Epi: A Package for Statistical Analysis in Epidemiology
Version 2.12

Functions for demographic and epidemiological analysis in the Lexis diagram, i.e. register and cohort follow-up data, in particular representation, manipulation and simulation of multi state data - the Lexis suite of functions, which includes interfaces to 'mstate', 'etm' and 'cmprsk' packages. Also contains functions for Age-Period-Cohort and Lee-Carter modeling and a function for interval censored data and some useful functions for tabulation and plotting, as well as a number of epidemiological data sets.

Browse man pages Browse package API and functions Browse package files

AuthorBendix Carstensen [aut, cre], Martyn Plummer [aut], Esa Laara [ctb], Michael Hills [ctb]
Date of publication2017-04-16 10:57:29 UTC
MaintainerBendix Carstensen <b@bxc.dk>
LicenseGPL-2
Version2.12
URL http://BendixCarstensen.com/Epi/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("Epi")

Man pages

apc.fit: Fit an Age-Period-Cohort model to tabular data.
apc.frame: Produce an empty frame for display of parameter-estimates...
apc.LCa: Fit Age-Period-Cohort models and Lee-Carter models with...
bdendo: A case-control study of endometrial cancer
bdendo11: A 1:1 subset of the endometrial cancer case-control study
B.dk: Births in Denmark by year and month of birth and sex
births: Births in a London Hospital
blcaIT: Bladder cancer mortality in Italian males
boxes.MS: Draw boxes and arrows for illustration of multistate models.
brv: Bereavement in an elderly cohort
cal.yr: Functions to convert character, factor and various date...
ccwc: Generate a nested case-control study
ci.cum: Compute cumulative sum of estimates.
ci.lin: Compute linear functions of parameters with standard errors...
ci.pd: Compute confidence limits for a difference of two independent...
clogistic: Conditional logistic regression
contr.cum: Contrast matrices
crr.Lexis: Fit a competing risks regression model (Fine-Gray model)...
cutLexis: Cut follow-up at a specified date for each person.
detrend: Projection of a model matrix on to the orthogonal complement...
diet: Diet and heart data
DMconv: Conversion to diabetes
DMepi: Epidmiological rates for diabetes in Denmark 1996-2015
DMlate: The Danish National Diabetes Register.
effx: Function to calculate effects
effx.match: Function to calculate effects for individually matched...
erl: Compute survival functions from rates and expected residual...
ewrates: Rates of lung and nasal cancer mortality, and total...
expand.data: Function to expand data for regression analysis of interval...
fit.add: Fit an addive excess risk model to interval censored data.
fit.baseline: Fit a piecewise contsnt intesity model for interval censored...
fit.mult: Fits a multiplicative relative risk model to interval...
float: Calculate floated variances
foreign.Lexis: Create a data structures suitable for use with packages...
ftrend: Fit a floating trend to a factor in generalized linear model
gen.exp: Generate covariates for drug-exposure follow-up from drug...
gmortDK: Population mortality rates for Denmark in 5-years age groups.
hivDK: hivDK: seroconversion in a cohort of Danish men
Icens: Fits a regression model to interval censored data.
LCa.fit: Fit Lee-Carter-type models for rates to arbitrarily shaped...
lep: An unmatched case-control study of leprosy incidence
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.
lls: Functions to manage and explore the workspace
lungDK: Male lung cancer incidence in Denmark
mcutLexis: Cut follow-up at multiple event dates and keep track of order...
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.
N2Y: Create risk time ("Person-Years") in Lexis triangles from...
NArray: Set up an array of NAs, solely from the list of dimnames
ncut: Function to group a variable in intervals.
N.dk: Population size in Denmark
nice: Nice breakpoints
nickel: A Cohort of Nickel Smelters in South Wales
Ns: Natural splines - (cubic splines linear beyond outermost...
occup: A small occupational cohort
pc.lines: Plot period and cohort effects in an APC-frame.
pctab: Create percentages in a table
plot.apc: Plot the estimates from a fitted Age-Period-Cohort model
plotEst: Plot estimates with confidence limits (forest plot)
plotevent: Plot Equivalence Classes
plot.Lexis: Lexis diagrams
projection.ip: Projection of columns of a matrix.
rateplot: Functions to plot rates from a table classified by age and...
rbind.Lexis: Combining a Lexis objects with data frames or other Lexis...
Relevel: Reorder and combine levels of a factor
rm.tr: Remove transitions from a Lexis object.
ROC: Function to compute and draw ROC-curves.
simLexis: Simulate a Lexis object representing follow-up in a...
splitLexis: Split follow-up time in a Lexis object
stack.Lexis: Functions to facilitate analysis of multistate models.
start.Lexis: Time series methods for Lexis objects
stattable: Tables of summary statistics
stattable.funs: Special functions for use in stat.table
S.typh: Salmonella Typhimurium outbreak 1996 in Denmark.
subset.Lexis: Subsetting Lexis (and stacked.Lexis) objects
summary.Lexis: Summarize transitions and risk time from a Lexis object
Termplot: A wrapper for 'termplot' that optionally (but by default)...
testisDK: Testis cancer incidence in Denmark, 1943-1996
thoro: Thorotrast Study
time.band: Extract time band data from a split Lexis object
time.scales: The time scales of a Lexis object
transform.Lexis: Transform a Lexis (or stacked.Lexis) objects
twoby2: Analysis of a two by two table
Y.dk: Population risk time in Denmark

