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||2016-10-04 14:35:49|
|Maintainer||Bendix Carstensen <firstname.lastname@example.org>|
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