(sd,digits=c(3,2))
regressionTable 53
regressionTable Regression table
Description
Tabulate the results of a regression analysis.
Usage
regressionTable(
object,
param.method = "coef",
confint.method = c("default", "profile", "robust", "simultaneous"),
pvalue.method = c("default", "robust", "simultaneous"),
intercept = 0L,
units = NULL,
noterms = NULL,
probindex = 0L,
...
)
Arguments
object Fitted regression model obtained with lm, glm or coxph.
param.method Method to obtain model coefficients.
confint.method Method to obtain confidence intervals. Default is ’default’ which leads to Wald
type intervals using the model based estimate of standard error. ’profile’ yields
profile likelihood confidence intervals, available from library MASS for lm and
glm objects. ’robust’ uses the sandwich form standard error to construct Wald
type intervals (see lava::estimate.default). ’simultaneous’ calls multcomp::glht
to obtain simultaneous confidence intervals.
pvalue.method Method to obtain p-values. If 'default' show raw p-values. If 'robust' use p-
value corresponding to robust standard error as provided by lava::estimate.default.
If 'simultaneous' call multcomp::glht to obtain p-values.
factor.reference
Style for showing results for categorical variables. If 'extraline' show an
additional line for the reference category. If 'inline' display as level vs. ref-
erence.
intercept Logical. If FALSE suppress intercept.
units List of units for continuous variables. See examples.
noterms Position of terms that should be ignored. E.g., for a Cox model with a cluster(id)
term, there will be no hazard ratio for variable id.
probindex Logical. If TRUE show coefficients on probabilistic index scale instead of hazard
ratio scale.
... Not yet used
54 regressionTable
Details
The basic use of this function is to generate a near publication worthy table from a regression
object. As with summary(object) reference levels of factor variables are not included. Expansion
of the table with such values can be performed using the "fixRegressionTable" function. Forest plot
can be added to the output with "plotRegressionTable".
regressionTable produces an object (list) with the parameters deriveds. The summary function
creates a data frame which can be used as a (near) publication ready table.
The table shows changes in mean for linear regression, odds ratios for logistic regression (family =
binomial) and hazard ratios for Cox regression.
Value
List of regression blocks
Author(s)
Examples
# linear regression
data(Diabetes)
f1 <- glm(bp.1s~age+gender+frame+chol,data=Diabetes)
summary(regressionTable(f1))
summary(regressionTable(f1,units=list("chol"="mmol/L","age"="years")))
## with interaction
f2 <- glm(bp.1s~age*gender+frame+chol,data=Diabetes)
#Add reference values
f3 <- glm(bp.1s~age+gender*frame+chol,data=Diabetes)
publish(f3)
regressionTable(f3)
# logistic regression
Diabetes$hyp1 <- factor(1*(Diabetes$bp.1s>140))
l1 <- glm(hyp1~age+gender+frame+chol,data=Diabetes,family="binomial")
regressionTable(l1)
publish(l1)
plot(regressionTable(l1))
## with interaction
l2 <- glm(hyp1~age+gender+frame*chol,data=Diabetes,family="binomial")
regressionTable(l2)
l3 <- glm(hyp1~age*gender+frame*chol,data=Diabetes,family="binomial")
regressionTable(l3)
# Cox regression
library(survival)
data(pbc)
SpaceT 55

c1 <- coxph(Surv(time,status!=0)~log(bili)+age+protime+sex+edema,data=pbc)
regressionTable(c1)
# with interaction
c2 <- coxph(Surv(time,status!=0)~log(bili)+age+protime*sex+edema,data=pbc)
regressionTable(c2)
c3 <- coxph(Surv(time,status!=0)~edema*log(bili)+age+protime+sex+edema+edema:sex,data=pbc)
regressionTable(c3)
if (requireNamespace("nlme",quietly=TRUE)){
## gls regression
library(lava)
library(nlme)
m <- lvm(Y ~ X1 + gender + group + Interaction)
distribution(m, ~gender) <- binomial.lvm()
distribution(m, ~group) <- binomial.lvm(size = 2)
constrain(m, Interaction ~ gender + group) <- function(x){x[,1]*x[,2]}
d <- sim(m, 1e2)
d$gender <- factor(d$gender, labels = letters[1:2])
d$group <- factor(d$group)
e.gls <- gls(Y ~ X1 + gender*group, data = d,