Functions

hivDK Man page
Aplot Man page Source code
B.dk Man page
COEF Source code
COEF.MIresult Source code
COEF.crr Source code
COEF.default Source code
COEF.lme Source code
COEF.lmerMod Source code
COEF.mer Source code
COEF.mipo Source code
COEF.polr Source code
Cplot Man page Source code
DMconv Man page
DMepi Man page
DMlate Man page
DMrand Man page
Icens Man page Source code
LCa.fit Man page Source code
Lexis Man page Source code
Lexis.diagram Man page Source code
Lexis.lines Man page Source code
Life.lines Man page Source code
M.dk Man page
N.dk Man page
N2Y Man page Source code
NArray Man page Source code
Ns Man page Source code
PY.ann Man page Source code
PY.ann.Lexis Man page Source code
Pplot Man page Source code
ROC Man page Source code
ROC.tic Source code
Relevel Man page Source code
Relevel.Lexis Man page
Relevel.factor Man page
S.typh Man page
Termplot Man page Source code
VCOV Source code
VCOV.MIresult Source code
VCOV.crr Source code
VCOV.default Source code
VCOV.gnlm Source code
VCOV.lme Source code
VCOV.lmerMod Source code
VCOV.mer Source code
VCOV.mipo Source code
VCOV.rq Source code
Wald Man page Source code
Y.dk Man page
ZArray Man page Source code
[.Lexis Man page
apc.LCa Man page Source code
apc.fit Man page Source code
apc.frame Man page Source code
apc.lines Man page
apc.plot Man page
array.subset Source code
as.Date.cal.yr Man page Source code
bdendo Man page
bdendo11 Man page
births Man page
blcaIT Man page
boxarr Man page Source code
boxes Man page Source code
boxes.Lexis Man page Source code
boxes.MS Man page Source code
boxes.matrix Man page Source code
breaks Man page Source code
brv Man page
cal.yr Man page Source code
cbind.Lexis Man page Source code
ccwc Man page Source code
check.time.scale Source code
chop.lex Source code
ci.cum Man page Source code
ci.exp Man page Source code
ci.lin Man page Source code
ci.mat Man page Source code
ci.pd Man page Source code
ci.pred Man page Source code
ci.ratio Man page Source code
clear Man page Source code
clogistic Man page Source code
coef.clogistic Source code
contr.2nd Man page Source code
contr.cum Man page Source code
contr.diff Man page Source code
contr.orth Man page Source code
count Man page Source code
countLexis Man page Source code
cp.lines Man page
cp.matlines Man page
cp.matpoints Man page
cp.points Man page
crr.Lexis Man page Source code
cutLexis Man page Source code
dbox Man page Source code
detrend Man page Source code
diet Man page
doCutLexis Source code
dur Man page Source code
effx Man page Source code
effx.match Man page Source code
entry Man page Source code
erl Man page Source code
erl1 Man page Source code
etm Man page Source code
etm.Lexis Man page Source code
etm.data.frame Source code
ewrates Man page
exit Man page Source code
expand.data Man page Source code
factorize Man page Source code
factorize.Lexis Man page
fillarr Man page Source code
fit.add Man page Source code
fit.baseline Man page Source code
fit.mult Man page Source code
