A Package for Statistical Analysis in Epidemiology

Documentation for package ‘Epi’ version 2.0

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

-- 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.
cbind.Lexis	Combining a Lexis objects with data frames or other Lexis objects
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 count 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
rbind.Lexis	Combining a Lexis objects with data frames or other Lexis objects
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

-- misc --

[.Lexis

Subsetting Lexis (and stacked.Lexis) objects