weights = varIdent(form = ~1|group))
regressionTable(e.gls)
summary(regressionTable(e.gls))
}
SpaceT A study was made of all 26 astronauts on the first eight space shut-
tle flights (Bungo et.al., 1985). On a voluntary basis 17 astronauts
consumed large quantities of salt and fluid prior to landing as a coun-
termeasure to space deconditioning, while nine did not.
Description
A study was made of all 26 astronauts on the first eight space shuttle flights (Bungo et.al., 1985).
On a voluntary basis 17 astronauts consumed large quantities of salt and fluid prior to landing as a
countermeasure to space deconditioning, while nine did not.
Format
A data frame with 52 observations on the following 4 variables:
Status Factor with levels Post (after flight) and Pre (before flight)
HR Supine heart rate(beats per minute)
Treatment Countermeasure salt/fluid (1= yes, 0=no)
ID Person id
56 spaghettiogram
References
Altman, Practical statistics for medical research, Page 223, Ex. 9.1. Bungo et.al., 1985
Examples
data(SpaceT)
spaghettiogram Spaghettiogram
Description
A spaghettiogram is showing repeated measures (longitudinal data)
Usage
spaghettiogram(
formula,
data,
xlim,
ylim,
xlab = "",
ylab = "",
axes = TRUE,
col,
lwd,
lty,
pch,
legend = FALSE,
add = FALSE,
background = TRUE,
...
)
Arguments
formula A formula which specifies the variables for the spaghettiograms. If Y ~ X +
id(Z) then for each value of Z the spaghettiogram is the graph (X,Y) in the
subset defined by the value of Z. Data are expected to be in the "long" format. Y
is a numeric vector and X is a factor whose levels define the X-axis. Each level
of the id-vector corresponds to one line (spaghetti) in the plot.
data data set in which variables X, Y and Z are defined.
xlim Limits for x-axis
ylim Limits for y-axis
xlab Label for x-axis
specialFrame 57
ylab Label for x-axis

axes Logical indicating if axes should be drawn.
col Colors for the spaghettiograms
lwd Widths for the spaghettiograms
lty Type for the spaghettiograms
pch Point-type for the spaghettiograms
legend If TRUE add a legend. Argument A of legend is controlled as legend.A. E.g.,
when legend.cex=2 legend will be called with argument cex=2.
add If TRUE add to existing plot device.
background Control the background color of the graph.
... used to transport arguments which are passed to the following subroutines: "plot",
"lines", "legend", "background", "axis1", "axis2".
Value
List with data of each subject
Examples
data(SpaceT)
Spaghettiogram(HR~Status+id(ID),
data=SpaceT)
specialFrame Special frame
Description
Extract data and design matrix including specials from call
Usage
specialFrame(
formula,
data,
unspecials.design = TRUE,
specials,
specials.factor = TRUE,
specials.design = FALSE,
strip.specials = TRUE,
strip.arguments = NULL,
strip.alias = NULL,
strip.unspecials = NULL,
drop.intercept = TRUE,
response = TRUE,
na.action = options()$na.action
)
58 specialFrame
Arguments
formula Formula whose left hand side specifies the event history, i.e., either via Surv()
or Hist().
data Data frame in which the formula is interpreted
unspecials.design
Passed as is to model.design.
specials Character vector of special function names. Usually the body of the special
functions is function(x)x but e.g., strata from the survival package does treat
the values
specials.factor
Passed as is to model.design.
specials.design
Passed as is to model.design
strip.specials Passed as specials to strip.terms
strip.arguments
Passed as arguments to strip.terms
strip.alias Passed as alias.names to strip.terms
strip.unspecials
Passed as unspecials to strip.terms
drop.intercept Passed as is to model.design
response If FALSE do not get response data.
na.action Decide what to do with missing values.
Details
Obtain a list with the data used for event history regression analysis. This function cannot be used
directly on the user level but inside a function to prepare data for survival analysis.
Value
A list which contains - the response - the design matrix (see model.design) - one entry for each
special (see model.design)
Author(s)
See Also
model.frame model.design Hist