fitClogit Source code
fixEvent Source code
float Man page
ftrend Man page
gen.exp Man page Source code
get.ests Source code
get.next Source code
gmortDK Man page
interp Source code
is.Lexis Source code
isInformative Source code
larray Source code
lep Man page
levels.Lexis Man page Source code
lines.Lexis Man page Source code
lines.Lexis.1D Source code
lines.Lexis.2D Source code
lines.apc Man page
lines.pState Man page Source code
linesEst Man page
lint Source code
lls Man page
lungDK Man page
match.cut Source code
mcutLexis Man page Source code
merge.Lexis Man page Source code
merge.data.frame Man page Source code
mh Man page Source code
mh.power Source code
model.terms Source code
mortDK Man page
msdata Man page Source code
msdata.Lexis Man page Source code
nState Man page Source code
ncut Man page Source code
nice Man page Source code
nickel Man page
ns.ld Source code
occup Man page
pState Man page Source code
pc.lines Man page
pc.matlines Man page
pc.matpoints Man page
pc.points Man page
pctab Man page Source code
percent Man page Source code
plot.LCa Man page Source code
plot.Lexis Man page Source code
plot.Lexis.1D Source code
plot.Lexis.2D Source code
plot.apc Man page
plot.pState Man page Source code
plotEst Man page Source code
plotevent Man page Source code
points.Lexis Man page Source code
points.Lexis.1D Source code
points.Lexis.2D Source code
pointsEst Man page
predict.LCa Man page Source code
pretty.print.stattable.1d Source code
pretty.print.stattable.2d Source code
print.Icens Man page Source code
print.LCa Man page Source code
print.clogistic Source code
print.floated Man page
print.mh Source code
print.stat.table Man page Source code
print.summary.Lexis Man page Source code
projection.ip Man page Source code
rateplot Man page Source code
ratio Man page Source code
rbind.Lexis Man page Source code
rm.tr Man page Source code
setStatus.default Source code
setStatus.factor Source code
setStatus.numeric Source code
show.apc.LCa Man page Source code
sim1 Source code
simLexis Man page Source code
simX Source code
split.lexis.1D Source code
split.to.width Source code
splitLexis Man page Source code
splitMatrix Source code
stack.Lexis Man page Source code
stat.table Man page Source code
status Man page Source code
std.vec Source code
steplines Source code
subset.Lexis Man page Source code
subset.stacked.Lexis Man page Source code
summary.Icens Source code
summary.LCa Man page Source code
summary.Lexis Man page Source code
surv1 Man page Source code
surv2 Man page Source code
tbox Man page Source code
testisDK Man page
thoro Man page
timeBand Man page Source code
timeScales Man page Source code
tmat Man page Source code
tmat.Lexis Man page Source code
transform.Lexis Man page Source code
transform.stacked.Lexis Man page Source code
twoby2 Man page Source code
use.amt.dpt Source code
use.only.amt Source code
valid.times Source code
vcov.clogistic Source code
wh.no Source code
yll Man page Source code

