# A Package for Statistical Analysis in Epidemiology

## Documentation for package ‘Epi’ version 1.1.71

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D E F G H I L M N O P R S T W Y Z

## -- A --

apc.fit | Fit an Age-Period-Cohort model to tabular data.
apc.frame | Produce an empty frame for display of parameter-estimates from Age-Period-Cohort-models.
apc.lines | Plot APC-estimates in an APC-frame.
apc.plot | Plot the estimates from a fitted Age-Period-Cohort model
Aplot | Functions to plot rates from a table classified by age and calendar time (period)
as.Date.cal.yr | Functions to convert character, factor and various date objects into a number, and vice versa.

## -- B --

B.dk | Births in Denmark by year and month of birth and sex
bdendo | A case-control study of endometrial cancer
bdendo11 | A 1:1 subset of the endometrial cancer case-control study
births | Births in a London Hospital
blcaIT | Bladder cancer mortality in Italian males
boxarr | Draw boxes and arrows for illustration of multistate models.
boxes | Draw boxes and arrows for illustration of multistate models.
boxes.Lexis | Draw boxes and arrows for illustration of multistate models.
boxes.matrix | Draw boxes and arrows for illustration of multistate models.
boxes.MS | Draw boxes and arrows for illustration of multistate models.
breaks | Extract time band data from a split Lexis object
brv | Bereavement in an elderly cohort

## -- C --

cal.yr | Functions to convert character, factor and various date objects into a number, and vice versa.
ccwc | Generate a nested case-control study
ci.cum | Compute cumulative sum of estimates.
ci.exp | Compute linear functions of parameters with standard errors and confidence limits
ci.lin | Compute linear functions of parameters with standard errors and confidence limits
ci.mat | Compute linear functions of parameters with standard errors and confidence limits
ci.pd | Compute confidence limits for a difference of two independent proportions.
ci.pred | Compute linear functions of parameters with standard errors and confidence limits
clear | Functions to manage and explore the workspace
clogistic | Conditional logistic regression
contr.2nd | Contrast matrices
contr.cum | Contrast matrices
contr.diff | Contrast matrices
contr.orth | Contrast matrices
count | Special functions for use in stat.table
countLexis | Cut follow-up at a specified date for each person.
cp.lines | Plot period and cohort effects in an APC-frame.
cp.matlines | Plot period and cohort effects in an APC-frame.
cp.matpoints | Plot period and cohort effects in an APC-frame.
cp.points | Plot period and cohort effects in an APC-frame.
Cplot | Functions to plot rates from a table classified by age and calendar time (period)
crr.Lexis | Fit a competing risks regression model (Fine-Gray model) using a Lexis object)
cutLexis | Cut follow-up at a specified date for each person.

## -- D --

dbox | Draw boxes and arrows for illustration of multistate models.
detrend | Projection of a model matrix on to the orthogonal complement of a trend.
diet | Diet and heart data
DMconv | Conversion to diabetes
DMlate | The Danish National Diabetes Register.
DMrand | The Danish National Diabetes Register.
dur | Time series methods for Lexis objects

## -- E --

effx | Function to calculate effects
effx.match | Function to calculate effects for individually matched case-control studies
entry | Time series methods for Lexis objects
etm | Create a data structures suitable for use with packages mstate, etm.
etm.Lexis | Create a data structures suitable for use with packages mstate, etm.
ewrates | Rates of lung and nasal cancer mortality, and total mortality.
exit | Time series methods for Lexis objects
expand.data | Function to expand data for regression analysis of interval censored data.

## -- F --

factorize | Transform a Lexis (or stacked.Lexis) objects
factorize.Lexis | Transform a Lexis (or stacked.Lexis) objects
fillarr | Draw boxes and arrows for illustration of multistate models.
fit.add | Fit an addive excess risk model to interval censored data.
fit.baseline | Fit a piecewise contsnt intesity model for interval censored data.
fit.mult | Fits a multiplicative relative risk model to interval censored data.
float | Calculate floated variances
ftrend | Fit a floating trend to a factor in generalized linear model

## -- G --

gen.exp | Generate covariates for drug-exposure follow-up from drug purchase records.
gmortDK | Population mortality rates for Denmark in 5-years age groups.

## -- H --

hivDK | hivDK: seroconversion in a cohort of Danish men

## -- I --

Icens | Fits a regression model to interval censored data.

