| Title: | Data Preparation, Estimation and Prediction in Multi-State Models |
|---|---|
| Description: | Contains functions for data preparation, descriptives, hazard estimation and prediction with Aalen-Johansen or simulation in competing risks and multi-state models, see Putter, Fiocco, Geskus (2007) <doi:10.1002/sim.2712>. |
| Authors: | Hein Putter [aut, cre], Liesbeth C. de Wreede [aut], Marta Fiocco [aut], Ronald B. Geskus [ctb], Edouard F. Bonneville [aut], Damjan Manevski [ctb] |
| Maintainer: | Hein Putter <[email protected]> |
| License: | GPL (>= 2) |
| Version: | 0.3.3 |
| Built: | 2024-10-09 05:16:23 UTC |
| Source: | https://github.com/hputter/mstate |
Functions for data preparation, descriptives, (hazard) estimation and prediction (Aalen-Johansen) in competing risks and multi-state models.
| Package: | mstate |
| Type: | Package |
| Version: | 0.2.10 |
| Date: | 2016-12-03 |
| License: | GPL 2.0 |
Liesbeth de Wreede, Marta Fiocco, Hein Putter. Maintainer: Hein Putter <[email protected]>
Putter H, Fiocco M, Geskus RB (2007). Tutorial in biostatistics: Competing risks and multi-state models. Statistics in Medicine 26, 2389–2430.
de Wreede LC, Fiocco M, and Putter H (2010). The mstate package for estimation and prediction in non- and semi-parametric multi-state and competing risks models. Computer Methods and Programs in Biomedicine 99, 261–274.
de Wreede LC, Fiocco M, and Putter H (2011). mstate: An R Package for the Analysis of Competing Risks and Multi-State Models. Journal of Statistical Software, Volume 38, Issue 7.
These data sets give the times (in years) from HIV infection to AIDS, SI switch and death in 329 men who have sex with men (MSM). Data are from the period until combination anti-retroviral therapy became available (1996). For more background information on the cohort, ccr5 and SI, see Geskus et al. (2000, 2003)
aidssi
| patnr: | Patient identification number |
| time: | Time from HIV infection to first of SI appearance and AIDS, or last follow-up |
| status: | Event indicator; 0 = censored, 1 = AIDS, 2 = SI appearance |
| cause: | Failure cause; factor with levels "event-free", "AIDS", "SI" |
| ccr5: | CCR5 genotype; factor with levels "WW" (wild type allele on both chromosomes), |
| "WM" (mutant allele on one chromosome) | |
aidssi2
| patnr: | Patient identification number |
| entry.time: | Time from HIV infection to cohort entry. Value is zero if HIV infection occurred while in follow-up. |
| aids.time: | Time from HIV infection to AIDS, or last follow-up if AIDS was not observed |
| aids.stat: | Event indicator with respect to AIDS, with values 0 (censored) and 1 (AIDS) |
| si.time: | Time from HIV infection to SI switch, or last follow-up if SI switch was not observed |
| si.stat: | Event indicator with respect to SI switch, with values 0 (no switch) and 1 (switch) |
| death.time: | Time from HIV infection to death, or last follow-up if death was not observed |
| death.stat: | Event indicator with respect to death; 0 = alive, 1 = dead |
| age.inf: | Age at HIV infection |
| ccr5: | CCR5 genotype; factor with levels "WW" (wild type allele on both chromosomes), |
| "WM" (mutant allele on one chromosome) | |
aidssi contains follow-up data until the first of AIDS and SI switch.
It was used as example for the competing risks analyses in Putter, Fiocco,
Geskus (2007) and in Geskus (2016).
aidssi2 extends the aidssi data set in three ways. First, it
considers events after the initial one. Second, it includes the entry times
of the individuals that entered the study after HIV infection. Third, age at
HIV infection has been added as extra covariable. Numbers differ slightly
from the aidssi data set. Some individuals were diagnosed with AIDS
only when they died and others had their last follow-up at AIDS diagnosis.
In order to prevent two transitions to happen at the same time, their time
to AIDS was shortened by 0.25 years. This data set was used as example for
the multi-state analyses in Geskus (2016).
Geskus RB (2000). On the inclusion of prevalent cases in HIV/AIDS natural history studies through a marker-based estimate of time since seroconversion. Statistics in Medicine 19, 1753–1769.
Geskus RB, Miedema FA, Goudsmit J, Reiss P, Schuitemaker H, Coutinho RA (2003). Prediction of residual time to AIDS and death based on markers and cofactors. Journal of AIDS 32, 514–521.
Geskus, Ronald B. (2016). Data Analysis with Competing Risks and Intermediate States. CRC Press, Boca Raton.
Putter H, Fiocco M, Geskus RB (2007). Tutorial in biostatistics: Competing risks and multi-state models. Statistics in Medicine 26, 2389–2430.
A data frame of 137 rows (patients) and 22 columns. The included variables are
Disease group; 1 = ALL, 2 = AML Low Risk, 3 = AML High Risk
Time in days to death or last follow-up
Disease-free survival time in days (time to relapse, death or last follow-up)
Death indicator; 1 = dead, 0 = alive
Relapse indicator; 1 = relapsed, 0 = disease-free
Disease-free survival indicator; 1 = dead or relapsed, 0 = alive and disease-free)
Time in days to Acute Graft-versus-Host Disease (AGVHD)
Acute GVHD indicator; 1 = Acute GVHD, 0 = No Acute GVHD
Time (days) to Chronic Graft-vrsus-Host Disease (CGVHD)
Chronic GVHD indicator; 1 = Chronic GVHD, 0 = No Chronic GVHD
Time (days) to platelet recovery
Platelet recovery indicator; 1 = platelets returned to normal, 0 = platelets never returned to normal
Patient age in years
Donor age in years
Patient sex; 1 = male, 0 = female
Donor sex; 1 = male, 0 = female
Patient CMV status; 1 = CMV positive, 0 = CMV negative
Donor CMV status; 1 = CMV positive, 0 = CMV negative
Waiting time to transplant in days
FAB; 1 = FAB grade 4 or 5 and AML, 0 = Otherwise
Hospital; 1 = The Ohio State University, 2 = Alferd , 3 = St. Vincent, 4 = Hahnemann
MTX used as a Graft-versus-Host prophylactic; 1 = yes, 0 = no
A data frame, see data.frame.
Klein and Moeschberger (1997). Survival Analysis Techniques for Censored and Truncated Data, Springer, New York.
This function converts a dataset that is in short format (one subject per line) into a counting process format with time-varying weights that correct for right censored and left truncated data. With this data set, analyses based on the subdistribution hazard can be performed.
## Default S3 method: crprep( Tstop, status, data, trans = 1, cens = 0, Tstart = 0, id, strata, keep, shorten = TRUE, rm.na = TRUE, origin = 0, prec.factor = 1000, ... )## Default S3 method: crprep( Tstop, status, data, trans = 1, cens = 0, Tstart = 0, id, strata, keep, shorten = TRUE, rm.na = TRUE, origin = 0, prec.factor = 1000, ... )
Tstop |
Either 1) a vector containing the time at which the follow-up
is ended, or 2) a character string indicating the column name in |
status |
Either 1) a vector describing status at end of follow-up,
having the same length as |
data |
Data frame in which to interpret |
trans |
Values of |
cens |
Value that denotes censoring in |
Tstart |
Either 1) a vector containing the time at which the follow-up
is started, having the same length as |
id |
Either 1) a vector, having the same length as |
strata |
Either 1) a vector of the same length as |
keep |
Either 1) a data frame or matrix or a numeric or factor vector
containing covariate(s) that need to be retained in the output dataset.
Number of rows/length should correspond with |
shorten |
Logical. If true, number of rows in output is reduced by collapsing rows within a subject in which weights do not change. |
rm.na |
Logical. If true, rows for which |
origin |
Substract origin time units from all Tstop and Tstart times. |
prec.factor |
Factor by which to multiply the machine's precision. Censoring and truncation times are shifted by prec.factor*precision if event times and censoring/truncation times are equal. |
... |
Further arguments to be passed to or from other methods. They are ignored in this function. |
For each event type as specified via trans, individuals with a
competing event remain in the risk set with weights that are determined by
the product-limit forms of the time-to-censoring and time-to-entry
estimates. Typically, their weights change over follow-up, and therefore
such individuals are split into several rows. Censoring weights are always
computed. Truncation weights are computed only if Tstart is
specified.
If several event types are specified at once, regression analyses using the
stacked format data set can be performed (see Putter et al. 2007 and Chapter
4 in Geskus 2016). The data set can also be used for a regression on the
cause-specific hazard by restricting to the subset subset=count==0.
Missing values are allowed in Tstop, status, Tstart,
strata and keep. Rows for which Tstart or Tstart
is missing are deleted.
There are two ways to supply the data. If given "by value" (option 1), the
actual data vectors are used. If given "by name" (option 2), the column
names are specified, which are read from the data set in data. In
general, the second option is preferred.
If data are given by value, the following holds for the naming of the
columns in the output data set. If keep, strata or id
is a vector from a (sub)-list, e.g. obj$name2$name1, then the column name is
based on the most inner part (i.e.\ "name1"). If it is a vector of the form
obj[,"name1"], then the column is named "name1". For all other vector
specifications, the name is copied as is. If keep is a data.frame or
a named matrix, the same names are used for the covariate columns in the
output data set. If keep is a matrix without names, then the covariate
columns are given the names "V1" until "Vk".
The current function does not allow to create a weighted data set in which the censoring and/or truncation mechanisms depend on covariates via a regression model.
A data frame in long (counting process) format containing the covariates (replicated per subject). The following column names are used:
Tstart |
start dates of dataset |
Tstop |
stop dates of dataset |
status |
status of the subject at the end of that row |
weight.cens |
weights due to censoring mechanism |
weight.trunc |
weights due to truncation mechanism (if present) |
count |
row number within subject and event type under consideration |
failcode |
event type under consideration |
The first column is the subject identifier. If the argument "id" is missing,
it has values 1:n and is named "id". Otherwise the information is taken from
the id argument.
Variables as specified in strata and/or keep are included as
well (see Details).
Ronald Geskus
Geskus RB (2011). Cause-Specific Cumulative Incidence Estimation and the Fine and Gray Model Under Both Left Truncation and Right Censoring. Biometrics 67, 39–49.
Geskus, Ronald B. (2016). Data Analysis with Competing Risks and Intermediate States. CRC Press, Boca Raton.
Putter H, Fiocco M, Geskus RB (2007). Tutorial in biostatistics: Competing risks and multi-state models. Statistics in Medicine 26, 2389–2430.
data(aidssi) aidssi.w <- crprep("time", "cause", data=aidssi, trans=c("AIDS","SI"), cens="event-free", id="patnr", keep="ccr5") # calculate cause-specific cumulative incidence, no truncation, # compare with Cuminc (also from mstate) ci <- Cuminc(aidssi$time, aidssi$status) sf <- survfit(Surv(Tstart,Tstop,status=="AIDS")~1, data=aidssi.w, weight=weight.cens, subset=failcode=="AIDS") plot(sf, fun="event", mark.time=FALSE) lines(CI.1~time,data=ci,type="s",col="red") sf <- survfit(Surv(Tstart,Tstop,status=="SI")~1, data=aidssi.w, weight=weight.cens, subset=failcode=="SI") plot(sf, fun="event", mark.time=FALSE) lines(CI.2~time,data=ci,type="s",col="red") # Fine and Gray regression for cause 1 cw <- coxph(Surv(Tstart,Tstop,status=="AIDS")~ccr5, data=aidssi.w, weight=weight.cens, subset=failcode=="AIDS") cw # This can be checked with the results of crr (cmprsk) # crr(ftime=aidssi$time, fstatus=aidssi$status, cov1=as.numeric(aidssi$ccr5)) # Gray's log-rank test aidssi.wCCR <- crprep("time", "cause", data=aidssi, trans=c("AIDS","SI"), cens="event-free", id="patnr", strata="ccr5") test.AIDS <- coxph(Surv(Tstart,Tstop,status=="AIDS")~ccr5, data=aidssi.wCCR, weights=weight.cens, subset=failcode=="AIDS") test.SI <- coxph(Surv(Tstart,Tstop,status=="SI")~ccr5, data=aidssi.wCCR, weights=weight.cens, subset=failcode=="SI") ## score test statistic and p-value c(test.AIDS$score, 1-pchisq(test.AIDS$score,1)) # AIDS c(test.SI$score, 1-pchisq(test.SI$score,1)) # SI # This can be compared with the results of cuminc (cmprsk) # with(aidssi, cuminc(time, status, group=ccr5)$Tests) # Note: results are not exactly the samedata(aidssi) aidssi.w <- crprep("time", "cause", data=aidssi, trans=c("AIDS","SI"), cens="event-free", id="patnr", keep="ccr5") # calculate cause-specific cumulative incidence, no truncation, # compare with Cuminc (also from mstate) ci <- Cuminc(aidssi$time, aidssi$status) sf <- survfit(Surv(Tstart,Tstop,status=="AIDS")~1, data=aidssi.w, weight=weight.cens, subset=failcode=="AIDS") plot(sf, fun="event", mark.time=FALSE) lines(CI.1~time,data=ci,type="s",col="red") sf <- survfit(Surv(Tstart,Tstop,status=="SI")~1, data=aidssi.w, weight=weight.cens, subset=failcode=="SI") plot(sf, fun="event", mark.time=FALSE) lines(CI.2~time,data=ci,type="s",col="red") # Fine and Gray regression for cause 1 cw <- coxph(Surv(Tstart,Tstop,status=="AIDS")~ccr5, data=aidssi.w, weight=weight.cens, subset=failcode=="AIDS") cw # This can be checked with the results of crr (cmprsk) # crr(ftime=aidssi$time, fstatus=aidssi$status, cov1=as.numeric(aidssi$ccr5)) # Gray's log-rank test aidssi.wCCR <- crprep("time", "cause", data=aidssi, trans=c("AIDS","SI"), cens="event-free", id="patnr", strata="ccr5") test.AIDS <- coxph(Surv(Tstart,Tstop,status=="AIDS")~ccr5, data=aidssi.wCCR, weights=weight.cens, subset=failcode=="AIDS") test.SI <- coxph(Surv(Tstart,Tstop,status=="SI")~ccr5, data=aidssi.wCCR, weights=weight.cens, subset=failcode=="SI") ## score test statistic and p-value c(test.AIDS$score, 1-pchisq(test.AIDS$score,1)) # AIDS c(test.SI$score, 1-pchisq(test.SI$score,1)) # SI # This can be compared with the results of cuminc (cmprsk) # with(aidssi, cuminc(time, status, group=ccr5)$Tests) # Note: results are not exactly the same
This function computes nonparametric cumulative incidence functions and associated standard errors for each value of a group variable.
