| AaJ.Lexis |
The Aalen-Johansen estimator of state probabilities from a multistate 'Lexis' object. |
| absorbing |
Time series and other methods for Lexis objects |
| addCov.Lexis |
Add covariates (typically clinical measurements) taken at known times to a Lexis object. |
| addDrug.Lexis |
Expand a Lexis object with information of drug exposure based on purchase dates and -amounts |
| after |
Time series and other methods for Lexis objects |
| 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.LCa |
Fit Age-Period-Cohort models and Lee-Carter models with effects modeled by natural splines. |
| 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.dk |
Births in Denmark by year and month of birth and sex |
| bdendo |
A case-control study of endometrial cancer |
| bdendo11 |
A case-control study of endometrial cancer |
| before |
Time series and other methods for Lexis objects |
| births |
Births in a London Hospital |
| blcaIT |
Bladder cancer mortality in Italian males |
| bootLexis |
Create a bootstrap sample of persons (as identified by 'lex.id') from a Lexis object |
| 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. |
| BrCa |
Clinical status, relapse, metastasis and death in 2982 women with breast cancer. |
| breaks |
Extract time band data from a split Lexis object |
| brv |
Bereavement in an elderly cohort |
| 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.Crisk |
Compute cumulative risks and expected sojourn times from models for cause-specific rates. |
| ci.cum |
Compute cumulative sum of estimates. |
| ci.eta |
Linear predictor ('eta') from a formula, coefficients, vcov and a prediction frame. |
| ci.exp |
Compute linear functions of parameters with standard errors and confidence limits, optionally transforming to a different scale. |
| ci.lin |
Compute linear functions of parameters with standard errors and confidence limits, optionally transforming to a different scale. |
| ci.mat |
Compute linear functions of parameters with standard errors and confidence limits, optionally transforming to a different scale. |
| 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, optionally transforming to a different scale. |
| ci.ratio |
Compute linear functions of parameters with standard errors and confidence limits, optionally transforming to a different scale. |
| ci.surv |
Compute cumulative sum of estimates. |
| clear |
Functions to manage and explore the workspace |
| clogistic |
Conditional logistic regression |
| coarse.Lexis |
Expand a Lexis object with information of drug exposure based on purchase dates and -amounts |
| 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. |
| coxph.Lexis |
Fit intensity models to follow-up data in Lexis objects |
| 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.matshade |
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. |
| effx |
Function to calculate effects |
| effx.match |
Function to calculate effects for individually matched case-control studies |
| entry |
Time series and other methods for Lexis objects |
| Epi |
Epi: Functions for manipulation and statistical analysis of epidemiological data |
| erl |
Compute survival functions from rates and expected residual lifetime in an illness-death model as well as years of life lost to disease. |
| erl1 |
Compute survival functions from rates and expected residual lifetime in an illness-death model as well as years of life lost to disease. |
| etm |
Create a data structures suitable for use with packages 'mstate' or 'etm'. |
| etm.Lexis |
Create a data structures suitable for use with packages 'mstate' or 'etm'. |
| ewrates |
Rates of lung and nasal cancer mortality, and total mortality. |
| exit |
Time series and other methods for Lexis objects |
| expand.data |
Function to expand data for regression analysis of interval censored data. |
| LCa.fit |
Fit Lee-Carter-type models for rates to arbitrarily shaped observations of rates in a Lexis diagram. |
| legendbox |
Draw a box with text explaining the numbers in and between boxes from 'boxes.MS' and 'boxes.Lexis' |
| lep |
An unmatched case-control study of leprosy incidence |
| levels.Lexis |
Transform a Lexis (or stacked.Lexis) object |
| Lexis |
Create a Lexis object of follow-up |
| Lexis.diagram |
Plot a Lexis diagram |
| Lexis.lines |
Draw life lines in a Lexis diagram. |
| Lexis2msm |
Convert a Lexis obejct to a data set suitable for input to the 'msm:msm' function. |
| lgrep |
Convenience versions of grep |
| 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.dk |
Mortality in Denmark 1974 ff. |
| mat2pol |
Plot columns of a matrix as stacked areas. |