## -- L --

lep | An unmatched case-control study of leprosy incidence
levels.Lexis | Transform a Lexis (or stacked.Lexis) objects
Lexis | Create a Lexis object
Lexis.diagram | Plot a Lexis diagram
Lexis.lines | Draw life lines in a Lexis diagram.
Life.lines | Compute dates/ages for life lines in a Lexis diagram
lines.apc | Plot APC-estimates in an APC-frame.
lines.Lexis | Lexis diagrams
lines.pState | Simulate a Lexis object representing follow-up in a multistate model.
linesEst | Plot estimates with confidence limits (forest plot)
lls | Functions to manage and explore the workspace
lungDK | Male lung cancer incidence in Denmark

## -- M --

M.dk | Mortality in Denmark 1974 ff.
merge.data.frame | Merge data frame with a Lexis object
merge.Lexis | Merge a Lexis object with a data frame
mh | Mantel-Haenszel analyses of cohort and case-control studies
mortDK | Population mortality rates for Denmark in 1-year age-classes.
msdata | Create a data structures suitable for use with packages mstate, etm.
msdata.Lexis | Create a data structures suitable for use with packages mstate, etm.

## -- N --

N.dk | Population size in Denmark
N2Y | Create risk time (Person-Years) in Lexis triangles from population data.
NArray | Set up an array of NAs, solely from the list of dimnames
ncut | Function to group a variable in intervals.
nice | Nice breakpoints
nickel | A Cohort of Nickel Smelters in South Wales
Ns | Natural splines - (cubic splines linear beyond outermost knots) with convenient specification of knots and possibility of centering and detrending.
nState | Simulate a Lexis object representing follow-up in a multistate model.

## -- O --

occup | A small occupational cohort

## -- P --

pc.lines | Plot period and cohort effects in an APC-frame.
pc.matlines | Plot period and cohort effects in an APC-frame.
pc.matpoints | Plot period and cohort effects in an APC-frame.
pc.points | Plot period and cohort effects in an APC-frame.
pctab | Create percentages in a table
percent | Special functions for use in stat.table
plot.apc | Plot the estimates from a fitted Age-Period-Cohort model
plot.Lexis | Lexis diagrams
plot.pState | Simulate a Lexis object representing follow-up in a multistate model.
plotEst | Plot estimates with confidence limits (forest plot)
plotevent | Plot Equivalence Classes
points.Lexis | Lexis diagrams
pointsEst | Plot estimates with confidence limits (forest plot)
Pplot | Functions to plot rates from a table classified by age and calendar time (period)
print.floated | Calculate floated variances
print.Icens | Fits a regression model to interval censored data.
print.stat.table | Tables of summary statistics
print.summary.Lexis | Summarize transitions and risk time from a Lexis object
projection.ip | Projection of columns of a matrix.
pState | Simulate a Lexis object representing follow-up in a multistate model.
PY.ann | Lexis diagrams
PY.ann.Lexis | Lexis diagrams

## -- R --

rateplot | Functions to plot rates from a table classified by age and calendar time (period)
ratio | Special functions for use in stat.table
Relevel | Reorder and combine levels of a factor
Relevel.factor | Reorder and combine levels of a factor
Relevel.Lexis | Transform a Lexis (or stacked.Lexis) objects
ROC | Function to compute and draw ROC-curves.

## -- S --

S.typh | Salmonella Typhimurium outbreak 1996 in Denmark.
simLexis | Simulate a Lexis object representing follow-up in a multistate model.
splitLexis | Split follow-up time in a Lexis object
stack.Lexis | Functions to facilitate analysis of multistate models.
stat.table | Tables of summary statistics
status | Time series methods for Lexis objects
subset.Lexis | Subsetting Lexis (and stacked.Lexis) objects
subset.stacked.Lexis | Subsetting Lexis (and stacked.Lexis) objects
summary.Lexis | Summarize transitions and risk time from a Lexis object

## -- T --

tbox | Draw boxes and arrows for illustration of multistate models.
Termplot | A wrapper for 'termplot' that optionally (but by default) exponentiates terms, and plot them on a common log-scale. Also scales x-axes to the same physical scale.
testisDK | Testis cancer incidence in Denmark, 1943-1996
thoro | Thorotrast Study
timeBand | Extract time band data from a split Lexis object
timeScales | The time scales of a Lexis object
tmat | Functions to facilitate analysis of multistate models.
tmat.Lexis | Functions to facilitate analysis of multistate models.
transform.Lexis | Transform a Lexis (or stacked.Lexis) objects
transform.stacked.Lexis | Transform a Lexis (or stacked.Lexis) objects
twoby2 | Analysis of a two by two table

## -- W --

Wald | Compute linear functions of parameters with standard errors and confidence limits

## -- Y --

Y.dk | Population risk time in Denmark

## -- Z --

ZArray | Set up an array of NAs, solely from the list of dimnames