Cuminc(time, status, data, group, na.status = c("remove", "extra"), ...)Cuminc(time, status, data, group, na.status = c("remove", "extra"), ...)
time |
Either 1) a numeric vector containing the failure times or 2) a string containing the column name indicating these failure times |
status |
Either 1) a numeric, factor or character vector containing the failure codes or 2) a string containing the column name indicating these failure codes |
data |
When appropriate, a data frame containing |
group |
Optionally, name of column in data indicating a grouping
variable; cumulative incidence functions are calculated for each value or
level of |
na.status |
One of |
... |
Allows extra arguments for future extensions, but for now just
used for backwards compatibility (e.g. allowing use of defunct |
The estimated cumulative incidences are as described in Putter, Fiocco & Geskus (2007); the standard errors are the square roots of the Greenwood variance estimators, see eg. Andersen, Borgan, Gill & Keiding (1993), de Wreede, Fiocco & Putter (2009), and they correspond to the variances in eg. Marubini & Valsecchi (1995). In case of no censoring, the estimated cumulative incidences and variances reduce to simple binomial frequencies and their variances.
An object of class "Cuminc", which is a data frame containing
the estimated failure-free probabilities and cumulative incidences and their
standard errors. The names of the dataframe are time, Surv,
seSurv, and cuminc and secuminc followed by the values
or levels of the failcodes. If group was specified, a
group variable is included with the same name and values/levels as
the original grouping variable, and with estimated cumulative incidences
(SE) for each value/level of group.
Cuminc is now simply a wrapper around survfit of the survival package with
type="mstate", only maintained for backward compatibility. The
survfit object is kept as attribute (attr("survfit")), and the print,
plot and summary functions are simply print, plot and summary applied to the
survfit object. Subsetting the "Cuminc" object results in subsetting
the data frame, not in subsetting the survfit object.
Hein Putter [email protected]
Andersen PK, Borgan O, Gill RD, Keiding N (1993). Statistical Models Based on Counting Processes. Springer, New York.
Marubini E, Valsecchi MG (1995). Analysing Survival Data from Clinical Trials and Observational Studies. Wiley, New York.
Putter H, Fiocco M, Geskus RB (2007). Tutorial in biostatistics: Competing risks and multi-state models. Statistics in Medicine 26, 2389–2430.
de Wreede L, Fiocco M, Putter H (2009). The mstate package for estimation and prediction in non- and semi-parametric multi-state models. Submitted.
### These data were used in Putter, Fiocco & Geskus (2007) data(aidssi) ci <- Cuminc(time=aidssi$time, status=aidssi$status) head(ci); tail(ci) ci <- Cuminc(time="time", status="status", data=aidssi, group="ccr5") head(ci); tail(ci) ### Some fake data fake <- data.frame(surv=c(seq(2,10,by=2),seq(1,13,by=3),seq(1,9,by=2),seq(1,13,by=3)), stat=rep(0:3,5),Tstage=c(1:4,rep(1:4,rep(4,4)))) fake$stat[fake$stat==0 & fake$Tstage==2] <- 3 fake$stat[fake$stat==3 & fake$Tstage==1] <- 2 fake Cuminc(time="surv", status="stat", data=fake) # If we remove all entries with status=0, # we should get binomial sample probabilities and corresponding SEs fake0 <- fake[fake$stat!=0,] Cuminc(time="surv", status="stat", data=fake0)### These data were used in Putter, Fiocco & Geskus (2007) data(aidssi) ci <- Cuminc(time=aidssi$time, status=aidssi$status) head(ci); tail(ci) ci <- Cuminc(time="time", status="status", data=aidssi, group="ccr5") head(ci); tail(ci) ### Some fake data fake <- data.frame(surv=c(seq(2,10,by=2),seq(1,13,by=3),seq(1,9,by=2),seq(1,13,by=3)), stat=rep(0:3,5),Tstage=c(1:4,rep(1:4,rep(4,4)))) fake$stat[fake$stat==0 & fake$Tstage==2] <- 3 fake$stat[fake$stat==3 & fake$Tstage==1] <- 2 fake Cuminc(time="surv", status="stat", data=fake) # If we remove all entries with status=0, # we should get binomial sample probabilities and corresponding SEs fake0 <- fake[fake$stat!=0,] Cuminc(time="surv", status="stat", data=fake0)
Given a dataset in long format, for instance generated by
msprep, this function cuts a multi-state data frame (object of
type "msdata") at a landmark time point LM. Administrative censoring can be
applied at time cens, equal for all individuals.
cutLMms(msdata, LM, cens)cutLMms(msdata, LM, cens)
msdata |
An object of class |
LM |
The landmark time point at which the cut is to be made |
cens |
The time point at which administrative censoring is to be applied; if missing, no administrative censoring will be applied |
The function has a similar purpose as the cutLM function in the
dynpred package. Only follow-up after a landmark time point LM is
considered, so all subjects who are no longer at risk are removed. Column
time is updated based on the new Tstart and Tstop.
An object of class "msdata" again, containing only follow-up
data after LM. The data frame contains an extra column Tentry with
the time of entry into the present state.
Hein Putter [email protected]
L. C. de Wreede, M. Fiocco, and H. Putter (2011). mstate: An R Package for the Analysis of Competing Risks and Multi-State Models. Journal of Statistical Software 38: 7.
tmat <- trans.illdeath(names=c("Tx","PR","RelDeath")) data(ebmt3) # data from Section 4 of Putter, Fiocco & Geskus (2007) msebmt <- msprep(time=c(NA,"prtime","rfstime"),status=c(NA,"prstat","rfsstat"), data=ebmt3,trans=tmat) # Cut at 5 years cutLMms(msebmt, LM=1826) events(cutLMms(msebmt, LM=1826))tmat <- trans.illdeath(names=c("Tx","PR","RelDeath")) data(ebmt3) # data from Section 4 of Putter, Fiocco & Geskus (2007) msebmt <- msprep(time=c(NA,"prtime","rfstime"),status=c(NA,"prstat","rfsstat"), data=ebmt3,trans=tmat) # Cut at 5 years cutLMms(msebmt, LM=1826) events(cutLMms(msebmt, LM=1826))
A data frame of 8966 patients transplanted at the EBMT. The included variables are
Patient identification number
Time in months from transplantation to death or last follow-up
Survival status; 0 = censored; 1,...,6 = death due to the following causes: Relapse (1), GvHD (2), Bacterial infections (3), Viral infections (4), Fungal infections (5), Other causes (6)
Cause of death as factor with levels "Alive", "Relapse", "GvHD", "Bacterial", "Viral", "Fungal", "Other"
Disease subclassification; factor with levels "AML", "ALL", "CML"
Donor-recipient gender match; factor with levels "No gender mismatch", "Gender mismatch"
T-cell depletion; factor with levels "No TCD", "TCD", "Unknown"
Year of transplantation; factor with levels "1985-1989", "1990-1994", "1995-1998"
Patient age at transplant; factor with levels "<=20", "20-40", ">40"
A data frame, see data.frame.
We acknowledge the European Society for Blood and Marrow Transplantation (EBMT) for making available these data. Disclaimer: these data were simplified for the purpose of illustration of the analysis of competing risks and multi-state models and do not reflect any real life situation. No clinical conclusions should be drawn from these data.
Fiocco M, Putter H, van Houwelingen JC (2005). Reduced rank proportional hazards model for competing risks. Biostatistics 6, 465–478.
A data frame of 2279 patients transplanted at the EBMT between 1985 and 1998. These data were used in Fiocco, Putter & van Houwelingen (2008), van Houwelingen & Putter (2008, 2012) and de Wreede, Fiocco & Putter (2011). The included variables are
Patient identification number
Time in days from transplantation to recovery or last follow-up
Recovery status; 1 = recovery, 0 = censored
Time in days from transplantation to adverse event (AE) or last follow-up
Adverse event status; 1 = adverse event, 0 = censored
Time in days from transplantation to both recovery and AE or last follow-up
Recovery and AE status; 1 = both recovery and AE, 0 = no recovery or no AE or censored
Time in days from transplantation to relapse or last follow-up
Relapse status; 1 = relapse, 0 = censored
Time in days from transplantation to death or last follow-up
Relapse status; 1 = dead, 0 = censored
Year of transplantation; factor with levels "1985-1989", "1990-1994", "1995-1998"
Patient age at transplant; factor with levels "<=20", "20-40", ">40"
Prophylaxis; factor with levels "no", "yes"
Donor-recipient gender match; factor with levels "no gender mismatch", "gender mismatch"
A data frame, see data.frame.
We acknowledge the European Society for Blood and Marrow Transplantation (EBMT) for making available these data. Disclaimer: these data were simplified for the purpose of illustration of the analysis of competing risks and multi-state models and do not reflect any real life situation. No clinical conclusions should be drawn from these data.
Fiocco M, Putter H, van Houwelingen HC (2008). Reduced-rank proportional hazards regression and simulation-based prediction for multi-state models. Statistics in Medicine 27, 4340–4358.
van Houwelingen HC, Putter H (2008). Dynamic predicting by landmarking as an alternative for multi-state modeling: an application to acute lymphoid leukemia data. Lifetime Data Anal 14, 447–463.
van Houwelingen HC, Putter H (2012). Dynamic Prediction in Clinical Survival Analaysis. Chapman & Hall/CRC Press, Boca Raton.
de Wreede LC, Fiocco M, and Putter H (2011). mstate: An R Package for the Analysis of Competing Risks and Multi-State Models. Journal of Statistical Software, Volume 38, Issue 7.
A data frame of 2204 patients transplanted at the EBMT between 1995 and 1998. These data were used in Section 4 of the tutorial on competing risks and multi-state models (Putter, Fiocco & Geskus, 2007). The included variables are
Patient identification number
Time in days from transplantation to platelet recovery or last follow-up
Platelet recovery status; 1 = platelet recovery, 0 = censored
Time in days from transplantation to relapse or death or last follow-up (relapse-free survival time)
Relapse-free survival status; 1 = relapsed or dead, 0 = censored
Disease subclassification; factor with levels "AML", "ALL", "CML"
Patient age at transplant; factor with levels "<=20", "20-40", ">40"
Donor-recipient gender match; factor with levels "No gender mismatch", "Gender mismatch"
T-cell depletion; factor with levels "No TCD", "TCD"
A data frame, see data.frame.
We acknowledge the European Society for Blood and Marrow Transplantation (EBMT) for making available these data. Disclaimer: these data were simplified for the purpose of illustration of the analysis of competing risks and multi-state models and do not reflect any real life situation. No clinical conclusions should be drawn from these data.
Putter H, Fiocco M, Geskus RB (2007). Tutorial in biostatistics: Competing risks and multi-state models. Statistics in Medicine 26, 2389–2430.
A data frame of 1977 patients transplanted for CML. The included variables are
Patient identification number
Time in days from transplantation to death or last follow-up
Survival status; 1 = death; 0 = censored
Time in days from transplantation to relapse or last follow-up
Relapse status; 1 = relapsed; 0 = censored
Calendar year of relapse; factor with levels "1993-1996"," 1997-1999", "2000-"
Patient age at transplant (years)
Gratwohl score; factor with levels "Low risk", "Medium risk", "High risk"
A data frame, see data.frame.
We acknowledge the European Society for Blood and Marrow Transplantation (EBMT) for making available these data. Disclaimer: these data were simplified for the purpose of illustration of the analysis of competing risks and multi-state models and do not reflect any real life situation. No clinical conclusions should be drawn from these data.
Given a "probtrans" object, ELOS calculates the (restricted) expected
length of stay in each of the states of the multi-state model.
ELOS(pt, tau)ELOS(pt, tau)
pt |
An object of class |
tau |
The horizon until which ELOS is calculated; if missing, the maximum of the observed transition times is taken |
The object pt needs to be a "probtrans" object, obtained with
forward prediction (the default, direction="forward", in the
call to probtrans). The restriction to tau is there
because, as in ordinary survival analysis, the probability of being in a
state can be positive until infinity, resulting in infinite values. The
(restricted, until tau) expected length of stay in state h, given in state g
at time s, is given by the integral from s to tau of P_gh(s,t), see for
instance Beyersmann and Putter (2014).
A K x K matrix (with K number of states), with the (g,h)'th element
containing E_gh(s,tau). The starting time point s is inferred from pt
(the smallest time point, should be equal to the predt value in the
call to probtrans. The row- and column names of the matrix
have been named "from1" until "fromK" and "in1" until "inK", respectively.
Hein Putter [email protected]
# transition matrix for illness-death model tmat <- trans.illdeath() # data in wide format, for transition 1 this is dataset E1 of # Therneau & Grambsch (2000) tg <- data.frame(illt=c(1,1,6,6,8,9),ills=c(1,0,1,1,0,1), dt=c(5,1,9,7,8,12),ds=c(1,1,1,1,1,1), x1=c(1,1,1,0,0,0),x2=c(6:1)) # data in long format using msprep tglong <- msprep(time=c(NA,"illt","dt"),status=c(NA,"ills","ds"), data=tg,keep=c("x1","x2"),trans=tmat) # events events(tglong) table(tglong$status,tglong$to,tglong$from) # expanded covariates tglong <- expand.covs(tglong,c("x1","x2")) # Cox model with different covariate cx <- coxph(Surv(Tstart,Tstop,status)~x1.1+x2.2+strata(trans), data=tglong,method="breslow") summary(cx) # new data, to check whether results are the same for transition 1 as # those in appendix E.1 of Therneau & Grambsch (2000) newdata <- data.frame(trans=1:3,x1.1=c(0,0,0),x2.2=c(0,1,0),strata=1:3) HvH <- msfit(cx,newdata,trans=tmat) # probtrans pt <- probtrans(HvH,predt=0) # ELOS until last observed time point ELOS(pt) # Restricted ELOS until tau=10 ELOS(pt, tau=10)# transition matrix for illness-death model tmat <- trans.illdeath() # data in wide format, for transition 1 this is dataset E1 of # Therneau & Grambsch (2000) tg <- data.frame(illt=c(1,1,6,6,8,9),ills=c(1,0,1,1,0,1), dt=c(5,1,9,7,8,12),ds=c(1,1,1,1,1,1), x1=c(1,1,1,0,0,0),x2=c(6:1)) # data in long format using msprep tglong <- msprep(time=c(NA,"illt","dt"),status=c(NA,"ills","ds"), data=tg,keep=c("x1","x2"),trans=tmat) # events events(tglong) table(tglong$status,tglong$to,tglong$from) # expanded covariates tglong <- expand.covs(tglong,c("x1","x2")) # Cox model with different covariate cx <- coxph(Surv(Tstart,Tstop,status)~x1.1+x2.2+strata(trans), data=tglong,method="breslow") summary(cx) # new data, to check whether results are the same for transition 1 as # those in appendix E.1 of Therneau & Grambsch (2000) newdata <- data.frame(trans=1:3,x1.1=c(0,0,0),x2.2=c(0,1,0),strata=1:3) HvH <- msfit(cx,newdata,trans=tmat) # probtrans pt <- probtrans(HvH,predt=0) # ELOS until last observed time point ELOS(pt) # Restricted ELOS until tau=10 ELOS(pt, tau=10)
Converts multi-state data back and forth between etm and msdata formats. Covariates have to be dealt with separately.
etm2msdata(etmdata, id, tra, covs)etm2msdata(etmdata, id, tra, covs)
etmdata |
Multi-state data in |
id |
Column name identifying the subject id |
tra |
Transition matrix in |
covs |
Vector of column names containing covariates to be included |
msdata2etm will convert from msdata format to etm
format; etm2msdata will convert from etm format to
msdata format. Both msdata2etm and etm2msdata work with
basic time-fixed covariates. Time-dependent covariates are not supported.