Files

inst
inst/CITATION
inst/doc
inst/doc/Follow-up.pdf
inst/doc/index.html
inst/doc/yll.pdf
inst/doc/yll.R
inst/doc/Follow-up.rnw
inst/doc/Follow-up.R
inst/doc/simLexis.pdf
inst/doc/simLexis.R
inst/doc/simLexis.rnw
inst/doc/yll.rnw
src
src/chinv2.c
src/chsolve2.c
src/cholesky2.c
src/clogit.c
src/init.c
NAMESPACE
data
data/lungDK.rda
data/diet.rda
data/lep.rda
data/hivDK.rda
data/testisDK.rda
data/S.typh.rda
data/ewrates.rda
data/blcaIT.rda
data/mortDK.rda
data/births.rda
data/bdendo11.rda
data/M.dk.rda
data/N.dk.rda
data/bdendo.rda
data/thoro.rda
data/occup.rda
data/brv.rda
data/DMepi.rda
data/Y.dk.rda
data/DMrand.rda
data/gmortDK.rda
data/B.dk.rda
data/nickel.rda
data/DMconv.rda
data/DMlate.rda
R
R/expand.data.r
R/clear.R
R/clogistic.R
R/detrend.R
R/lexis.R
R/ncut.r
R/Life.lines.R
R/twoby2.R
R/rateplot.R
R/cal.yr.R
R/splitLexis.R
R/effx.r
R/N2Y.r
R/contr.orth.R
R/stattable.R
R/factorize.R
R/apc.fit.R
R/ROC.R
R/ci.mat.R
R/effx.match.r
R/apc.frame.R
R/Ns.r
R/Termplot.R
R/foreign.R
R/contr.diff.R
R/ci.cum.R
R/plotEst.R
R/crr.Lexis.r
R/float.R
R/cutLexis.R
R/contr.2nd.R
R/boxes.MS.R
R/erl.R
R/ccwc.R
R/summary.Lexis.r
R/gen.exp.R
R/Icens.R
R/pctab.R
R/simLexis.R
R/apc.LCa.R
R/Lexis.lines.R
R/mcutLexis.R
R/Pplot.R
R/lls.R
R/mh.R
R/LCa.fit.R
R/fit.baseline.R
R/print.Icens.r
R/NArray.R
R/print.floated.R
R/ftrend.R
R/Relevel.R
R/contr.cum.R
R/ci.lin.R
R/fit.mult.r
R/Wald.R
R/plotevent.r
R/ci.pd.R
R/Cplot.R
R/rm.tr.R
R/fit.add.r
R/as.Date.cal.yr.R
R/projection.ip.r
R/Lexis.diagram.R
R/apc.plot.R
R/Aplot.R
R/stack.Lexis.R
R/summary.Icens.r
vignettes
vignettes/index.html
vignettes/Follow-up.rnw
vignettes/simLexis.rnw
vignettes/yll.rnw
MD5
build
build/vignette.rds
DESCRIPTION
man
man/Lexis.lines.Rd
man/cutLexis.Rd
man/bdendo.Rd
man/ci.cum.Rd
man/blcaIT.Rd
man/N.dk.Rd
man/lls.Rd
man/time.scales.Rd
man/pc.lines.Rd
man/Lexis.Rd
man/DMlate.Rd
man/mh.Rd
man/Y.dk.Rd
man/effx.Rd
man/lines.apc.Rd
man/mcutLexis.Rd
man/testisDK.Rd
man/stack.Lexis.Rd
man/fit.mult.Rd
man/hivDK.Rd
man/boxes.MS.Rd
man/plotEst.Rd
man/rm.tr.Rd
man/foreign.Lexis.Rd
man/splitLexis.Rd
man/cal.yr.Rd
man/nickel.Rd
man/time.band.Rd
man/Termplot.Rd
man/diet.Rd
man/ci.pd.Rd
man/subset.Lexis.Rd
man/ewrates.Rd
man/start.Lexis.Rd
man/merge.Lexis.Rd
man/simLexis.Rd
man/stattable.funs.Rd
man/thoro.Rd
man/lungDK.Rd
man/births.Rd
man/transform.Lexis.Rd
man/B.dk.Rd
man/crr.Lexis.rd
man/nice.Rd
man/occup.Rd
man/projection.ip.rd
man/S.typh.Rd
man/erl.Rd
man/pctab.Rd
man/effx.match.Rd
man/stattable.Rd
man/brv.Rd
man/rbind.Lexis.Rd
man/detrend.Rd
man/bdendo11.Rd
man/ftrend.Rd
man/ROC.Rd
man/Icens.Rd
man/Lexis.diagram.Rd
man/apc.LCa.Rd
man/fit.add.Rd
man/N2Y.Rd
man/plotevent.rd
man/Life.lines.Rd
man/float.Rd
man/gmortDK.Rd
man/M.dk.Rd
man/apc.fit.Rd
man/twoby2.Rd
man/Ns.Rd
man/apc.frame.Rd
man/mortDK.Rd
man/NArray.Rd
man/rateplot.Rd
man/contr.cum.Rd
man/summary.Lexis.rd
man/DMconv.Rd
man/DMepi.Rd
man/merge.data.frame.Rd
man/Relevel.Rd
man/ci.lin.Rd
man/fit.baseline.rd
man/plot.apc.Rd
man/lep.Rd
man/ccwc.Rd
man/clogistic.Rd
man/ncut.Rd
man/expand.data.rd
man/plot.Lexis.Rd
man/gen.exp.Rd
man/LCa.fit.Rd
CHANGES
Epi documentation built on May 19, 2017, 6:54 p.m.