splinePlot.lrm 59
Examples
## Here are some data with an event time and no competing risks
## and two covariates X1 and X2.
## Suppose we want to declare that variable X1 is treated differently
## than variable X2. For example, X1 could be a cluster variable, or
## X1 should have a proportional effect on the outcome.
d <- data.frame(y=1:7,
X2=c(2.24,3.22,9.59,4.4,3.54,6.81,5.05),
X3=c(1,1,1,1,0,0,1),
X4=c(44.69,37.41,68.54,38.85,35.9,27.02,41.84),
X1=factor(c("a","b","a","c","c","a","b"),
levels=c("c","a","b")))
## define special functions prop and cluster
prop <- function(x)x
cluster <- function(x)x
## We pass a formula and the data
e <- specialFrame(y~prop(X1)+X2+cluster(X3)+X4,
data=d,
specials=c("prop","cluster"))
## The first element is the response
e$response
## The other elements are the design, i.e., model.matrix for the non-special covariates
e$design
## and a data.frame for the special covariates
e$prop
## The special covariates can be returned as a model.matrix
e2 <- specialFrame(y~prop(X1)+X2+cluster(X3)+X4,
data=d,
specials=c("prop","cluster"),
specials.design=TRUE)
e2$prop
## and the non-special covariates can be returned as a data.frame
e3 <- specialFrame(y~prop(X1)+X2+cluster(X3)+X4,
data=d,
specials=c("prop","cluster"),
specials.design=TRUE,
unspecials.design=FALSE)
e3$design
splinePlot.lrm Plot predictions of logistic regression
Description
Plotting the prediction of a logistic regression model with confidence bands against one continuous
variable.
60 splinePlot.lrm
Usage
splinePlot.lrm(
object,
xvar,
xvalues,
xlim = range(xvalues),
ylim,
xlab = xvar,
ylab = scale[[1]],
col = 1,
lty = 1,
lwd = 3,
confint = TRUE,
newdata = NULL,
scale = c("risk", "odds"),
add = FALSE,
...
)
Arguments
object Logistic regression model fitted with rms::lrm
xvar Name of the variable to show on x-axis
xvalues Sequence of xvar values
xlim x-axis limits
ylim y-axis limits
xlab x-axis labels
ylab y-axis labels
col color of the line
lty line style
lwd line width
confint Logical. If TRUE show confidence shadows
newdata How to adjust
scale Character string that determines the outcome scale (y-axis). Choose between
"risk" and "odds".
add Logical. If TRUE add lines to an existing graph
... Further arguments passed to plot. Only if add is FALSE.
Details
Function which extracts from a logistic regression model fitted with rms::lrm the predicted risks
or odds.
stripes 61
Author(s)
Examples
data(Diabetes)
Diabetes$hypertension= 1*(Diabetes$bp.1s>140)
library(rms)
uu <- datadist(Diabetes)
options(datadist="uu")
fit=lrm(hypertension~rcs(age)+gender+hdl,data=Diabetes)
splinePlot.lrm(fit,xvar="age",xvalues=seq(30,50,1))
stripes Background and grid color control.
Description
Some users like background colors, and it may be helpful to have grid lines to read off e.g. proba-
bilities from a Kaplan-Meier graph. Both things can be controlled with this function. However, it
mainly serves plot.prodlim.
Usage
stripes(
xlim,
ylim,
col = "white",
lwd = 1,
gridcol = "gray77",
fill = "white",
horizontal = NULL,
vertical = NULL,
border = "black",
xpd = FALSE
)
Arguments
xlim Limits for the horizontal x-dimension. Defaults to par("usr")[1:2].
ylim Limits for the vertical y-dimension.
col Colors use for the stripes. Can be a vector of colors which are then repeated
appropriately.
lwd Line width
gridcol Color of grid lines
fill Color to fill the background rectangle given by par("usr").
62 subgroupAnalysis
horizontal Numerical values at which to show horizontal grid lines, and at which to change
the color of the stripes.
vertical Numerical values at which to show vertical grid lines.
border If a fill color is provided, the color of the border around the background.
xpd From help(par): A logical value or NA. If FALSE, all plotting is clipped to
the plot region, if TRUE, all plotting is clipped to the figure region, and if NA,
all plotting is clipped to the device region. See also clip.
Author(s)
Examples
plot(0,0)
backGround(bg="beige",fg="red",vertical=0,horizontal=0)
plot(0,0)
stripes(col=c("yellow","green"),gridcol="red",xlim=c(-1,1),horizontal=seq(0,1,.1))
stripes(col=c("yellow","green"),gridcol="red",horizontal=seq(0,1,.1))
subgroupAnalysis Subgroup Analysis - Interactions and estimates
Description
The function can examine Cox regression, logistic regression and Poisson regression (Poisson re-
gression for survival analysis) where the effect of one variable is of particular interest. This function
systematically checks for effect modification with a list of other variables.
In randomised studies the main regression analysis is often univariate and includes only the exposure
of interest. In observational studies the main regression analysis can readily be adjusted for other
variables including those which may modify the effect of the variable of interest.
Usage
subgroupAnalysis(object,data,treatment,
subgroups, confint.method="default",factor.reference="extraline")
Arguments
object - glm, coxph or cph object for which subgroups should be analyzed.
data - Dataset including all relevant variables
treatment - Must be numeric - 0/1
subgroupAnalysis 63
subgroups - A vector of variable names presenting the factor variables where subgroups
should be formed. These variables should all be "factors"
confint.method "default" creates Wald type confidence interval, "robust", creates creates robust
standard errors - see regressionTable function.
factor.reference
"extraline" creates an extraline for the reference, "inline" avoids this line.
Details
The function can only handle a bivariate treatment, which MUST coded as zero or one. The p-value
for interaction is obtained with a likelihood ratio test comparing the main regression analysis with
the interaction model.
There are plot and print functions available for the function see helppages for plot.subgroupAnalysis
and print.subgroupAnalysis
Value
A data.frame with subsgroup specifications, number in each subgroup, parameter estimates and
p-value for interaction. A forest plot can be obtained with "plotConfidence".
Author(s)
See Also
coxph, glm, plotConfidence
Examples
#load libraries
library(data.table)
library(Publish)
library(survival)
data.table::setDT(traceR)
labels=c("slim","fat")))]
traceR[,sex:=as.factor(sex)] # all subgroup variables needs to be factor
traceR[observationTime==0,observationTime:=1]
# remove missing covariate values
traceR=na.omit(traceR)
# univariate analysis of smoking in subgroups of age and sex
# Main regression analysis is a simple/univariate Cox regression
subgroups=c("smoking","sex","wmi2","abd2"))
sub_cox
64 summary.ci
# to see how the results are obtained consider the variable: smoking
fit_cox_smoke <- coxph(Surv(observationTime,dead)~treatment*smoking,data=traceR)
# the last three rows of the following output:
publish(fit_cox_smoke)
# are included in the first 3 rows of the result of the sub group analysis:
sub_cox[1:3,]
# the p-value is obtained as:
fit_cox_smoke_add <- coxph(Surv(observationTime,dead)~treatment+smoking,data=traceR)
anova(fit_cox_smoke_add,fit_cox_smoke,test="Chisq")
# Note that a real subgroup analysis would be to subset the data