The function msdata2etm will work for transition-specific covariates,
but the result does not really make much sense when used in etm.
Hein Putter [email protected]
# Transition matrix for illness-death model tmat <- trans.illdeath() # Data in wide format, for transition 1 this is dataset E1 of # Therneau & Grambsch (T&G) tg <- data.frame(id=1:6,illt=c(1,1,6,6,8,9),ills=c(1,0,1,1,0,1), dt=c(5,1,9,7,8,12),ds=c(1,1,1,1,1,1), x1=c(1,1,1,0,0,0),x2=c(6:1)) # Data in long format using msprep tglong <- msprep(time=c(NA,"illt","dt"),status=c(NA,"ills","ds"), data=tg,keep=c("x1","x2"),trans=tmat, id="id") # Same thing in etm format tra <- trans2tra(tmat) tgetm <- msdata2etm(tglong, id="id") tgetm <- msdata2etm(tglong, id="id", covs=c("x1", "x2")) # with covariates # And back etm2msdata(tgetm, id="id", tra=tra) etm2msdata(tgetm, id="id", tra=tra, covs=c("x1", "x2")) # with covariates# Transition matrix for illness-death model tmat <- trans.illdeath() # Data in wide format, for transition 1 this is dataset E1 of # Therneau & Grambsch (T&G) tg <- data.frame(id=1:6,illt=c(1,1,6,6,8,9),ills=c(1,0,1,1,0,1), dt=c(5,1,9,7,8,12),ds=c(1,1,1,1,1,1), x1=c(1,1,1,0,0,0),x2=c(6:1)) # Data in long format using msprep tglong <- msprep(time=c(NA,"illt","dt"),status=c(NA,"ills","ds"), data=tg,keep=c("x1","x2"),trans=tmat, id="id") # Same thing in etm format tra <- trans2tra(tmat) tgetm <- msdata2etm(tglong, id="id") tgetm <- msdata2etm(tglong, id="id", covs=c("x1", "x2")) # with covariates # And back etm2msdata(tgetm, id="id", tra=tra) etm2msdata(tgetm, id="id", tra=tra, covs=c("x1", "x2")) # with covariates
Given a dataset in long format, for instance generated by
msprep, and a transition matrix for the multi-state model,
this function counts the number of observed transitions in the multi-state
model and gives their percentages.
events(msdata)events(msdata)
msdata |
An object of class |
Although msdata does not need to be the result of a call to
msprep, it does need to be an object of class "msdata",
which is essentially a data frame in long format, with one row for each
transition for which the subject is at risk. The columns from,
to, and status need to be present, with appropriate meaning,
see msprep. The msdata argument needs to have a
"trans" attributes, which holds the transition matrix of the
multi-state model.
A list containing two tables, the first, called Frequencies,
with the number of observed transitions in the multi-state model occurring
in msdata, the second, called Proportions, with the
corresponding proportions.
Hein Putter [email protected]
tmat <- trans.illdeath(names=c("Tx","PR","RelDeath")) data(ebmt3) # data from Section 4 of Putter, Fiocco & Geskus (2007) msebmt <- msprep(time=c(NA,"prtime","rfstime"),status=c(NA,"prstat","rfsstat"), data=ebmt3,trans=tmat) events(msebmt) # see Fig 13 of Putter, Fiocco & Geskus (2007)tmat <- trans.illdeath(names=c("Tx","PR","RelDeath")) data(ebmt3) # data from Section 4 of Putter, Fiocco & Geskus (2007) msebmt <- msprep(time=c(NA,"prtime","rfstime"),status=c(NA,"prstat","rfsstat"), data=ebmt3,trans=tmat) events(msebmt) # see Fig 13 of Putter, Fiocco & Geskus (2007)
Given a competing risks dataset in stacked format, and one or more covariates, this function adds type-specific covariates to the dataset. The original dataset with the type-specific covariates appended is returned.
expand.covs(data, ...)expand.covs(data, ...)
data |
An object of class |
... |
Further arguments to be passed to or from other methods. They are ignored in this function. |
Type-specific covariates can be used to analyse separate effects on all
event types in a single analysis based on a stacked data set (Putter, Fiocco
& Geskus (2007) and Geskus (2016)). It is only unambiguously defined for
numeric covariates or for explicit codings. Rows that contain the data for
that specific event type have the value copied from the original covariate
in case it is numeric. In all other rows it has the value zero. If the
covariate is a factor, it will be expanded on the design matrix given by
model.matrix. For standard "treatment
contrasts" this means that dummy variables are created. If the covariate is
a factor, the column name combines the name of the covariate with the
specific event type. If longnames=TRUE, both parts are
intersected by the specific labels in the coding. Missing values in the
basic covariates are allowed and result in missing values in the expanded
covariates.
An data frame object of the same class as the data argument,
containing the design matrix for the type-specific covariates, either on its
own (append=FALSE) or appended to the data
(append=TRUE).
Ronald Geskus and Hein Putter [email protected]
Putter H, Fiocco M, Geskus RB (2007). Tutorial in biostatistics: Competing risks and multi-state models. Statistics in Medicine 26, 2389–2430.
Geskus, Ronald B. (2016). Data Analysis with Competing Risks and Intermediate States. CRC Press, Boca Raton.
# small data set in stacked format tg <- data.frame(time=c(5,5,1,1,9,9),status=c(1,0,2,2,0,1),failcode=rep(c("I","II"),3), x1=c(1,1,2,2,2,2),x2=c(3,3,2,2,1,1)) tg$x1 <- factor(tg$x1,labels=c("male","female")) # expanded covariates expand.covs(tg,covs=c("x1","x2")) expand.covs(tg,covs=c("x1","x2"),longnames=TRUE) expand.covs(tg,covs=c("x1","x2"),append=FALSE)# small data set in stacked format tg <- data.frame(time=c(5,5,1,1,9,9),status=c(1,0,2,2,0,1),failcode=rep(c("I","II"),3), x1=c(1,1,2,2,2,2),x2=c(3,3,2,2,1,1)) tg$x1 <- factor(tg$x1,labels=c("male","female")) # expanded covariates expand.covs(tg,covs=c("x1","x2")) expand.covs(tg,covs=c("x1","x2"),longnames=TRUE) expand.covs(tg,covs=c("x1","x2"),append=FALSE)
Given a multi-state dataset in long format, and one or more covariates, this function adds transition-specific covariates, expanding the original covariate(s), to the dataset. The original dataset with the transition-specific covariates appended is returned.
## S3 method for class 'msdata' expand.covs(data, covs, append = TRUE, longnames = TRUE, ...)## S3 method for class 'msdata' expand.covs(data, covs, append = TRUE, longnames = TRUE, ...)
data |
An object of class |
covs |
A character vector containing the names of the covariates in
|
append |
Logical value indicating whether or not the design matrix for
the expanded covariates should be appended to the data (default= |
longnames |
Logical value indicating whether or not the labels are to
be used for the names of the expanded covariates that are categorical
(default= |
... |
Further arguments to be passed to or from other methods. They are ignored in this function. |
For a given basic covariate Z, the transition-specific covariate for
transition s is called Z.s. The concept of transition-specific
covariates in the context of multi-state models was introduced by Andersen,
Hansen & Keiding (1991), see also Putter, Fiocco & Geskus (2007). It is only
unambiguously defined for numeric covariates or for explicit codings. Then
it will take the value 0 for all rows in the long format dataframe for which
trans does not equal s. For the rows for which trans
equals s, the original value of Z is copied. In
expand.covs, when a given covariate is a factor, it will be expanded
on the design matrix given by
model.matrix. Missing values in the basic
covariates are allowed and result in missing values in the expanded
covariates.
An object of class 'msdata', containing the design matrix for the
transition- specific covariates, either on its own
(append=FALSE) or appended to the data
(append=TRUE).
Hein Putter [email protected]
Andersen PK, Hansen LS, Keiding N (1991). Non- and semi-parametric estimation of transition probabilities from censored observation of a non-homogeneous Markov process. Scandinavian Journal of Statistics 18, 153–167.
Putter H, Fiocco M, Geskus RB (2007). Tutorial in biostatistics: Competing risks and multi-state models. Statistics in Medicine 26, 2389–2430.
# transition matrix for illness-death model tmat <- trans.illdeath() # small data set in wide format tg <- data.frame(illt=c(1,1,6,6,8,9),ills=c(1,0,1,1,0,1), dt=c(5,1,9,7,8,12),ds=c(1,1,1,1,1,1), x1=c(1,1,1,2,2,2),x2=c(6:1)) tg$x1 <- factor(tg$x1,labels=c("male","female")) # data in long format using msprep tglong <- msprep(time=c(NA,"illt","dt"), status=c(NA,"ills","ds"),data=tg, keep=c("x1","x2"),trans=tmat) # expanded covariates expand.covs(tglong,c("x1","x2"),append=FALSE) expand.covs(tglong,"x1") expand.covs(tglong,"x1",longnames=FALSE)# transition matrix for illness-death model tmat <- trans.illdeath() # small data set in wide format tg <- data.frame(illt=c(1,1,6,6,8,9),ills=c(1,0,1,1,0,1), dt=c(5,1,9,7,8,12),ds=c(1,1,1,1,1,1), x1=c(1,1,1,2,2,2),x2=c(6:1)) tg$x1 <- factor(tg$x1,labels=c("male","female")) # data in long format using msprep tglong <- msprep(time=c(NA,"illt","dt"), status=c(NA,"ills","ds"),data=tg, keep=c("x1","x2"),trans=tmat) # expanded covariates expand.covs(tglong,c("x1","x2"),append=FALSE) expand.covs(tglong,"x1") expand.covs(tglong,"x1",longnames=FALSE)
A function that calculates the excess and population hazards for a given transition. Code is based on function rs.surv from the relsurv package.
haz_function( formula = formula(data), data, ratetable = relsurv::slopop, na.action, add.times, rmap, include.all.times = FALSE )haz_function( formula = formula(data), data, ratetable = relsurv::slopop, na.action, add.times, rmap, include.all.times = FALSE )
formula |
A non-parametric Surv-based formula, e.g. Surv(times, status)~1 |
data |
A subset of the msprep object (dataset) where there's only data for the chosen transition |
ratetable |
A table of event rates, organized as a ratetable object, such as slopop |
na.action |
A missing-data filter function, applied to the model.frame, after any subset argument has been used. Default is options()$na.action |
add.times |
Additional times at which the hazards should be evaluated |
rmap |
An optional list to be used if the variables are not organized and named in the same way as in the ratetable object |
include.all.times |
Should hazards be evaluated at all times in seq(minimum time, maximum time, by=1). Default is FALSE |
A list containing the needed hazards.
Damjan Manevski [email protected]
A data frame of 488 liver cirrhosis patients from a randomized clinical trial concerning prednisone treatment in these patients. The dataset is in long format. The included variables are
Patient identification number
Starting state
Receiving state
Transition number
Starting time
Transition time
Status variable; 1=transition, 0=censored
Treatment; factor with levels "Placebo", "Prednisone"
A data frame, see data.frame.
This data was kindly provided by Per Kragh Andersen. It was introduced in Andersen, Borgan, Gill & Keiding (1993), Example 1.3.12, and used as illustration for computation of transition probabilities in multi-state models, see Sections IV.4 (Example IV.4.4) and VII.2 (Example VII.2.10).
Andersen PK, Borgan O, Gill RD, Keiding N (1993). Statistical Models Based on Counting Processes. Springer, New York.
This function implements the landmark Aalen-Johansen method of Putter & Spitoni (2016) for non-parametric estimation of transition probabilities in non-Markov models.
LMAJ(msdata, s, from, method = c("aalen", "greenwood"))LMAJ(msdata, s, from, method = c("aalen", "greenwood"))
msdata |
An |
s |
The prediction time point s from which transition probabilities are to be obtained |
from |
Either a single state or a set of states in the state space 1,...,S |
method |
The method for calculating variances, as in
|
A data frame containing estimates and associated standard errors of
the transition probabilities P(X(t)=k | X(s) in from) with s
and from the arguments of the function.
Hein Putter [email protected]
Edouard F. Bonneville [email protected]