| matshade |
Plot confidence intervals as shaded areas around lines. |
| mcutLexis |
Cut follow-up at multiple event dates and keep track of order of events |
| 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' or 'etm'. |
| msdata.Lexis |
Create a data structures suitable for use with packages 'mstate' or 'etm'. |
| 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. |
| ngrep |
Convenience versions of grep |
| nice |
Nice breakpoints |
| nickel |
A Cohort of Nickel Smelters in South Wales |
| nid |
Create a bootstrap sample of persons (as identified by 'lex.id') from a Lexis object |
| nid.Lexis |
Create a bootstrap sample of persons (as identified by 'lex.id') from a Lexis object |
| Ns |
Natural splines - (cubic splines linear beyond outermost knots) with convenient specification of knots and possibility of centering, detrending and clamping. |
| nState |
Simulate a Lexis object representing follow-up in a multistate model. |
| 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.matshade |
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.LCa |
Fit Lee-Carter-type models for rates to arbitrarily shaped observations of rates in a Lexis diagram. |
| plot.Lexis |
Lexis diagrams |
| plot.pState |
Simulate a Lexis object representing follow-up in a multistate model. |
| plotCIF |
Plotting Aalen-Johansen curves for competing events |
| plotEst |
Plot estimates with confidence limits (forest plot) |
| plotevent |
Plot Equivalence Classes |
| points.Lexis |
Lexis diagrams |
| pointsEst |
Plot estimates with confidence limits (forest plot) |
| poisreg |
Family Object for Poisson Regression |
| Pplot |
Functions to plot rates from a table classified by age and calendar time (period) |
| pr |
Diabetes prevance as of 2010-01-01 in Denmark |
| preceding |
Time series and other methods for Lexis objects |
| predict.LCa |
Fit Lee-Carter-type models for rates to arbitrarily shaped observations of rates in a Lexis diagram. |
| print.floated |
Calculate floated variances |
| print.Icens |
Fits a regression model to interval censored data. |
| print.LCa |
Fit Lee-Carter-type models for rates to arbitrarily shaped observations of rates in a Lexis diagram. |
| print.Lexis |
Create a Lexis object of follow-up |
| print.mh |
Mantel-Haenszel analyses of cohort and case-control studies |
| 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 |
| S.typh |
Salmonella Typhimurium outbreak 1996 in Denmark. |
| show.apc.LCa |
Fit Age-Period-Cohort models and Lee-Carter models with effects modeled by natural splines. |
| simLexis |
Simulate a Lexis object representing follow-up in a multistate model. |
| sortLexis |
Transform a Lexis (or stacked.Lexis) object |
| splitLexis |
Split follow-up time in a Lexis object |
| st2alb |
Clinical trial: Steno2 baseline and follow-up. |
| st2clin |
Clinical trial: Steno2 baseline and follow-up. |
| stack.Lexis |
Functions to facilitate analysis of multistate models. |
| stackedCIF |
Plotting Aalen-Johansen curves for competing events |
| stat.table |
Tables of summary statistics |
| status |
Time series and other methods for Lexis objects |
| steno2 |
Clinical trial: Steno2 baseline and follow-up. |
| subset.Lexis |
Subsetting Lexis (and stacked.Lexis) objects |
| subset.stacked.Lexis |
Subsetting Lexis (and stacked.Lexis) objects |
| succeeding |
Time series and other methods for Lexis objects |
| summary.Icens |
Fits a regression model to interval censored data. |
| summary.LCa |
Fit Lee-Carter-type models for rates to arbitrarily shaped observations of rates in a Lexis diagram. |
| summary.Lexis |
Summarize transitions and risk time from a Lexis object |
| surv1 |
Compute survival functions from rates and expected residual lifetime in an illness-death model as well as years of life lost to disease. |
| surv2 |
Compute survival functions from rates and expected residual lifetime in an illness-death model as well as years of life lost to disease. |
| 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 |
| thinCol |
Is 'x' in the column span of matrix 'A' and what columns are linearly dependent? |
| thoro |
Thorotrast Study |
| timeBand |
Extract time band data from a split Lexis object |
| timeScales |
The time scales of a Lexis object |
| timeSince |
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) object |
| transform.stacked.Lexis |
Transform a Lexis (or stacked.Lexis) object |
| transient |
Time series and other methods for Lexis objects |
| tsNA20 |
The time scales of a Lexis object |
| twoby2 |
Analysis of a two by two table |
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