fit_cox1a <- coxph(Surv(observationTime,dead)~treatment,data=traceR[smoking=="never"])
fit_cox1b <- coxph(Surv(observationTime,dead)~treatment,data=traceR[smoking=="current"])
fit_cox1c <- coxph(Surv(observationTime,dead)~treatment,data=traceR[smoking=="prior"])
## when the main analysis is already adjusted

fit_cox_adj <- coxph(Surv(observationTime,dead)~treatment+smoking+sex+wmi2+abd2,
data=traceR)
sub_cox_adj <- subgroupAnalysis(fit_cox_adj,traceR,treatment="treatment",
subgroups=c("smoking","sex","wmi2","abd2")) # subgroups as character string
sub_cox_adj
# When both start and end are in the Surv statement:

traceR[,null:=0]
fit_cox2 <- coxph(Surv(null,observationTime,dead)~treatment+smoking+sex+wmi2+abd2,data=traceR)
summary(regressionTable(fit_cox))
sub_cox2 <- subgroupAnalysis(fit_cox2,traceR,treatment="treatment",
subgroups=c("smoking","sex","wmi2","abd2"))
# Analysis with Poisson - and the unrealistic assumption of constant hazard
# and adjusted for age in all subgroups
fit_p <- glm(dead~treatment+age+offset(log(observationTime)),family="poisson",
data=traceR)
sub_pois <- subgroupAnalysis(fit_p,traceR,treatment="treatment",
subgroups=~smoking+sex+wmi2+abd2)
# Analysis with logistic regression - and very wrongly ignoring censoring
fit_log <- glm(dead~treatment+age,family="binomial",data=traceR)
sub_log <- subgroupAnalysis(fit_log,traceR,treatment="treatment",
subgroups=~smoking+sex+wmi2+abd2, factor.reference="inline")
summary.ci Summarize confidence intervals
Description
Summarize confidence intervals