H. Putter and C. Spitoni (2016). Estimators of transition probabilities in non-Markov multi-state models. Submitted.
data(prothr) tmat <- attr(prothr, "trans") pr0 <- subset(prothr, treat=="Placebo") attr(pr0, "trans") <- tmat pr1 <- subset(prothr, treat=="Prednisone") attr(pr1, "trans") <- tmat c0 <- coxph(Surv(Tstart, Tstop, status) ~ strata(trans), data=pr0) c1 <- coxph(Surv(Tstart, Tstop, status) ~ strata(trans), data=pr1) msf0 <- msfit(c0, trans=tmat) msf1 <- msfit(c1, trans=tmat) # Comparison as in Figure 2 of Titman (2015) # Aalen-Johansen pt0 <- probtrans(msf0, predt=1000)[[2]] pt1 <- probtrans(msf1, predt=1000)[[2]] par(mfrow=c(1,2)) plot(pt0$time, pt0$pstate1, type="s", lwd=2, xlim=c(1000,4000), ylim=c(0,0.61), xlab="Time since randomisation (days)", ylab="Probability") lines(pt1$time, pt1$pstate1, type="s", lwd=2, lty=3) legend("topright", c("Placebo", "Prednisone"), lwd=2, lty=1:2, bty="n") title(main="Aalen-Johansen") # Landmark Aalen-Johansen LMpt0 <- LMAJ(msdata=pr0, s=1000, from=2) LMpt1 <- LMAJ(msdata=pr1, s=1000, from=2) plot(LMpt0$time, LMpt0$pstate1, type="s", lwd=2, xlim=c(1000,4000), ylim=c(0,0.61), xlab="Time since randomisation (days)", ylab="Probability") lines(LMpt1$time, LMpt1$pstate1, type="s", lwd=2, lty=3) legend("topright", c("Placebo", "Prednisone"), lwd=2, lty=1:2, bty="n") title(main="Landmark Aalen-Johansen")data(prothr) tmat <- attr(prothr, "trans") pr0 <- subset(prothr, treat=="Placebo") attr(pr0, "trans") <- tmat pr1 <- subset(prothr, treat=="Prednisone") attr(pr1, "trans") <- tmat c0 <- coxph(Surv(Tstart, Tstop, status) ~ strata(trans), data=pr0) c1 <- coxph(Surv(Tstart, Tstop, status) ~ strata(trans), data=pr1) msf0 <- msfit(c0, trans=tmat) msf1 <- msfit(c1, trans=tmat) # Comparison as in Figure 2 of Titman (2015) # Aalen-Johansen pt0 <- probtrans(msf0, predt=1000)[[2]] pt1 <- probtrans(msf1, predt=1000)[[2]] par(mfrow=c(1,2)) plot(pt0$time, pt0$pstate1, type="s", lwd=2, xlim=c(1000,4000), ylim=c(0,0.61), xlab="Time since randomisation (days)", ylab="Probability") lines(pt1$time, pt1$pstate1, type="s", lwd=2, lty=3) legend("topright", c("Placebo", "Prednisone"), lwd=2, lty=1:2, bty="n") title(main="Aalen-Johansen") # Landmark Aalen-Johansen LMpt0 <- LMAJ(msdata=pr0, s=1000, from=2) LMpt1 <- LMAJ(msdata=pr1, s=1000, from=2) plot(LMpt0$time, LMpt0$pstate1, type="s", lwd=2, xlim=c(1000,4000), ylim=c(0,0.61), xlab="Time since randomisation (days)", ylab="Probability") lines(LMpt1$time, LMpt1$pstate1, type="s", lwd=2, lty=3) legend("topright", c("Placebo", "Prednisone"), lwd=2, lty=1:2, bty="n") title(main="Landmark Aalen-Johansen")
Log-rank based test for the validity of the Markov assumption
MarkovTest( data, id, formula = NULL, transition, grid, B = 1000, fn = list(function(x) mean(abs(x), na.rm = TRUE)), fn2 = list(function(x) mean(x, na.rm = TRUE)), min_time = 0, other_weights = NULL, dist = c("poisson", "normal") )MarkovTest( data, id, formula = NULL, transition, grid, B = 1000, fn = list(function(x) mean(abs(x), na.rm = TRUE)), fn2 = list(function(x) mean(x, na.rm = TRUE)), min_time = 0, other_weights = NULL, dist = c("poisson", "normal") )
data |
Multi-state data in |
id |
Column name in |
formula |
Right-hand side of the formula. If NULL will fit with no covariates (formula="1" will also work), offset terms can also be specified. |
transition |
Transition number of the transition to be tested (in the
transition matrix as attribute to |
grid |
Grid of time points at which to compute the statistic |
B |
Number of wild bootstrap replications to perform |
fn |
A list of summary functions to be applied to the individual zbar traces (or a list of lists) |
fn2 |
A list of summary functions to be applied to the overall chi-squared trace |
min_time |
The minimum time for calculating optimal weights |
other_weights |
Other (than optimal) weights can be specified here |
dist |
Distribution of wild bootstrap random weights, either "poisson" for centred Poisson (default), or "normal" for standard normal |
Function MarkovTest performs the log-rank test described in Titman & Putter (2020). Function optimal_weights_matrix implements the optimal weighting for the state-specific trace. Function optimal_weights_multiple implements the optimal weighting for the chi-squared trace.
MarkovTest returns an object of class "MarkovTest", which is a list with the following items:
orig_stat |
Summary statistic for each of the starting states |
orig_ch_stat |
Overall chi-squared summary statistic |
p_stat_wb |
P-values corresponding to each of the summary statistics for each starting state |
p_ch_stat_wb |
P-values for overall chi-squared summary statistic |
b_stat_wb |
Bootstrap summary statistics for each of the starting states |
zbar |
Individual traces for each of the starting states |
nobs_grid |
The number of events after time s for each s in the grid |
Nsub |
Number of patients who are ever at risk of the transition of interest |
est_quant |
Pointwise 2.5 and 97.5 quantile limits for each of the traces |
obs_chisq_trace |
Trace of the chi-squared statistic |
nch_wb_trace |
Individual values of the chi-squared statistic trace for the wild bootstrap samples |
n_wb_trace |
Individual values of the log-rank z statistic traces for the wild bootstrap samples |
est_cov |
Estimated covariance matrix between the log-rank statistics at each grid point |
transition |
The transition number tested |
from |
The from state of the transition tested |
to |
The to state of the transition tested |
B |
The number of wild bootstrap replications |
dist |
The distribution used in the wild bootstrap |
qualset |
Set of qualifying states corresponding to the components of the above traces |
coxfit |
Fitted coxph object |
fn |
List of functions applied to state-specific trace |
fn2 |
List of functions applied to overall trace |
Andrew Titman [email protected], transported to mstate by Hein Putter [email protected]
Titman AC, Putter H (2020). General tests of the Markov property in multi-state models. Biostatistics To appear.
## Not run: # Example provided by the prothrombin data data("prothr") # Apply Markov test to grid of monthly time points over the first 7.5 years year <- 365.25 month <- year / 12 grid <- month * (1 : 90) # Markov test for transition 1 (wild bootstrap based on 25 replications, 1000 recommended) MT <- MarkovTest(prothr, id = "id", transition = 1, grid = grid, B = 25) # Plot traces plot(MT, grid, what="states", idx=1:10, states=rownames(attr(prothr, "trans")), xlab="Days since randomisation", ylab="Log-rank test statistic", main="Transition Normal -> Low") plot(MT, grid,what="overall", idx=1:10, xlab="Days since randomisation", ylab="Chi-square test statistic", main="Transition Normal -> Low") # Example using optimal weights and adjustment for covariates oweights_fun <- optimal_weights_matrix(prothr, id = "id", grid=grid, transition = 1, other_weights=list( function(x) mean(abs(x),na.rm=TRUE), function(x) max(abs(x),na.rm=TRUE))) oweights_chi <- optimal_weights_multiple(prothr, id = "id", grid=grid, transition = 1) # Formula in MarkovTest only works for continuous covariates and dummy coded variables # No factors allowed prothr$prednisone <- as.numeric(prothr$treat == "Prednisone") MT <- MarkovTest(prothr, id = "id", formula = "prednisone", transition = 1, grid = grid, B = 25, fn = oweights_fun, fn2 = list( function(x) weighted.mean(x, w=oweights_chi, na.rm=TRUE), function(x) mean(x, na.rm=TRUE), function(x) max(x, na.rm=TRUE))) ## End(Not run)## Not run: # Example provided by the prothrombin data data("prothr") # Apply Markov test to grid of monthly time points over the first 7.5 years year <- 365.25 month <- year / 12 grid <- month * (1 : 90) # Markov test for transition 1 (wild bootstrap based on 25 replications, 1000 recommended) MT <- MarkovTest(prothr, id = "id", transition = 1, grid = grid, B = 25) # Plot traces plot(MT, grid, what="states", idx=1:10, states=rownames(attr(prothr, "trans")), xlab="Days since randomisation", ylab="Log-rank test statistic", main="Transition Normal -> Low") plot(MT, grid,what="overall", idx=1:10, xlab="Days since randomisation", ylab="Chi-square test statistic", main="Transition Normal -> Low") # Example using optimal weights and adjustment for covariates oweights_fun <- optimal_weights_matrix(prothr, id = "id", grid=grid, transition = 1, other_weights=list( function(x) mean(abs(x),na.rm=TRUE), function(x) max(abs(x),na.rm=TRUE))) oweights_chi <- optimal_weights_multiple(prothr, id = "id", grid=grid, transition = 1) # Formula in MarkovTest only works for continuous covariates and dummy coded variables # No factors allowed prothr$prednisone <- as.numeric(prothr$treat == "Prednisone") MT <- MarkovTest(prothr, id = "id", formula = "prednisone", transition = 1, grid = grid, B = 25, fn = oweights_fun, fn2 = list( function(x) weighted.mean(x, w=oweights_chi, na.rm=TRUE), function(x) mean(x, na.rm=TRUE), function(x) max(x, na.rm=TRUE))) ## End(Not run)
A function that upgrades the transMat object so that the population and excess-related transitions are included in the transition matrix.
modify_transMat(trans, split.transitions)modify_transMat(trans, split.transitions)
trans |
The original transition matrix (usually generated using function transMat from mstate). Also often present in the msfit object. |
split.transitions |
The transitions that should be split. |
An upgraded transition matrix that contains the population and excess transitions.
Damjan Manevski [email protected]
# transition matrix for illness-death model trans <- transMat(list(c(2,3),c(4), c(), c()), names = c("Alive", "Relapse","Non-relapse mortality", "Death after relapse")) split.transitions <- c(2,3) modify_transMat(trans, split.transitions)# transition matrix for illness-death model trans <- transMat(list(c(2,3),c(4), c(), c()), names = c("Alive", "Relapse","Non-relapse mortality", "Death after relapse")) split.transitions <- c(2,3) modify_transMat(trans, split.transitions)
A generic nonparametric bootstrapping function for multi-state models.
msboot(theta, data, B = 5, id = "id", verbose = 0, ...)msboot(theta, data, B = 5, id = "id", verbose = 0, ...)
theta |
A function of |
data |
An object of class 'msdata', such as output from
|
B |
The number of bootstrap replications; the default is taken to be quite small (5) since bootstrapping can be time-consuming |
id |
Character string indicating which column identifies the subjects to be resampled |
verbose |
The level of output; default 0 = no output, 1 = print the replication |
... |
Any further arguments to the function |
The function msboot samples randomly with replacement subjects from
the original dataset data. The individuals are identified with
id, and bootstrap datasets are produced by concatenating all selected
rows.
Matrix of dimension (length of output of theta) x B, with b'th column being the value of theta for the b'th bootstrap dataset
Marta Fiocco, Hein Putter <[email protected]>
Fiocco M, Putter H, van Houwelingen HC (2008). Reduced-rank proportional hazards regression and simulation-based prediction for multi-state models. Statistics in Medicine 27, 4340–4358.
tmat <- trans.illdeath() data(ebmt1) covs <- c("score","yrel") msebmt <- msprep(time=c(NA,"rel","srv"),status=c(NA,"relstat","srvstat"), data=ebmt1,id="patid",keep=covs,trans=tmat) # define a function (this one returns vector of regression coef's) regcoefvec <- function(data) { cx <- coxph(Surv(Tstart,Tstop,status)~score+strata(trans), data=data,method="breslow") return(coef(cx)) } regcoefvec(msebmt) set.seed(1234) msboot(theta=regcoefvec,data=msebmt,id="patid")tmat <- trans.illdeath() data(ebmt1) covs <- c("score","yrel") msebmt <- msprep(time=c(NA,"rel","srv"),status=c(NA,"relstat","srvstat"), data=ebmt1,id="patid",keep=covs,trans=tmat) # define a function (this one returns vector of regression coef's) regcoefvec <- function(data) { cx <- coxph(Surv(Tstart,Tstop,status)~score+strata(trans), data=data,method="breslow") return(coef(cx)) } regcoefvec(msebmt) set.seed(1234) msboot(theta=regcoefvec,data=msebmt,id="patid")
A helper nonparametric bootstrapping function for variances in extended multi-state models using relative survival. This implementation is written based on function mstate:::msboot.
msboot.relsurv( theta, data, B = 10, id = "id", verbose = 0, transmat, all_times, split.transitions, rmap, time.format, boot_orig_msfit, ratetable = relsurv::slopop, add.times, ... )msboot.relsurv( theta, data, B = 10, id = "id", verbose = 0, transmat, all_times, split.transitions, rmap, time.format, boot_orig_msfit, ratetable = relsurv::slopop, add.times, ... )
theta |
A function of data and perhaps other arguments, returning the value of the statistic to be bootstrapped |
data |
An object of class 'msdata', such as output from msprep |
B |
The number of bootstrap replications; the default is B=10 |
id |
Character string indicating which column identifies the subjects to be resampled |
verbose |
The level of output; default 0 = no output, 1 = print the replication |
transmat |
The transition matrix of class transMat |
all_times |
All times at which the hazards have to be evaluated |
split.transitions |
An integer vector containing the numbered transitions that should be split. Use same numbering as in the given transition matrix |
rmap |
An optional list to be used if the variables in the dataset are not organized (and named) in the same way as in the ratetable object |
time.format |
Define the time format which is used in the dataset Possible options: c('days', 'years', 'months'). Default is 'days' |
boot_orig_msfit |
Logical, if true, do the bootstrap for the basic msfit model |
ratetable |
The population mortality table. A table of event rates, organized as a ratetable object, see for example relsurv::slopop. Default is slopop |
add.times |
Additional times at which hazards should be evaluated |
... |
Any further arguments to the function theta |
A list of size B containing the results for every bootstrap replication.
Damjan Manevski [email protected], Marta Fiocco, Hein Putter [email protected]
Helper function used for calling inside msboot.relsurv (used for every bootstrap dataset). This function is used for calculating split hazards and evaluating them at all needed times.
msboot.relsurv.boot( data, transmat, all_times, split.transitions, rmap, time.format, boot_orig_msfit = FALSE, ratetable = relsurv::slopop, add.times )msboot.relsurv.boot( data, transmat, all_times, split.transitions, rmap, time.format, boot_orig_msfit = FALSE, ratetable = relsurv::slopop, add.times )
data |
An object of class 'msdata' containing a bootstrapped sample |
transmat |
The transition matrix of class transMat |
all_times |
All times at which the hazards have to be evaluated |
split.transitions |
An integer vector containing the numbered transitions that should be split. Use same numbering as in the given transition matrix |
rmap |
An optional list to be used if the variables in the dataset are not organized (and named) in the same way as in the ratetable object |
time.format |
Define the time format which is used in the dataset Possible options: c('days', 'years', 'months'). Default is 'days' |
boot_orig_msfit |
Logical, if true, do the bootstrap for the basic msfit model |
ratetable |
The population mortality table. A table of event rates, organized as a ratetable object, see for example relsurv::slopop. Default is slopop |
add.times |
Additional times at which hazards should be evaluated |
A list of calculated values for the given bootstrap sample.
Damjan Manevski [email protected]
msdata to etm format
msdata2etm(msdata, id, covs)msdata2etm(msdata, id, covs)
msdata |
Multi-state data in |
id |
Column name identifying the subject id |
covs |
Vector of column names containing covariates to be included |
This function computes subject-specific or overall cumulative transition hazards for each of the possible transitions in the multi-state model. If requested, also the variances and covariances of the estimated cumulative transition hazards are calculated.
msfit( object, newdata, variance = TRUE, vartype = c("aalen", "greenwood"), trans )msfit( object, newdata, variance = TRUE, vartype = c("aalen", "greenwood"), trans )
object |
A |
newdata |
A data frame with the same variable names as those that
appear in the |
variance |
A logical value indicating whether the (co-)variances of the
subject-specific transition hazards should be computed. Default is
|
vartype |
A character string specifying the type of variances to be
computed (so only needed if |
trans |
Transition matrix describing the states and transitions in the
multi-state model. See |
The data frame needs to have one row for each transition in the multi-state
model. An additional column strata (numeric) is needed to describe
for each transition to which stratum it belongs. The name has to be
strata, even if in the original coxph call another variable
was used. For details refer to de Wreede, Fiocco & Putter (2010). So far,
the results have been checked only for the "breslow" method of
dealing with ties in coxph, so this is
recommended.
An object of class "msfit", which is a list containing
Haz |
A data frame with |
varHaz |
A data frame with
|
trans |
The transition matrix used |
Hein Putter [email protected]
Putter H, Fiocco M, Geskus RB (2007). Tutorial in biostatistics: Competing risks and multi-state models. Statistics in Medicine 26, 2389–2430.
