Epi: A Package for Statistical Analysis in Epidemiology

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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 multistate 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 some epidemiological datasets.

Author
Bendix Carstensen [aut, cre], Martyn Plummer [aut], Esa Laara [ctb], Michael Hills [ctb]
Date of publication
2016-10-02 09:22:48
Maintainer
Bendix Carstensen <bxc@steno.dk>
License
GPL-2
Version
2.6
URLs

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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
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
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...
fit.add
Fit an addive excess risk model to interval censored data.
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
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)
plot.Lexis
Lexis diagrams
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
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

Files in this package

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