summary.ci 65
Usage
summary(object, format = "[u;l]", se = FALSE, print = TRUE, ...)
Arguments
object Object of class ci containing point estimates and the corresponding confidence
intervals
format A string which indicates the format used for confidence intervals. The string
is passed to formatCI with two arguments: the lower and the upper limit. For
example '(l;u)' yields confidence intervals with round parenthesis in which
the upper and the lower limits are separated by semicolon.
se If TRUE add standard error.
print Logical: if FALSE do not actually print confidence intervals but just return them
invisibly.
... used to control formatting of numbers
Details
This format of the confidence intervals is user-manipulable.
Value
Formatted confidence intervals
Author(s)
See Also
ci plot.ci format.ci
Examples
library(lava)
m <- lvm(Y~X)
m <- categorical(m,Y~X,K=4)
set.seed(4)
d <- sim(m,24)
ci.mean(Y~X,data=d)
x <- summary(ci.mean(Y~X,data=d),digits=2)
x
x <- summary(ci.mean(Y~X,data=d),format="(u,l)",digits=2)
x <- summary(ci.mean(Y~X,data=d),format="(u,l)",digits=1,se=TRUE)
x <- summary(ci.mean(Y~X,data=d),format="(u,l)",digits=1,handler="format")
x <- summary(ci.mean(Y~X,data=d),format="(u,l)",digits=1,handler="prettyNum")
66 summary.regressionTable
summary.regressionTable
Formatting regression tables
Description
Preparing regression results for publication
Usage
## S3 method for class 'regressionTable'
summary(object, show.missing = "ifany", print = TRUE, ...)
Arguments
object object obtained with regressionTable or summary.regressionTable.
show.missing Decide if number of missing values are shown. Either logical or character. If
'ifany' then number missing values are shown if there are some.
print If TRUE print results.
... Used to control formatting of parameter estimates, confidence intervals and p-
values. See examples.
Value
List with two elements:
• regressionTable: the formatted regression table (a data.frame)
• rawTable: table with the unformatted values (a data.frame)
Author(s)
See Also
publish.glm publish.coxph
Examples
library(survival)
data(pbc)
fit = coxph(Surv(time,status!=0)~age+sex+edema+log(bili)+log(albumin)+log(protime),
data=pbc)
u=summary(regressionTable(fit))
u$regressionTable
u$rawTable
summary(regressionTable(fit),handler="prettyNum")
summary.subgroupAnalysis 67
summary(regressionTable(fit),handler="format")
summary(regressionTable(fit),handler="sprintf",digits=c(2,2),pValue.stars=TRUE)
summary(regressionTable(fit),handler="sprintf",digits=c(2,2),pValue.stars=TRUE,ci.format="(l,u)")
summary.subgroupAnalysis
summary.subgroupAnalysis
Description
This function operates on a "subgroupAnalysis" object to produce a formatted table.
Usage
summary(
object,
digits = 3,
eps = 0.001,
subgroup.p = FALSE,
keep.digital = FALSE,
...
)
Arguments
object - a subgroupAnalysis object
digits - number of digits for risk ratios
eps - lowest value of p to be shown exactly, others will be "<eps"
subgroup.p - present p-values for analyses in subgroups
keep.digital - prevents formatting risk ratio and confidence limits. Useful for cases when fur-
ther manipulations of rows and columns prior to adding a forest plot is relevant.
... - not currently used
Details
This function produces a formatted or unformatted table of a subgroupAnalysis object. A forest
plot can be added with the plot function.
Value
A data.frame with formatted values for subgroups
Author(s)
68 summary.univariateTable
See Also
subgroupAnalysis
Examples
#load libraries
library(Publish)
library(survival)
library(data.table)
setDT(traceR)
labels=c("slim","fat")))]
traceR[,sex:=as.factor(sex)] # all subgroup variables needs to be factor
traceR[observationTime==0,observationTime:=1]
# univariate analysis of smoking in subgroups of age and sex
# Basic model from randomised study - but observed for 12 years
subgroup=c("smoking","sex","wmi2","abd2")) # subgroups as character string
summary(sub_cox)