Therneau TM, Grambsch PM (2000). Modeling Survival Data: Extending the Cox Model. Springer, New York.
de Wreede LC, Fiocco M, and Putter H (2010). The mstate package for estimation and prediction in non- and semi-parametric multi-state and competing risks models. Computer Methods and Programs in Biomedicine 99, 261–274.
de Wreede LC, Fiocco M, and Putter H (2011). mstate: An R Package for the Analysis of Competing Risks and Multi-State Models. Journal of Statistical Software, Volume 38, Issue 7.
# transition matrix for illness-death model tmat <- trans.illdeath() # data in wide format, for transition 1 this is dataset E1 of # Therneau & Grambsch (2000) tg <- data.frame(illt=c(1,1,6,6,8,9),ills=c(1,0,1,1,0,1), dt=c(5,1,9,7,8,12),ds=c(1,1,1,1,1,1), x1=c(1,1,1,0,0,0),x2=c(6:1)) # data in long format using msprep tglong <- msprep(time=c(NA,"illt","dt"),status=c(NA,"ills","ds"), data=tg,keep=c("x1","x2"),trans=tmat) # events events(tglong) table(tglong$status,tglong$to,tglong$from) # expanded covariates tglong <- expand.covs(tglong,c("x1","x2")) # Cox model with different covariate cx <- coxph(Surv(Tstart,Tstop,status)~x1.1+x2.2+strata(trans), data=tglong,method="breslow") summary(cx) # new data, to check whether results are the same for transition 1 as # those in appendix E.1 of Therneau & Grambsch (2000) newdata <- data.frame(trans=1:3,x1.1=c(0,0,0),x2.2=c(0,1,0),strata=1:3) msfit(cx,newdata,trans=tmat)# transition matrix for illness-death model tmat <- trans.illdeath() # data in wide format, for transition 1 this is dataset E1 of # Therneau & Grambsch (2000) tg <- data.frame(illt=c(1,1,6,6,8,9),ills=c(1,0,1,1,0,1), dt=c(5,1,9,7,8,12),ds=c(1,1,1,1,1,1), x1=c(1,1,1,0,0,0),x2=c(6:1)) # data in long format using msprep tglong <- msprep(time=c(NA,"illt","dt"),status=c(NA,"ills","ds"), data=tg,keep=c("x1","x2"),trans=tmat) # events events(tglong) table(tglong$status,tglong$to,tglong$from) # expanded covariates tglong <- expand.covs(tglong,c("x1","x2")) # Cox model with different covariate cx <- coxph(Surv(Tstart,Tstop,status)~x1.1+x2.2+strata(trans), data=tglong,method="breslow") summary(cx) # new data, to check whether results are the same for transition 1 as # those in appendix E.1 of Therneau & Grambsch (2000) newdata <- data.frame(trans=1:3,x1.1=c(0,0,0),x2.2=c(0,1,0),strata=1:3) msfit(cx,newdata,trans=tmat)
A function that takes a fitted msfit object and upgrades it using relative survival, where chosen transitions are split in population and excess transitions. This upgraded msfit object contains the split hazards based on the transition matrix (transMat). The (co)variance matrix is also upgraded, if provided.
msfit.relsurv( msfit.obj, data, split.transitions, ratetable = relsurv::slopop, rmap, time.format = "days", var.pop.haz = c("fixed", "bootstrap", "both"), B = 10, seed = NULL, add.times, substitution = TRUE, link_trans_ind = FALSE )msfit.relsurv( msfit.obj, data, split.transitions, ratetable = relsurv::slopop, rmap, time.format = "days", var.pop.haz = c("fixed", "bootstrap", "both"), B = 10, seed = NULL, add.times, substitution = TRUE, link_trans_ind = FALSE )
msfit.obj |
The msfit object which has to be upgraded |
data |
The data used for fitting the msfit model |
split.transitions |
An integer vector containing the numbered transitions that should be split. Use same numbering as in the given transition matrix |
ratetable |
The population mortality table. A table of event rates, organized as a ratetable object, see for example relsurv::slopop. Default is slopop |
rmap |
An optional list to be used if the variables in the data are not organized (and named) in the same way as in the ratetable object |
time.format |
Define the time format which is used in the data. Possible options: c('days', 'years', 'months'). Default is 'days' |
var.pop.haz |
If 'fixed' (default), the Greenwood estimator for the variances is used, where it is assumed that the variance of the population hazards is zero. If 'bootstrap', one gets boostrap estimates for all all transitions. Option 'both' gives both variance estimates |
B |
Number of bootstrap replications. Relevant only if var.pop.haz == 'bootstrap' or 'both'. Default is B=10. |
seed |
Set seed |
add.times |
Additional times at which hazards should be evaluated |
substitution |
Whether function substitute should be used for rmap argument. Default is TRUE |
link_trans_ind |
Choose whether the linkage between the old and new transition matrix should be saved. Default is FALSE. |
Returns a msfit object that contains estimates for the extended model with split (population and excess) transitions.
Damjan Manevski [email protected]
Manevski D, Putter H, Pohar Perme M, Bonneville EF, Schetelig J, de Wreede LC (2021). Integrating relative survival in multi-state models – a non-parametric approach. https://arxiv.org/abs/2106.12399
## Not run: library(mstate) # Load dataset: data("ebmt1") # Transition matrix: tmat <- transMat(list(c(2,3),c(4), c(), c()), names = c("Alive relapse-free", "Relapse","NRM", "DaR")) # Data in long format using msprep df <- msprep(time=c(NA,"rel","srv","srv"), status=c(NA,"relstat","srvstat","srvstat"), data=ebmt1, trans=tmat) # Generate demographic covariates (which are usually present in datasets) # and based on them estimate the population hazard. set.seed(510) df$age <- runif(nrow(df), 45, 65) df$sex <- sample(c("male", "female"), size = nrow(df), replace = TRUE) df$dateHCT <- sample(seq(as.Date('1990/01/01'), as.Date('2000/01/01'), by="day"), nrow(df), replace = TRUE) # generate years # Cox object: cx <- coxph(Surv(Tstart,Tstop,status)~strata(trans), data=df,method="breslow") # Basic multi-state model: mod <- msfit(cx,trans=tmat) # Extended multi-state model, where the two transition # reaching death are split in excess and population parts. # We assume patients live like in the Slovene population, # thus we use Slovene mortality tables in this example. # Variances estimated using 25 bootstrap replications. mod.relsurv <- msfit.relsurv(msfit.obj = mod, data=df, split.transitions = c(2,3), ratetable = relsurv::slopop, rmap = list(age=age*365.241, year=dateHCT), time.format = "days", var.pop.haz = "bootstrap", B = 25) # Estimate transition probabilities: pt <- probtrans(mod.relsurv, predt=0, method='greenwood') # Estimated cumulative hazards with the corresponding # bootstrap standard errors at 300, 600, 900 days: summary(object = mod.relsurv, times = c(300, 600, 900), conf.type = 'log') # Estimated transition probabilities together with the corresponding # bootstrap standard errors and log.boot confidence intervals # at 300, 600, 900 days: summary(object = pt, times = c(300, 600, 900), conf.type = 'log') # Plot the measures: plot(mod.relsurv, use.ggplot = TRUE) plot(pt, use.ggplot = TRUE) ## End(Not run)## Not run: library(mstate) # Load dataset: data("ebmt1") # Transition matrix: tmat <- transMat(list(c(2,3),c(4), c(), c()), names = c("Alive relapse-free", "Relapse","NRM", "DaR")) # Data in long format using msprep df <- msprep(time=c(NA,"rel","srv","srv"), status=c(NA,"relstat","srvstat","srvstat"), data=ebmt1, trans=tmat) # Generate demographic covariates (which are usually present in datasets) # and based on them estimate the population hazard. set.seed(510) df$age <- runif(nrow(df), 45, 65) df$sex <- sample(c("male", "female"), size = nrow(df), replace = TRUE) df$dateHCT <- sample(seq(as.Date('1990/01/01'), as.Date('2000/01/01'), by="day"), nrow(df), replace = TRUE) # generate years # Cox object: cx <- coxph(Surv(Tstart,Tstop,status)~strata(trans), data=df,method="breslow") # Basic multi-state model: mod <- msfit(cx,trans=tmat) # Extended multi-state model, where the two transition # reaching death are split in excess and population parts. # We assume patients live like in the Slovene population, # thus we use Slovene mortality tables in this example. # Variances estimated using 25 bootstrap replications. mod.relsurv <- msfit.relsurv(msfit.obj = mod, data=df, split.transitions = c(2,3), ratetable = relsurv::slopop, rmap = list(age=age*365.241, year=dateHCT), time.format = "days", var.pop.haz = "bootstrap", B = 25) # Estimate transition probabilities: pt <- probtrans(mod.relsurv, predt=0, method='greenwood') # Estimated cumulative hazards with the corresponding # bootstrap standard errors at 300, 600, 900 days: summary(object = mod.relsurv, times = c(300, 600, 900), conf.type = 'log') # Estimated transition probabilities together with the corresponding # bootstrap standard errors and log.boot confidence intervals # at 300, 600, 900 days: summary(object = pt, times = c(300, 600, 900), conf.type = 'log') # Plot the measures: plot(mod.relsurv, use.ggplot = TRUE) plot(pt, use.ggplot = TRUE) ## End(Not run)
This function converts a dataset which is in wide format (one subject per line, multiple columns indicating time and status for different states) into a dataset in long format (one line for each transition for which a subject is at risk). Selected covariates are replicated per subjects.
msprep(time, status, data, trans, start, id, keep)msprep(time, status, data, trans, start, id, keep)
time |
Either 1) a matrix or data frame of dimension n x S (n being the
number of individuals and S the number of states in the multi-state model),
containing the times at which the states are visited or last follow-up time,
or 2) a character vector of length S containing the column names indicating
these times. In the latter cases, some elements of |
status |
Either 1) a matrix or data frame of dimension n x S,
containing, for each of the states, event indicators taking the value 1 if
the state is visited or 0 if it is not (censored), or 2) a character vector
of length S containing the column names indicating these status variables.
In the latter cases, some elements of |
data |
Data frame (not a tibble) in wide format in which to interpret
|
trans |
Transition matrix describing the states and transitions in the
multi-state model. If S is the number of states in the multi-state model,
|
start |
List with elements |
id |
Either 1) a vector of length n containing the subject
identifications, or 2) a character string indicating the column name
containing these subject ids. If not provided, |
keep |
Either 1) a data frame or matrix with n rows or a numeric or
factor vector of length n containing covariate(s) that need to be retained
in the output dataset, or 2) a character vector containing the column names
of these covariates in |
For msprep, the transition matrix should correspond to an
irreversible acyclic Markov chain. In particular, on the diagonals only
NAs are allowed.
The transition matrix, if irreversible and acyclic, will have starting
states, i.e. states into which no transitions are possible. For these
starting states NAs are allowed in the time and status
arguments, either as columns, when specified as matrix or data frame, or as
elements of the character vector when specified as character vector.
The function msprep uses a recursive algorithm through calls to the
recursive function msprepEngine. First, with the current transition
matrix, all starting states are detected (defined as states into which there
are no transitions). For each of these starting states, all subjects
starting from that state are selected and for each subject the next visited
state is detected by looking at all transitions from that starting state and
determining the smallest transition time with status=1. The recursive
msprepEngine is called again with the starting states deleted from
the transition matrix and with subjects deleted that either reached an
absorbing state or that were censored. For the remaining subjects the
starting states and times are updated in the next call. Datasets returned
from the msprepEngine calls are appended to the current dataset in
long format and finally sorted.
A warning is issued for a subject, if multiple transitions exist with the
same smallest transition time (and status=0). In such cases the next
transition cannot be determined unambiguously, and the state with the
smallest number is chosen. In our experience, occasionally the shortest
transition time has status=0, while a higher transition time has
status=1. Then this larger transition time and the corresponding
transition is selected. No warning is issued for these data inconsistencies.
An object of class "msdata", which is a data frame in long
(counting process) format containing the subject id, the covariates
(replicated per subject), and
from |
the starting state |
to |
the receiving state |
trans |
the transition number |
Tstart |
the starting time of the transition |
Tstop |
the stopping time of the transition |
status |
status variable, with 1 indicating an event (transition), 0 a censoring |
The "msdata" object has the transition
matrix as "trans" attribute.
Hein Putter [email protected] and Marta Fiocco
Putter H, Fiocco M, Geskus RB (2007). Tutorial in biostatistics: Competing risks and multi-state models. Statistics in Medicine 26, 2389–2430.
# transition matrix for illness-death model tmat <- trans.illdeath() # some data in wide format tg <- data.frame(stt=rep(0,6),sts=rep(0,6), illt=c(1,1,6,6,8,9),ills=c(1,0,1,1,0,1), dt=c(5,1,9,7,8,12),ds=c(1,1,1,1,1,1), x1=c(1,1,1,2,2,2),x2=c(6:1)) tg$x1 <- factor(tg$x1,labels=c("male","female")) tg$patid <- factor(2:7,levels=1:8,labels=as.character(1:8)) # define time, status and covariates also as matrices tt <- matrix(c(rep(NA,6),tg$illt,tg$dt),6,3) st <- matrix(c(rep(NA,6),tg$ills,tg$ds),6,3) keepmat <- data.frame(gender=tg$x1,age=tg$x2) # data in long format using msprep msprep(time=tt,status=st,trans=tmat,keep=as.matrix(keepmat)) msprep(time=c(NA,"illt","dt"),status=c(NA,"ills","ds"),data=tg, id="patid",keep=c("x1","x2"),trans=tmat) # Patient no 5, 6 now start in state 2 at time t=4 and t=10 msprep(time=tt,status=st,trans=tmat,keep=keepmat, start=list(state=c(1,1,1,1,2,2),time=c(0,0,0,0,4,10)))# transition matrix for illness-death model tmat <- trans.illdeath() # some data in wide format tg <- data.frame(stt=rep(0,6),sts=rep(0,6), illt=c(1,1,6,6,8,9),ills=c(1,0,1,1,0,1), dt=c(5,1,9,7,8,12),ds=c(1,1,1,1,1,1), x1=c(1,1,1,2,2,2),x2=c(6:1)) tg$x1 <- factor(tg$x1,labels=c("male","female")) tg$patid <- factor(2:7,levels=1:8,labels=as.character(1:8)) # define time, status and covariates also as matrices tt <- matrix(c(rep(NA,6),tg$illt,tg$dt),6,3) st <- matrix(c(rep(NA,6),tg$ills,tg$ds),6,3) keepmat <- data.frame(gender=tg$x1,age=tg$x2) # data in long format using msprep msprep(time=tt,status=st,trans=tmat,keep=as.matrix(keepmat)) msprep(time=c(NA,"illt","dt"),status=c(NA,"ills","ds"),data=tg, id="patid",keep=c("x1","x2"),trans=tmat) # Patient no 5, 6 now start in state 2 at time t=4 and t=10 msprep(time=tt,status=st,trans=tmat,keep=keepmat, start=list(state=c(1,1,1,1,2,2),time=c(0,0,0,0,4,10)))
Given cumulative transition hazards sample paths through the multi-state model.
mssample( Haz, trans, history = list(state = 1, time = 0, tstate = NULL), beta.state = NULL, clock = c("forward", "reset"), output = c("state", "path", "data"), tvec, cens = NULL, M = 10, do.trace = NULL )mssample( Haz, trans, history = list(state = 1, time = 0, tstate = NULL), beta.state = NULL, clock = c("forward", "reset"), output = c("state", "path", "data"), tvec, cens = NULL, M = 10, do.trace = NULL )
Haz |
Cumulative hazards to be sampled from. These should be given as a
data frame with columns |
trans |
Transition matrix describing the multi-state model. See
|
history |
A list with elements The elements |
beta.state |
A matrix of dimension (no states) x (no transitions)
specifying estimated effects of times at which earlier states were reached
on subsequent transitions. If these are not in the model, the value
|
clock |
Character argument, either |
output |
One of |
tvec |
A numeric vector of time points at which the states or paths
should be evaluated. Ignored if |
cens |
An independent censoring distribution, given as a data frame with time and Haz |
M |
The number of sampled trajectories through the multi-state model. The default is 10, since the procedure can become quite time-consuming |
do.trace |
An integer, specifying that the replication number should be
written to the console every |
The procedure is described in detail in Fiocco, Putter & van Houwelingen
(2008). The argument beta.state and the element tstate from
the argument history are meant to incorporate situations where the
time at which some previous states were visited may affect future transition
rates. The relation between time of visit of state s and transition
k is assumed to be linear on the log-hazards; the corresponding
regression coefficient is to be supplied as the (s,k)-element of
beta.state, which is 0 if no such effect has been included in the
model. If no such effects are present, then beta.state=NULL
(default) suffices. In the tstate element of history, the
s-th element is the time at which state s was visited. This is
only relevant for states which have been visited prior to the beginning of
sampling, i.e. before the time element of history; the
elements of tstate are internally updated when in the sampling
process new states are visited (only if beta.state is not NULL
to avoid unnecessary computations).
M simulated paths through the multi-state model given by
trans and Haz. It is either a data frame with columns
time, pstate1, ..., pstateS for S states when
output="state", or with columns time, ppath1,...,
ppathP for the P paths specified in paths(trans) when
output="path". When output="data", the sampled paths are
stored in an "msdata" object, a data frame in long format such as
that obtained by msprep. This may be useful for
(semi-)parametric bootstrap procedures, in which case cens may be
used as censoring distribution (assumed to be independent of all transition
times and independent of any covariates).
Marta Fiocco, Hein Putter [email protected]
Fiocco M, Putter H, van Houwelingen HC (2008). Reduced-rank proportional hazards regression and simulation-based prediction for multi-state models. Statistics in Medicine 27, 4340–4358.
# transition matrix for illness-death model tmat <- trans.illdeath() # data in wide format, for transition 1 this is dataset E1 of # Therneau & Grambsch (T&G) tg <- data.frame(illt=c(1,1,6,6,8,9),ills=c(1,0,1,1,0,1), dt=c(5,1,9,7,8,12),ds=c(1,1,1,1,1,1), x1=c(1,1,1,0,0,0),x2=c(6:1)) # data in long format using msprep tglong <- msprep(time=c(NA,"illt","dt"),status=c(NA,"ills","ds"), data=tg,keep=c("x1","x2"),trans=tmat) # expanded covariates tglong <- expand.covs(tglong,c("x1","x2")) # Cox model with different covariate cx <- coxph(Surv(Tstart,Tstop,status)~x1.1+x2.2+strata(trans), data=tglong,method="breslow") # new data, to check whether results are the same for transition 1 as T&G newdata <- data.frame(trans=1:3,x1.1=c(0,0,0),x2.2=c(0,1,0),strata=1:3) fit <- msfit(cx,newdata,trans=tmat) tv <- unique(fit$Haz$time) # mssample set.seed(1234) mssample(Haz=fit$Haz,trans=tmat,tvec=tv,M=100) set.seed(1234) paths(tmat) mssample(Haz=fit$Haz,trans=tmat,tvec=tv,M=100,output="path") set.seed(1234) mssample(Haz=fit$Haz,trans=tmat,tvec=tv,M=100,output="data",do.trace=25)# transition matrix for illness-death model tmat <- trans.illdeath() # data in wide format, for transition 1 this is dataset E1 of # Therneau & Grambsch (T&G) tg <- data.frame(illt=c(1,1,6,6,8,9),ills=c(1,0,1,1,0,1), dt=c(5,1,9,7,8,12),ds=c(1,1,1,1,1,1), x1=c(1,1,1,0,0,0),x2=c(6:1)) # data in long format using msprep tglong <- msprep(time=c(NA,"illt","dt"),status=c(NA,"ills","ds"), data=tg,keep=c("x1","x2"),trans=tmat) # expanded covariates tglong <- expand.covs(tglong,c("x1","x2")) # Cox model with different covariate cx <- coxph(Surv(Tstart,Tstop,status)~x1.1+x2.2+strata(trans), data=tglong,method="breslow") # new data, to check whether results are the same for transition 1 as T&G newdata <- data.frame(trans=1:3,x1.1=c(0,0,0),x2.2=c(0,1,0),strata=1:3) fit <- msfit(cx,newdata,trans=tmat) tv <- unique(fit$Haz$time) # mssample set.seed(1234) mssample(Haz=fit$Haz,trans=tmat,tvec=tv,M=100) set.seed(1234) paths(tmat) mssample(Haz=fit$Haz,trans=tmat,tvec=tv,M=100,output="path") set.seed(1234) mssample(Haz=fit$Haz,trans=tmat,tvec=tv,M=100,output="data",do.trace=25)
For a given multi-state model, specified through a transition matrix,
paths recursively finds all the possible trajectories or paths
through that multi-state starting from a specified state. DO NOT USE for
reversible or cyclic multi-state models.
paths(trans, start = 1)paths(trans, start = 1)
trans |
The transition matrix describing the multi-state model, see
|
start |
The starting state for the trajectories |
The function is recursive. It starts in start, looks at what states
can be visited from start, and appends the results of the next call
to the current value (matrix). If the transition matrix contains loops, the
function will find infinitely many paths, so do not use paths for
reversible or cyclic multi-state models. A warning is not yet incorporated!
A matrix, each row of which specifies a possible path through the multi-state model.
Hein Putter <[email protected]>
tmat <- matrix(NA,5,5) tmat[1,2:3] <- 1:2 tmat[1,5] <- 3 tmat[2,4:5] <- 4:5 tmat[3,4:5] <- 6:7 tmat[4,5] <- 8 paths(tmat) paths(tmat, start=3)tmat <- matrix(NA,5,5) tmat[1,2:3] <- 1:2 tmat[1,5] <- 3 tmat[2,4:5] <- 4:5 tmat[3,4:5] <- 6:7 tmat[4,5] <- 8 paths(tmat) paths(tmat, start=3)
Plot the estimates of the non-parametric Aalen-Johansen estimate of the
cumulative incidence functions (competing risks data). Note this is a method
for mstate::Cuminc and not cmprsk::cuminc. Both return the same
estimates, though the former does so in a dataframe, and the latter in the list.
## S3 method for class 'Cuminc' plot( x, use.ggplot = FALSE, xlab = "Time", ylab = "Probability", xlim, ylim, lty, legend, cols, conf.type = c("log", "plain", "none"), conf.int = 0.95, legend.pos = "right", facet = FALSE, ... )## S3 method for class 'Cuminc' plot( x, use.ggplot = FALSE, xlab = "Time", ylab = "Probability", xlim, ylim, lty, legend, cols, conf.type = c("log", "plain", "none"), conf.int = 0.95, legend.pos = "right", facet = FALSE, ... )
x |
Object of class |
use.ggplot |
Default FALSE, set TRUE for ggplot version of plot |
xlab |
A title for the x-axis; default is |
ylab |
A title for the y-axis; default is |
xlim |
The x limits of the plot(s), default is range of time |
ylim |
The y limits of the plot(s); if ylim is specified for type="separate", then all plots use the same ylim for y limits |
lty |
The line type, see |
legend |
Character vector corresponding to number of absorbing states.
In case of a grouped |
cols |
Vector (numeric or character) specifying colours of the lines |
conf.type |
Type of confidence interval - either "log" or "plain" . See function details for details. |
conf.int |
Confidence level (%) from 0-1 for probabilities, default is 0.95 (95% CI). Setting to 0 removes the CIs. |
legend.pos |
The position of the legend, see |
facet |
Logical, in case of group used for |
... |
Further arguments to plot or print method |
Grouped cumulative incidences can be plotted either in the same plot or in facets,
see the facet argument.
A ggplot object if use.ggplot = T used, otherwise NULL.
Edouard F. Bonneville [email protected]
library(ggplot2) data("aidssi") head(aidssi) si <- aidssi # No grouping cum_incid <- Cuminc( time = "time", status = "status", data = si ) plot( x = cum_incid, use.ggplot = TRUE, conf.type = "none", lty = 1:2, conf.int = 0.95 ) # With grouping cum_incid_grp <- Cuminc( time = "time", status = "status", group = "ccr5", data = si ) plot( x = cum_incid_grp, use.ggplot = TRUE, conf.type = "none", lty = 1:4, facet = TRUE )library(ggplot2) data("aidssi") head(aidssi) si <- aidssi # No grouping cum_incid <- Cuminc( time = "time", status = "status", data = si ) plot( x = cum_incid, use.ggplot = TRUE, conf.type = "none", lty = 1:2, conf.int = 0.95 ) # With grouping cum_incid_grp <- Cuminc( time = "time", status = "status", group = "ccr5", data = si ) plot( x = cum_incid_grp, use.ggplot = TRUE, conf.type = "none", lty = 1:4, facet = TRUE )
Plot method for an object of class 'MarkovTest'. It plots the trace of the
log-rank statistics provided by MarkovTest.
## S3 method for class 'MarkovTest' plot( x, y, what = c("states", "overall"), idx = NULL, quantiles = TRUE, qsup, states, xlab, ylab, main, ... )## S3 method for class 'MarkovTest' plot( x, y, what = c("states", "overall"), idx = NULL, quantiles = TRUE, qsup, states, xlab, ylab, main, ... )
x |
Object of class 'MarkovTest' |
y |
The grid at which |
what |
Choose "states" for plotting state-specific traces, and "overall" for the overall chi-squared trace |
idx |
Vector of indices of wild bootstrap traces to plot |
quantiles |
Boolean whether or not to plot the 2.5 and 97.5 percent
quantiles, default is |
qsup |
The index of the function in either |
states |
Number of the qualifying state(s) to plot trace for |
xlab |
Text for x-axis label |
ylab |
Text for y-axis label |
main |
Text for title (main) |
... |
Further arguments to plot |
No return value
Hein Putter [email protected]
## Not run: # Example provided by the prothrombin data data("prothr") # Apply Markov test to grid of monthly time points over the first 7.5 years year <- 365.25 month <- year / 12 grid <- month * (1:90) # Markov test for transition 1 (wild bootstrap based on 100 replications) MT <- MarkovTest(prothr, id = "id", transition = 1, grid = grid, B = 100) plot(MT, grid, what="states", idx=1:50, states=rownames(attr(prothr, "trans")), xlab="Days since randomisation", ylab="Log-rank test statistic", main="Transition Normal -> Low") plot(MT, grid,what="overall", idx=1:50, xlab="Days since randomisation", ylab="Chi-square test statistic", main="Transition Normal -> Low") plot(MT, grid, what="states", quantiles=FALSE) # only trace plot(MT, grid, what="states") # trace plus quantiles (default) plot(MT, grid, what="states", idx=1:10) # trace plus quantiles, plus first 10 bootstrap traces plot(MT, grid, what="overall", quantiles=FALSE) # only trace plot(MT, grid, what="overall") # trace plus quantiles (default) plot(MT, grid, what="overall", idx=1:10) # trace plus quantiles, plus first 10 bootstrap traces ## End(Not run)## Not run: # Example provided by the prothrombin data data("prothr") # Apply Markov test to grid of monthly time points over the first 7.5 years year <- 365.25 month <- year / 12 grid <- month * (1:90) # Markov test for transition 1 (wild bootstrap based on 100 replications) MT <- MarkovTest(prothr, id = "id", transition = 1, grid = grid, B = 100) plot(MT, grid, what="states", idx=1:50, states=rownames(attr(prothr, "trans")), xlab="Days since randomisation", ylab="Log-rank test statistic", main="Transition Normal -> Low") plot(MT, grid,what="overall", idx=1:50, xlab="Days since randomisation", ylab="Chi-square test statistic", main="Transition Normal -> Low") plot(MT, grid, what="states", quantiles=FALSE) # only trace plot(MT, grid, what="states") # trace plus quantiles (default) plot(MT, grid, what="states", idx=1:10) # trace plus quantiles, plus first 10 bootstrap traces plot(MT, grid, what="overall", quantiles=FALSE) # only trace plot(MT, grid, what="overall") # trace plus quantiles (default) plot(MT, grid, what="overall", idx=1:10) # trace plus quantiles, plus first 10 bootstrap traces ## End(Not run)
Plot method for an object of class "msfit". It plots the estimated
cumulative transition intensities in the multi-state model.