summary.univariateTable
Preparing univariate tables for publication
Description
Summary function for univariate table
Usage
## S3 method for class 'univariateTable'
summary(
object,
n = "inNames",
drop.reference = FALSE,
pvalue.stars = FALSE,
pvalue.digits = 4,
show.missing = c("ifany", "always", "never"),
show.pvalues,
show.totals,
...
)
summary.univariateTable 69
Arguments
object univariateTable object as obtained with function univariateTable.
n If not missing, show the number of subjects in each column. If equal to "inNames",
show the numbers in parentheses in the column names. If missing the value
object$n is used.
drop.reference Logical or character (vector). Decide if line with reference level should be sup-
pressed for factors. If TRUE or "all" suppress for all categorical factors. If
'binary' suppress only for binary variables. Can be character vector in which
case reference lines are suppressed for variables that are included in the vector.
pvalue.stars If TRUE use symnum to parse p-values otherwise use format.pval.
pvalue.digits Passed to format.pval.
show.missing Decides if number of missing values are shown in table. Defaults to "ifany",
and can also be set to "always" or "never".
show.pvalues Logical. If set to FALSE the column p-values is removed. If missing the value
object$compare.groups[[1]]==TRUE is used.
show.totals Logical. If set to FALSE the column Totals is removed. If missing the value
object$show.totals is used.
... passed on to labelUnits. This overwrites labels stored in object$labels
Details
Collects results of univariate table in a matrix.
Value
Summary table
Author(s)
Examples
data(Diabetes)
u <- univariateTable(gender~age+location+Q(BMI)+height+weight,
data=Diabetes)
summary(u)
summary(u,n=NULL)
summary(u,pvalue.digits=2,"age"="Age (years)","height"="Body height (cm)")
u2 <- univariateTable(location~age+AgeGroups+gender+height+weight,
data=Diabetes)
summary(u2)
summary(u2,drop.reference=TRUE)
## same but more flexible
summary(u2,drop.reference=c("binary"))
## same but even more flexible
summary(u2,drop.reference=c("gender"))
70 sutable
sutable Fast summary of a univariate table
Description
First apply univariateTable then call summary.
Usage
sutable(...)
Arguments
... Unnamed arguments and are passed to univariateTable as well as named ar-
guments that match univariateTable’s arguments, other arguments are passed
to summary.univariateTable
Value
Summary table
Author(s)
See Also
summary.univariateTable univariateTable
Examples
data(Diabetes)
sutable(gender~age+location+Q(BMI)+height+weight,data=Diabetes,BMI="Body mass index (kg/m^2)")
table2x2 71
table2x2 2x2 table calculus for teaching
Description
2x2 table calculus for teaching
Usage
table2x2(
x,
digits = 1,
stats = c("table", "rd", "rr", "or", "chisq", "fisher")
)
Arguments
x 2x2 table
digits rounding digits
stats subset or all of c("table","rd","or","rr","chisq","fisher") where rd=
risk difference, rr = risk ratio, or = odds ratio, chisq = chi-square test, fisher=
fisher’s exact test and table = the 2x2 table
Details
2x2 table calculus for teaching
Value
see example
Author(s)
Examples
table2x2(table("marker"=rbinom(100,1,0.4),"response"=rbinom(100,1,0.1)))
table2x2(matrix(c(71,18,38,8),ncol=2),stats="table")
table2x2(matrix(c(71,18,38,8),ncol=2),stats=c("rr","fisher"))
72 trace
trace trace data
Description
These data are from screening to the TRACE study, a comparison between the angiotensin convert-
ing enzyme inhibitor trandolapril and placebo ford large myocardial infarctions. A total of 6676
patients were screened for the study. Survival has been followed for the screened population for 16
years. The current data has been prepared for a poisson regression to examine survival. The data
has been "split" in 0.5 year intervals (plitLexis function from Epi package) and then collapsed on
all variables (aggregate function).
Format
Time Time after myocardial infarction, in 6 months intervals