## S3 method for class 'msfit' plot( x, type = c("single", "separate"), cols, xlab = "Time", ylab = "Cumulative hazard", ylim, lwd, lty, legend, legend.pos = "right", bty = "n", use.ggplot = FALSE, xlim, scale_type = "fixed", conf.int = 0.95, conf.type = "none", ... )## S3 method for class 'msfit' plot( x, type = c("single", "separate"), cols, xlab = "Time", ylab = "Cumulative hazard", ylim, lwd, lty, legend, legend.pos = "right", bty = "n", use.ggplot = FALSE, xlim, scale_type = "fixed", conf.int = 0.95, conf.type = "none", ... )
x |
Object of class |
type |
One of |
cols |
A vector specifying colors for the different transitions;
default is 1:K (K no of transitions), when type= |
xlab |
A title for the x-axis; default is |
ylab |
A title for the y-axis; default is |
ylim |
The y limits of the plot(s); if ylim is specified for type="separate", then all plots use the same ylim for y limits |
lwd |
The line width, see |
lty |
The line type, see |
legend |
Character vector of length equal to the number of transitions,
to be used in a legend; if missing, these will be taken from the row- and
column-names of the transition matrix contained in |
legend.pos |
The position of the legend, see |
bty |
The box type of the legend, see |
use.ggplot |
Default FALSE, set TRUE for ggplot version of plot |
xlim |
Limits of x axis, relevant if use_ggplot = T |
scale_type |
"fixed", "free", "free_x" or "free_y", see scales argument of facet_wrap(). Only relevant for use_ggplot = T. |
conf.int |
Confidence level (%) from 0-1 for the cumulative hazard, default is 0.95. Only relevant for use_ggplot = T |
conf.type |
Type of confidence interval - either "log" or "plain" . See
function details of |
... |
Further arguments to plot |
No return value
Hein Putter [email protected]
Edouard F. Bonneville [email protected]
# transition matrix for illness-death model tmat <- trans.illdeath() # data in wide format, for transition 1 this is dataset E1 of # Therneau & Grambsch (2000) tg <- data.frame(illt=c(1,1,6,6,8,9),ills=c(1,0,1,1,0,1), dt=c(5,1,9,7,8,12),ds=c(1,1,1,1,1,1), x1=c(1,1,1,0,0,0),x2=c(6:1)) # data in long format using msprep tglong <- msprep(time=c(NA,"illt","dt"),status=c(NA,"ills","ds"), data=tg,keep=c("x1","x2"),trans=tmat) # events events(tglong) table(tglong$status,tglong$to,tglong$from) # expanded covariates tglong <- expand.covs(tglong,c("x1","x2")) # Cox model with different covariate cx <- coxph(Surv(Tstart,Tstop,status)~x1.1+x2.2+strata(trans), data=tglong,method="breslow") summary(cx) # new data, to check whether results are the same for transition 1 as # those in appendix E.1 of Therneau & Grambsch (2000) newdata <- data.frame(trans=1:3,x1.1=c(0,0,0),x2.2=c(0,1,0),strata=1:3) msf <- msfit(cx,newdata,trans=tmat) # standard plot plot(msf) # specifying line width, color, and legend plot(msf,lwd=2,col=c("darkgreen","darkblue","darkred"),legend=c("1->2","1->3","2->3")) # separate plots par(mfrow=c(2,2)) plot(msf,type="separate",lwd=2) par(mfrow=c(1,1)) # ggplot version - see vignette for details library(ggplot2) plot(msf, use.ggplot = TRUE)# transition matrix for illness-death model tmat <- trans.illdeath() # data in wide format, for transition 1 this is dataset E1 of # Therneau & Grambsch (2000) tg <- data.frame(illt=c(1,1,6,6,8,9),ills=c(1,0,1,1,0,1), dt=c(5,1,9,7,8,12),ds=c(1,1,1,1,1,1), x1=c(1,1,1,0,0,0),x2=c(6:1)) # data in long format using msprep tglong <- msprep(time=c(NA,"illt","dt"),status=c(NA,"ills","ds"), data=tg,keep=c("x1","x2"),trans=tmat) # events events(tglong) table(tglong$status,tglong$to,tglong$from) # expanded covariates tglong <- expand.covs(tglong,c("x1","x2")) # Cox model with different covariate cx <- coxph(Surv(Tstart,Tstop,status)~x1.1+x2.2+strata(trans), data=tglong,method="breslow") summary(cx) # new data, to check whether results are the same for transition 1 as # those in appendix E.1 of Therneau & Grambsch (2000) newdata <- data.frame(trans=1:3,x1.1=c(0,0,0),x2.2=c(0,1,0),strata=1:3) msf <- msfit(cx,newdata,trans=tmat) # standard plot plot(msf) # specifying line width, color, and legend plot(msf,lwd=2,col=c("darkgreen","darkblue","darkred"),legend=c("1->2","1->3","2->3")) # separate plots par(mfrow=c(2,2)) plot(msf,type="separate",lwd=2) par(mfrow=c(1,1)) # ggplot version - see vignette for details library(ggplot2) plot(msf, use.ggplot = TRUE)
Plot method for an object of class 'probtrans'. It plots the transition
probabilities as estimated by probtrans.
## S3 method for class 'probtrans' plot( x, from = 1, type = c("filled", "single", "separate", "stacked"), ord, cols, xlab = "Time", ylab = "Probability", xlim, ylim, lwd, lty, cex, legend, legend.pos = "right", bty = "n", xaxs = "i", yaxs = "i", use.ggplot = FALSE, conf.int = 0.95, conf.type = c("log", "plain", "none"), label, ... )## S3 method for class 'probtrans' plot( x, from = 1, type = c("filled", "single", "separate", "stacked"), ord, cols, xlab = "Time", ylab = "Probability", xlim, ylim, lwd, lty, cex, legend, legend.pos = "right", bty = "n", xaxs = "i", yaxs = "i", use.ggplot = FALSE, conf.int = 0.95, conf.type = c("log", "plain", "none"), label, ... )
x |
Object of class 'probtrans', containing estimated transition probabilities |
from |
The starting state from which the probabilities are used to plot |
type |
One of |
ord |
A vector of length equal to the number of states, specifying the
order of plotting in case type= |
cols |
A vector specifying colors for the different transitions;
default is a palette from green to red, when type= |
xlab |
A title for the x-axis; default is |
ylab |
A title for the y-axis; default is |
xlim |
The x limits of the plot(s), default is range of time |
ylim |
The y limits of the plot(s); if ylim is specified for type="separate", then all plots use the same ylim for y limits |
lwd |
The line width, see |
lty |
The line type, see |
cex |
Character size, used in text; only used when
type= |
legend |
Character vector of length equal to the number of transitions, to be used in a legend; if missing, numbers will be used; this and the legend arguments following are ignored when type="separate" |
legend.pos |
The position of the legend, see |
bty |
The box type of the legend, see |
xaxs |
See |
yaxs |
See |
use.ggplot |
Default FALSE, set TRUE for ggplot version of plot |
conf.int |
Confidence level (%) from 0-1 for probabilities, default is 0.95 (95% CI). Setting to 0 removes the CIs. |
conf.type |
Type of confidence interval - either "log" or "plain" . See function details for details. |
label |
Only relevant for type = "filled" or "stacked", set to "annotate" to have state labels on plot, or leave unspecified. |
... |
Further arguments to plot |
Regarding confidence intervals: let denote a predicted probability,
its estimated standard error,
and denote the critical value of the standard normal
distribution at confidence level .
The confidence interval of type "plain" is then
The confidence interval of type "log", based on the Delta method, is then
No return value
Hein Putter [email protected]
Edouard F. Bonneville [email protected]
# transition matrix for illness-death model tmat <- trans.illdeath() # data in wide format, for transition 1 this is dataset E1 of # Therneau and Grambsch (2000) tg <- data.frame(illt=c(1,1,6,6,8,9),ills=c(1,0,1,1,0,1), dt=c(5,1,9,7,8,12),ds=c(1,1,1,1,1,1), x1=c(1,1,1,0,0,0),x2=c(6:1)) # data in long format using msprep tglong <- msprep(time=c(NA,"illt","dt"),status=c(NA,"ills","ds"), data=tg,keep=c("x1","x2"),trans=tmat) # events events(tglong) table(tglong$status,tglong$to,tglong$from) # expanded covariates tglong <- expand.covs(tglong,c("x1","x2")) # Cox model with different covariate cx <- coxph(Surv(Tstart,Tstop,status)~x1.1+x2.2+strata(trans), data=tglong,method="breslow") summary(cx) # new data, to check whether results are the same for transition 1 as # those in appendix E.1 of Therneau and Grambsch (2000) newdata <- data.frame(trans=1:3,x1.1=c(0,0,0),x2.2=c(0,1,0),strata=1:3) msf <- msfit(cx,newdata,trans=tmat) # probtrans pt <- probtrans(msf,predt=0) # default plot plot(pt,ord=c(2,3,1),lwd=2,cex=0.75) # filled plot plot(pt,type="filled",ord=c(2,3,1),lwd=2,cex=0.75) # single plot plot(pt,type="single",lwd=2,col=rep(1,3),lty=1:3,legend.pos=c(8,1)) # separate plots par(mfrow=c(2,2)) plot(pt,type="sep",lwd=2) par(mfrow=c(1,1)) # ggplot version - see vignette for details library(ggplot2) plot(pt, ord=c(2,3,1), use.ggplot = TRUE)# transition matrix for illness-death model tmat <- trans.illdeath() # data in wide format, for transition 1 this is dataset E1 of # Therneau and Grambsch (2000) tg <- data.frame(illt=c(1,1,6,6,8,9),ills=c(1,0,1,1,0,1), dt=c(5,1,9,7,8,12),ds=c(1,1,1,1,1,1), x1=c(1,1,1,0,0,0),x2=c(6:1)) # data in long format using msprep tglong <- msprep(time=c(NA,"illt","dt"),status=c(NA,"ills","ds"), data=tg,keep=c("x1","x2"),trans=tmat) # events events(tglong) table(tglong$status,tglong$to,tglong$from) # expanded covariates tglong <- expand.covs(tglong,c("x1","x2")) # Cox model with different covariate cx <- coxph(Surv(Tstart,Tstop,status)~x1.1+x2.2+strata(trans), data=tglong,method="breslow") summary(cx) # new data, to check whether results are the same for transition 1 as # those in appendix E.1 of Therneau and Grambsch (2000) newdata <- data.frame(trans=1:3,x1.1=c(0,0,0),x2.2=c(0,1,0),strata=1:3) msf <- msfit(cx,newdata,trans=tmat) # probtrans pt <- probtrans(msf,predt=0) # default plot plot(pt,ord=c(2,3,1),lwd=2,cex=0.75) # filled plot plot(pt,type="filled",ord=c(2,3,1),lwd=2,cex=0.75) # single plot plot(pt,type="single",lwd=2,col=rep(1,3),lty=1:3,legend.pos=c(8,1)) # separate plots par(mfrow=c(2,2)) plot(pt,type="sep",lwd=2) par(mfrow=c(1,1)) # ggplot version - see vignette for details library(ggplot2) plot(pt, ord=c(2,3,1), use.ggplot = TRUE)
Print method for an object of class 'MarkovTest'
## S3 method for class 'MarkovTest' print(x, ...)## S3 method for class 'MarkovTest' print(x, ...)
x |
Object of class 'markovTest', as obtained by call to
|
... |
Further arguments to print |
No return value
Hein Putter [email protected]
## Not run: # Example provided by the prothrombin data data("prothr") # Apply Markov test to grid of monthly time points over the first 7.5 years year <- 365.25 month <- year / 12 grid <- month * (1:90) # Markov test for transition 1 (wild bootstrap based on 25 replications for brevity) MT <- MarkovTest(prothr, id = "id", transition = 1, grid = grid, B = 25) MT ## End(Not run)## Not run: # Example provided by the prothrombin data data("prothr") # Apply Markov test to grid of monthly time points over the first 7.5 years year <- 365.25 month <- year / 12 grid <- month * (1:90) # Markov test for transition 1 (wild bootstrap based on 25 replications for brevity) MT <- MarkovTest(prothr, id = "id", transition = 1, grid = grid, B = 25) MT ## End(Not run)
Print method for an object of class 'msdata'
## S3 method for class 'msdata' print(x, trans = FALSE, ...)## S3 method for class 'msdata' print(x, trans = FALSE, ...)
x |
Object of class 'msdata', as prepared for instance by
|
trans |
Boolean specifying whether or not the transition matrix should
be printed as well; default is |
... |
Further arguments to print |
No return value
Hein Putter [email protected]
# transition matrix for illness-death model tmat <- trans.illdeath() # some data in wide format tg <- data.frame(stt=rep(0,6),sts=rep(0,6), illt=c(1,1,6,6,8,9),ills=c(1,0,1,1,0,1), dt=c(5,1,9,7,8,12),ds=c(1,1,1,1,1,1), x1=c(1,1,1,2,2,2),x2=c(6:1)) tg$x1 <- factor(tg$x1,labels=c("male","female")) tg$patid <- factor(2:7,levels=1:8,labels=as.character(1:8)) # define time, status and covariates also as matrices tt <- matrix(c(rep(NA,6),tg$illt,tg$dt),6,3) st <- matrix(c(rep(NA,6),tg$ills,tg$ds),6,3) keepmat <- data.frame(gender=tg$x1,age=tg$x2) # data in long format using msprep msp <- msprep(time=tt,status=st,trans=tmat,keep=as.matrix(keepmat)) print(msp) print(msp, trans=TRUE)# transition matrix for illness-death model tmat <- trans.illdeath() # some data in wide format tg <- data.frame(stt=rep(0,6),sts=rep(0,6), illt=c(1,1,6,6,8,9),ills=c(1,0,1,1,0,1), dt=c(5,1,9,7,8,12),ds=c(1,1,1,1,1,1), x1=c(1,1,1,2,2,2),x2=c(6:1)) tg$x1 <- factor(tg$x1,labels=c("male","female")) tg$patid <- factor(2:7,levels=1:8,labels=as.character(1:8)) # define time, status and covariates also as matrices tt <- matrix(c(rep(NA,6),tg$illt,tg$dt),6,3) st <- matrix(c(rep(NA,6),tg$ills,tg$ds),6,3) keepmat <- data.frame(gender=tg$x1,age=tg$x2) # data in long format using msprep msp <- msprep(time=tt,status=st,trans=tmat,keep=as.matrix(keepmat)) print(msp) print(msp, trans=TRUE)
Print method for summary.msfit object
## S3 method for class 'summary.msfit' print(x, complete = FALSE, ...)## S3 method for class 'summary.msfit' print(x, complete = FALSE, ...)
x |
Object of class 'summary.msfit', to be printed |
complete |
Whether or not the complete estimated cumulative transition
intensities should be printed ( |
... |
Further arguments to print |
## Not run: # If all time points should be printed, specify complete=TRUE in the print statement print(x, complete=TRUE) ## End(Not run)## Not run: # If all time points should be printed, specify complete=TRUE in the print statement print(x, complete=TRUE) ## End(Not run)
Print method for a summary.probtrans object
## S3 method for class 'summary.probtrans' print(x, complete = FALSE, ...)## S3 method for class 'summary.probtrans' print(x, complete = FALSE, ...)
x |
Object of class 'summary.probtrans', to be printed |
complete |
Whether or not the complete estimated transition
probabilities should be printed ( |
... |
Further arguments to print |
## Not run: # If all time points should be printed, specify complete=TRUE in the print statement print(x, complete=TRUE) ## End(Not run)## Not run: # If all time points should be printed, specify complete=TRUE in the print statement print(x, complete=TRUE) ## End(Not run)
This function computes subject-specific or overall transition probabilities in multi-state models. If requested, also standard errors are calculated.
probtrans( object, predt, direction = c("forward", "fixedhorizon"), method = c("aalen", "greenwood"), variance = TRUE, covariance = FALSE )probtrans( object, predt, direction = c("forward", "fixedhorizon"), method = c("aalen", "greenwood"), variance = TRUE, covariance = FALSE )
object |
msfit object containing estimated cumulative hazards for each of the transitions in the multi-state model and, if standard errors are requested, (co)variances of these cumulative hazards for each pair of transitions |
predt |
A positive number indicating the prediction time. This is
either the time at which the prediction is made (if |
direction |
One of |
method |
A character string specifying the type of variances to be
computed (so only needed if either |
variance |
Logical value indicating whether standard errors are to be
calculated (default is |
covariance |
Logical value indicating whether covariances of transition
probabilities for different states are to be calculated (default is
|
For details refer to de Wreede, Fiocco & Putter (2010).
An object of class "probtrans", which is a list of which item
[[s]] contains a data frame with the estimated transition probabilities (and
standard errors if variance=TRUE) from state s. If
covariance=TRUE, item varMatrix contains an array of
dimension K^2 x K^2 x (nt+1) (with K the number of states and nt the
distinct transition time points); the time points correspond to those in the
data frames with the estimated transition probabilities. Finally, there are
items trans, method, predt, direction, recording
the transition matrix, and the method, predt and direction arguments used in
the call to probtrans. Plot and summary methods have been defined for
"probtrans" objects.