smoking Smoking status. A factor with levels (Never, Current, Previous)
sex A factor with levels (Female, Male)
age Age in years at the time of myocardial infarction
ObsTime Cumulative risk time in each split
dead Count of deaths
References
Kober et al 1995 Am. J. Cardiol 76,1-5
Examples
data(trace)
Units(trace,list("age"="years"))
summary(rtf)
publish(fit)
traceR 73
traceR traceR data
Description
These data are from the TRACE randomised trial, a comparison between the angiotensin converting
enzyme inhibitor trandolapril and placebo ford large myocardial infarctions. In all, 1749 patients
were randomised. The current data are from a 15 year follow-up.
Format
A data frame with 1749 observations on the following variables.
weight Weight in kilo

height Height in meters
abdominalCircumference in centimeters
seCreatinine in mmol per liter
wallMotionIndex left ventricular function 0-2, 0 worst, 2 normal
observationTime time to death or censor
age age in years
sex 0=female,1=male
smoking 0=never,1=prior,2=current
dead 0=censor,1=dead
treatment placebo or trandolapril
References
Kober et al 1995 NEJM 333,1670
Examples
data(trace)
Units(trace,list("age"="years"))
summary(rtf)
publish(fit)
74 univariateTable
Units Add units to data set
Description
Add variable units to data.frame (or data.table).
Usage
Units(object, units)
Arguments
object A data.frame or data.table
units Named list of units. Names are variable names. If omitted, show existing units.
Details
If the object has units existing units are replaced by given units.
Value
The object augmented with attribute "units"
Author(s)
Examples
data(Diabetes)
Diabetes <- Units(Diabetes,list(BMI="kg/m^2"))
Units(Diabetes)
Diabetes <- Units(Diabetes,list(bp.1s="mm Hg",bp.2s="mm Hg"))
Units(Diabetes)
univariateTable Univariate table
Description
Categorical variables are summarized using counts and frequencies and compared .
univariateTable 75
Usage
univariateTable(
formula,
data = parent.frame(),
summary.format = "mean(x) (sd(x))",
Q.format = "median(x) [iqr(x)]",
freq.format = "count(x) (percent(x))",
column.percent = TRUE,
digits = c(1, 1, 3),
big.mark = ",",
short.groupnames,
compare.groups = TRUE,
show.totals = TRUE,
n = "inNames",
outcome = NULL,
...
)
Arguments
formula Formula specifying the grouping variable (strata) on the left hand side (can be
omitted) and on the right hand side the variables for which to obtain (descriptive)
statistics.
data Data set in which formula is evaluated
summary.format Format for the numeric (non-factor) variables. Default is mean (SD). If differ-
ent formats are desired, either special Q can be used or the function is called
multiple times and the results are rbinded. See examples.
Q.format Format for quantile summary of numerical variables: Default is median (inter
quartile range).
freq.format Format for categorical variables. Default is count (percentage).
column.percent Logical, if TRUE and the default freq.format is used then column percentages are
given instead of row percentages for categorical variables (factors).
digits Number of digits
big.mark For formatting large numbers (i.e., greater than 1,000). "" turn this off.
short.groupnames
If TRUE group names are abbreviated.
compare.groups Method used to compare groups. If "logistic" and there are exactly two
groups logistic regression is used instead of t-tests and Wilcoxon rank tests to
compare numeric variables across groups.
show.totals If TRUE show a column with totals.
n If TRUE show the number of subjects as a separate row. If equal to "inNames",
show the numbers in parentheses in the column names. If FALSE do not show
number of subjects.
outcome Outcome data used to calculate p-values when compare groups method is 'logistic'
or 'cox'.
... saved as part of the result to be passed on to labelUnits
76 univariateTable
Details
This function can generate the baseline demographic characteristics that forms table 1 in many
publications. It is also useful for generating other tables of univariate statistics.
The result of the function is an object (list) which containe the various data generated. In most
applications the summary function should be applied which generates a data.frame with a (nearly)
publication ready table. Standard manipulation can be used to modify, add or remove columns/rows
and for users not accustomed to R the table generated can be exported to a text file which can be
read by other software, e.g., via write.csv(table,file="path/to/results/table.csv")
By default, continuous variables are summarized by means and standard deviations and compared
with t-tests. When continuous variables are summarized by medians and interquartile ranges the De-
viations from the above defaults are obtained when the arguments summary.format and freq.format
are combined with suitable summary functions.
Value
List with one summary table element for each variable on the right hand side of formula. The
summary tables can be combined with rbind. The function summary.univariateTable combines
the tables, and shows p-values in custom format.
Author(s)
Thomas A. Gerds
See Also
summary.univariateTable, publish.univariateTable
Examples
data(Diabetes)
library(data.table)
univariateTable(~age,data=Diabetes)
univariateTable(~gender,data=Diabetes)
univariateTable(~age+gender+ height+weight,data=Diabetes)
## same thing but less typing
utable(~age+gender+ height+weight,data=Diabetes)
## summary by location:
univariateTable(location~Q(age)+gender+height+weight,data=Diabetes)
## continuous variables marked with Q() are (by default) summarized
## with median (IQR) and kruskal.test (with two groups equivalent to wilcox.test)
## variables not marked with Q() are (by default) summarized
## with mean (sd) and anova.glm(...,test="Chisq")
## the p-value of anova(glm()) with only two groups is similar
## but not exactly equal to that of a t.test
## categorical variables are (by default) summarized by count
## (percent) and chi-square tests (\code{chisq.test}). When \code{compare.groups ='logistic'}
## anova(glm(...,family=binomial,test="Chisq")) is used to calculate p-values.
## export result to csv

univariateTable 77
table1 = summary(univariateTable(location~age+gender+height+weight,data=Diabetes),
show.pvalues=FALSE)
# write.csv(table1,file="~/table1.csv",rownames=FALSE)
## change labels and values

utable(location~age+gender+height+weight,data=Diabetes,
age="Age (years)",gender="Sex",
gender.female="Female",
gender.male="Male",
height="Body height (inches)",
weight="Body weight (pounds)")
## Use quantiles and rank tests for some variables and mean and standard deviation for others
univariateTable(gender~Q(age)+location+Q(BMI)+height+weight,
data=Diabetes)
## Factor with more than 2 levels

Diabetes$AgeGroups <- cut(Diabetes$age,
c(19,29,39,49,59,69,92),
include.lowest=TRUE)
univariateTable(location~AgeGroups+gender+height+weight,
data=Diabetes)
## Row percent
univariateTable(location~gender+age+AgeGroups,
data=Diabetes,
column.percent=FALSE)
## change of frequency format

univariateTable(location~gender+age+AgeGroups,
data=Diabetes,
column.percent=FALSE,
freq.format="percent(x) (n=count(x))")
## changing Labels
u <- univariateTable(location~gender+AgeGroups+ height + weight,
data=Diabetes,
column.percent=TRUE,
freq.format="count(x) (percent(x))")
summary(u,"AgeGroups"="Age (years)","height"="Height (inches)")
## more than two groups

Diabetes$frame=factor(Diabetes$frame,levels=c("small","medium","large"))
univariateTable(frame~gender+BMI+age,data=Diabetes)
Diabetes$sex=as.numeric(Diabetes$gender)
univariateTable(frame~sex+gender+BMI+age,
data=Diabetes,freq.format="count(x) (percent(x))")
## multiple summary formats

## suppose we want for some reason mean (range) for age
## and median (range) for BMI.
## method 1:
78 univariateTable
univariateTable(frame~Q(age)+BMI,
data=Diabetes,
Q.format="mean(x) (range(x))",
summary.format="median(x) (range(x))")
## method 2:
u1 <- summary(univariateTable(frame~age,
data=na.omit(Diabetes),
summary.format="mean(x) (range(x))"))
u2 <- summary(univariateTable(frame~BMI,
data=na.omit(Diabetes),
summary.format="median(x) (range(x))"))
publish(rbind(u1,u2),digits=2)
## Large number format (big.mark)

Diabetes$AGE <- 1000*Diabetes$age
u3 <- summary(univariateTable(frame~AGE,
data=Diabetes,big.mark="'"))
Index
∗ datasets print.table2x2, 34
CiTable, 7 print.univariateTable, 35
Diabetes, 9 pubformat, 35
trace, 72 publish, 36
traceR, 73 Publish-package, 3
∗ survival publish.CauseSpecificCox, 37
stripes, 61 publish.ci, 38
publish.coxph, 39
acut, 3 publish.glm, 41
anova.coxph, 12 publish.htest, 43
publish.matrix, 44, 49
ci.mean, 6
publish.MIresult, 46
ci.mean.default, 6
publish.riskRegression, 49
CiTable, 7
publish.Score, 50
coxphSeries, 8
publish.summary.aov, 51
Diabetes, 9 publish.survdiff, 52
fixRegressionTable, 10 regressionTable, 53
followupTable, 11
formatCI, 12, 39, 65 segments, 27
SpaceT, 55
glmSeries, 14 Spaghettiogram (spaghettiogram), 56
spaghettiogram, 56
labelUnits, 15 specialFrame, 57
lazyDateCoding, 16 splinePlot.lrm, 59
lazyFactorCoding, 17 strata, 58
model.design, 58 strip.terms, 58
stripes, 61
org, 18 subgroupAnalysis, 62
summary.ci, 64
parseInteractionTerms, 18 summary.regressionTable, 66
plot.ci, 20 summary.subgroupAnalysis, 67
plot.prodlim, 61 summary.univariateTable, 68
plot.regressionTable, 22 sutable, 70
plot.subgroupAnalysis, 23
plotConfidence, 24 table2x2, 71
print.ci, 32 trace, 72
print.subgroupAnalysis, 33 traceR, 73
print.summary.regressionTable
(summary.regressionTable), 66 Units, 74
79
80 INDEX
univariateTable, 74
utable, 12
utable (univariateTable), 74

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Package ‘Publish’

Publish-package Publish package

acut Automatic selection and formatting of breaks in cut

format.low string used specifically on the lowest label.

## The default uses format similar to cut

## The formatting can easily be changed

## Manually setting format and breaks

BMI.groups <- acut(Diabetes$BMI,

## Instead of using the quantiles, we can specify equally spaced breaks,

## This can be changes with the breaks argument.

## Of course We can also supply the breaks manually.

ci.mean Compute mean values with confidence intervals

ci.mean.default Compute mean values with confidence intervals

CiTable CiTable data

coxphSeries Run a series of Cox regression models

coxphSeries(formula, data, vars, ...)

matrix with results

Thomas Alexander Gerds

## control the logistic regression analyses for age and gender

Diabetes Diabetes data of Dr John Schorling

weight.europe weight (kg)

fixRegressionTable Expand regression coefficient table

followupTable Summary tables for a given followup time point.

formatCI Formatting confidence intervals

# change of handler function

glmSeries Run a series of generalized linear regression analyses

## pass labels immediately to utable

## sometimes useful to state explicitly which variables value

lazyDateCoding Efficient coding of date variables

lazyFactorCoding Efficient coding of factor levels

org Wrapper function for publish with output format org

Wrapper for publish(...,org=TRUE)

x object to format as org

Thomas Alexander Gerds

parseInteractionTerms Parse interaction terms

Parse interaction terms for regression tables

terms Terms of a formula

List of contrasts which can be passed to lava::estimate.

Thomas A. Gerds <tag@biostat.ku.dk>

tt2 <- terms(formula(SBP~age*factor(sex)+BMI))

plot.ci Plot confidence intervals

Function to plot confidence intervals

## S3 method for class 'ci'

plot.regressionTable Plotting regression coefficients with confidence limits

## S3 method for class 'subgroupAnalysis'

plotConfidence Plot confidence intervals

## A first draft version of the plot is obtained as follows

## if argument labels is a named list the table is subdivided:

## The graph consist of at most three columns:

## The relative size of the columns needs to be controlled manually

## The actual size of the current graphics device determines

## Another good news is that all figures can be controlled separately

## More control of the x-axis and confidence intervals that

## Controlling the labels and their titles

## For factor reference groups, one may want to replace the

## changing the style of the graphical confidence intervals

## Finally, vertical columns can be delimited with background color

threegreens <- c(prodlim::dimColor("green",density=55),