Liesbeth de Wreede and Hein Putter [email protected]
Andersen PK, Borgan O, Gill RD, Keiding N (1993). Statistical Models Based on Counting Processes. Springer, New York.
Putter H, Fiocco M, Geskus RB (2007). Tutorial in biostatistics: Competing risks and multi-state models. Statistics in Medicine 26, 2389–2430.
Therneau TM, Grambsch PM (2000). Modeling Survival Data: Extending the Cox Model. Springer, New York.
de Wreede LC, Fiocco M, and Putter H (2010). The mstate package for estimation and prediction in non- and semi-parametric multi-state and competing risks models. Computer Methods and Programs in Biomedicine 99, 261–274.
de Wreede LC, Fiocco M, and Putter H (2011). mstate: An R Package for the Analysis of Competing Risks and Multi-State Models. Journal of Statistical Software, Volume 38, Issue 7.
# transition matrix for illness-death model tmat <- trans.illdeath() # data in wide format, for transition 1 this is dataset E1 of # Therneau & Grambsch (2000) tg <- data.frame(illt=c(1,1,6,6,8,9),ills=c(1,0,1,1,0,1), dt=c(5,1,9,7,8,12),ds=c(1,1,1,1,1,1), x1=c(1,1,1,0,0,0),x2=c(6:1)) # data in long format using msprep tglong <- msprep(time=c(NA,"illt","dt"),status=c(NA,"ills","ds"), data=tg,keep=c("x1","x2"),trans=tmat) # events events(tglong) table(tglong$status,tglong$to,tglong$from) # expanded covariates tglong <- expand.covs(tglong,c("x1","x2")) # Cox model with different covariate cx <- coxph(Surv(Tstart,Tstop,status)~x1.1+x2.2+strata(trans), data=tglong,method="breslow") summary(cx) # new data, to check whether results are the same for transition 1 as # those in appendix E.1 of Therneau & Grambsch (2000) newdata <- data.frame(trans=1:3,x1.1=c(0,0,0),x2.2=c(0,1,0),strata=1:3) HvH <- msfit(cx,newdata,trans=tmat) # probtrans pt <- probtrans(HvH,predt=0) # predictions from state 1 pt[[1]]# transition matrix for illness-death model tmat <- trans.illdeath() # data in wide format, for transition 1 this is dataset E1 of # Therneau & Grambsch (2000) tg <- data.frame(illt=c(1,1,6,6,8,9),ills=c(1,0,1,1,0,1), dt=c(5,1,9,7,8,12),ds=c(1,1,1,1,1,1), x1=c(1,1,1,0,0,0),x2=c(6:1)) # data in long format using msprep tglong <- msprep(time=c(NA,"illt","dt"),status=c(NA,"ills","ds"), data=tg,keep=c("x1","x2"),trans=tmat) # events events(tglong) table(tglong$status,tglong$to,tglong$from) # expanded covariates tglong <- expand.covs(tglong,c("x1","x2")) # Cox model with different covariate cx <- coxph(Surv(Tstart,Tstop,status)~x1.1+x2.2+strata(trans), data=tglong,method="breslow") summary(cx) # new data, to check whether results are the same for transition 1 as # those in appendix E.1 of Therneau & Grambsch (2000) newdata <- data.frame(trans=1:3,x1.1=c(0,0,0),x2.2=c(0,1,0),strata=1:3) HvH <- msfit(cx,newdata,trans=tmat) # probtrans pt <- probtrans(HvH,predt=0) # predictions from state 1 pt[[1]]
This function estimates regression coefficients in reduced rank proportional hazards models for competing risks and multi-state models.
redrank( redrank, full = ~1, data, R, strata = NULL, Gamma.start, method = "breslow", eps = 1e-05, print.level = 1 )redrank( redrank, full = ~1, data, R, strata = NULL, Gamma.start, method = "breslow", eps = 1e-05, print.level = 1 )
redrank |
Survival formula, starting with either Surv(time,status) ~ or with Surv(Tstart,Tstop,status) ~, followed by a formula containing covariates for which a reduced rank estimate is to be found |
full |
Optional, formula specifying that part which needs to be retained in the model (so not subject to reduced rank) |
data |
Object of class 'msdata', as prepared for instance by
|
R |
Numeric, indicating the rank of the solution |
strata |
Name of covariate to be used inside the
|
Gamma.start |
A matrix of dimension K x R, with K the number of transitions and R the rank, to be used as starting value |
method |
The method for handling ties in
|
eps |
Numeric value determining when the iterative algorithm is
finished (when for two subsequent iterations the difference in
log-likelihood is smaller than |
print.level |
Determines how much output is written to the screen; 0: no output, 1: iterations, for each iteration solutions of Alpha, Gamma, log-likelihood, 2: also the Cox regression results |
For details refer to Fiocco, Putter & van Houwelingen (2005, 2008).
A list with elements
Alpha |
the Alpha matrix |
Gamma |
the Gamma matrix |
Beta |
the Beta matrix corresponding to
|
Beta2 |
the Beta matrix corresponding to
|
cox.itr1 |
the |
alphaX |
the
matrix of prognostic scores given by |
niter |
the number of iterations needed to reach convergence |
df |
the number of regression parameters estimated |
loglik |
the log-likelihood |
Marta Fiocco and Hein Putter [email protected]
Fiocco M, Putter H, van Houwelingen JC (2005). Reduced rank proportional hazards model for competing risks. Biostatistics 6, 465–478.
Fiocco M, Putter H, van Houwelingen HC (2008). Reduced-rank proportional hazards regression and simulation-based prediction for multi-state models. Statistics in Medicine 27, 4340–4358.
Putter H, Fiocco M, Geskus RB (2007). Tutorial in biostatistics: Competing risks and multi-state models. Statistics in Medicine 26, 2389–2430.
## Not run: # This reproduces the results in Fiocco, Putter & van Houwelingen (2005) # Takes a while to run data(ebmt2) # transition matrix for competing risks tmat <- trans.comprisk(6,names=c("Relapse","GvHD","Bacterial","Viral","Fungal","Other")) # preparing long dataset ebmt2$stat1 <- as.numeric(ebmt2$status==1) ebmt2$stat2 <- as.numeric(ebmt2$status==2) ebmt2$stat3 <- as.numeric(ebmt2$status==3) ebmt2$stat4 <- as.numeric(ebmt2$status==4) ebmt2$stat5 <- as.numeric(ebmt2$status==5) ebmt2$stat6 <- as.numeric(ebmt2$status==6) covs <- c("dissub","match","tcd","year","age") ebmtlong <- msprep(time=c(NA,rep("time",6)), stat=c(NA,paste("stat",1:6,sep="")), data=ebmt2,keep=covs,trans=tmat) # The reduced rank 2 solution rr2 <- redrank(Surv(Tstart,Tstop,status) ~ dissub+match+tcd+year+age, data=ebmtlong, R=2) rr3$Alpha; rr3$Gamma; rr3$Beta; rr3$loglik # The reduced rank 3 solution rr3 <- redrank(Surv(Tstart,Tstop,status) ~ dissub+match+tcd+year+age, data=ebmtlong, R=3) rr3$Alpha; rr3$Gamma; rr3$Beta; rr3$loglik # The reduced rank 3 solution, with no reduction on age rr3 <- redrank(Surv(Tstart,Tstop,status) ~ dissub+match+tcd+year, full=~age, data=ebmtlong, R=3) rr3$Alpha; rr3$Gamma; rr3$Beta; rr3$loglik # The full rank solution fullrank <- redrank(Surv(Tstart,Tstop,status) ~ dissub+match+tcd+year+age, data=ebmtlong, R=6) fullrank$Beta; fullrank$loglik ## End(Not run)## Not run: # This reproduces the results in Fiocco, Putter & van Houwelingen (2005) # Takes a while to run data(ebmt2) # transition matrix for competing risks tmat <- trans.comprisk(6,names=c("Relapse","GvHD","Bacterial","Viral","Fungal","Other")) # preparing long dataset ebmt2$stat1 <- as.numeric(ebmt2$status==1) ebmt2$stat2 <- as.numeric(ebmt2$status==2) ebmt2$stat3 <- as.numeric(ebmt2$status==3) ebmt2$stat4 <- as.numeric(ebmt2$status==4) ebmt2$stat5 <- as.numeric(ebmt2$status==5) ebmt2$stat6 <- as.numeric(ebmt2$status==6) covs <- c("dissub","match","tcd","year","age") ebmtlong <- msprep(time=c(NA,rep("time",6)), stat=c(NA,paste("stat",1:6,sep="")), data=ebmt2,keep=covs,trans=tmat) # The reduced rank 2 solution rr2 <- redrank(Surv(Tstart,Tstop,status) ~ dissub+match+tcd+year+age, data=ebmtlong, R=2) rr3$Alpha; rr3$Gamma; rr3$Beta; rr3$loglik # The reduced rank 3 solution rr3 <- redrank(Surv(Tstart,Tstop,status) ~ dissub+match+tcd+year+age, data=ebmtlong, R=3) rr3$Alpha; rr3$Gamma; rr3$Beta; rr3$loglik # The reduced rank 3 solution, with no reduction on age rr3 <- redrank(Surv(Tstart,Tstop,status) ~ dissub+match+tcd+year, full=~age, data=ebmtlong, R=3) rr3$Alpha; rr3$Gamma; rr3$Beta; rr3$loglik # The full rank solution fullrank <- redrank(Surv(Tstart,Tstop,status) ~ dissub+match+tcd+year+age, data=ebmtlong, R=6) fullrank$Beta; fullrank$loglik ## End(Not run)
Summary method for a summary.Cuminc object
## S3 method for class 'Cuminc' summary(object, ...)## S3 method for class 'Cuminc' summary(object, ...)
object |
Object of class 'Cuminc', to be summarised |
... |
Further arguments to summarise |
Summary method for an object of class 'msfit'. It prints a selection of the estimated cumulative transition intensities, and, if requested, also of the (co)variances.
## S3 method for class 'msfit' summary( object, times, transitions, variance = TRUE, conf.int = 0.95, conf.type = c("log", "none", "plain"), extend = FALSE, ... )## S3 method for class 'msfit' summary( object, times, transitions, variance = TRUE, conf.int = 0.95, conf.type = c("log", "none", "plain"), extend = FALSE, ... )
object |
Object of class 'msfit', containing estimated cumulative transition intensities for all transitions in a multi-state model |
times |
Time points at which to evaluate the cumulative transition hazards |
transitions |
The transition for which to summarize the cumulative transition hazards |
variance |
Whether or not the standard errors of the estimated
cumulative transition intensities should be printed; default is |
conf.int |
The proportion to be covered by the confidence intervals, default is 0.95 |
conf.type |
The type of confidence interval, one of "log", "none", or "plain". Defaults to "log" |
extend |
logical value: if |
... |
Further arguments to summary |
Function summary.msfit returns an object of class
"summary.msfit", which is a list (for each from state) of cumulative
transition hazaards at the specified (or all) time points. The print
method of a summary.probtrans doesn't return a value.
Hein Putter [email protected]
# Start with example from msfit tmat <- trans.illdeath() tg <- data.frame(illt=c(1,1,6,6,8,9),ills=c(1,0,1,1,0,1), dt=c(5,1,9,7,8,12),ds=c(1,1,1,1,1,1), x1=c(1,1,1,0,0,0),x2=c(6:1)) tglong <- msprep(time=c(NA,"illt","dt"),status=c(NA,"ills","ds"), data=tg,keep=c("x1","x2"),trans=tmat) tglong <- expand.covs(tglong,c("x1","x2")) cx <- coxph(Surv(Tstart,Tstop,status)~x1.1+x2.2+strata(trans), data=tglong,method="breslow") newdata <- data.frame(trans=1:3,x1.1=c(0,0,0),x2.2=c(0,1,0),strata=1:3) msf <- msfit(cx,newdata,trans=tmat) # Default, all transitions, with SE summary(msf) summary(msf, conf.type="plain") # Only transitions 1 and 3 summary(msf, tra=c(1, 3)) # Default is 95% confidence interval, change here to 90% summary(msf, conf.int=0.90) # Do not show variances (nor confidence intervals) summary(msf, variance=FALSE) # Cumulative hazards only at specified time points summary(msf, times=seq(0, 15, by=3)) # Last specified time point is larger than last observed, not printed # Use extend=TRUE as in summary.survfit summary(msf, times=seq(0, 15, by=3), extend=TRUE) # Different types of confidence intervals, default is log summary(msf, times=seq(0, 15, by=3), conf.type="plain") summary(msf, times=seq(0, 15, by=3), conf.type="no") # When the number of time points specified is larger than 12, head and tail is shown x <- summary(msf, times=seq(5, 8, by=0.25)) x# Start with example from msfit tmat <- trans.illdeath() tg <- data.frame(illt=c(1,1,6,6,8,9),ills=c(1,0,1,1,0,1), dt=c(5,1,9,7,8,12),ds=c(1,1,1,1,1,1), x1=c(1,1,1,0,0,0),x2=c(6:1)) tglong <- msprep(time=c(NA,"illt","dt"),status=c(NA,"ills","ds"), data=tg,keep=c("x1","x2"),trans=tmat) tglong <- expand.covs(tglong,c("x1","x2")) cx <- coxph(Surv(Tstart,Tstop,status)~x1.1+x2.2+strata(trans), data=tglong,method="breslow") newdata <- data.frame(trans=1:3,x1.1=c(0,0,0),x2.2=c(0,1,0),strata=1:3) msf <- msfit(cx,newdata,trans=tmat) # Default, all transitions, with SE summary(msf) summary(msf, conf.type="plain") # Only transitions 1 and 3 summary(msf, tra=c(1, 3)) # Default is 95% confidence interval, change here to 90% summary(msf, conf.int=0.90) # Do not show variances (nor confidence intervals) summary(msf, variance=FALSE) # Cumulative hazards only at specified time points summary(msf, times=seq(0, 15, by=3)) # Last specified time point is larger than last observed, not printed # Use extend=TRUE as in summary.survfit summary(msf, times=seq(0, 15, by=3), extend=TRUE) # Different types of confidence intervals, default is log summary(msf, times=seq(0, 15, by=3), conf.type="plain") summary(msf, times=seq(0, 15, by=3), conf.type="no") # When the number of time points specified is larger than 12, head and tail is shown x <- summary(msf, times=seq(5, 8, by=0.25)) x
Summary method for an object of class 'probtrans'. It prints a selection of the estimated transition probabilities, and, if requested, also of the variances.
## S3 method for class 'probtrans' summary( object, times, from = 1, to = 0, variance = TRUE, conf.int = 0.95, conf.type = c("log", "none", "plain"), extend = FALSE, ... )## S3 method for class 'probtrans' summary( object, times, from = 1, to = 0, variance = TRUE, conf.int = 0.95, conf.type = c("log", "none", "plain"), extend = FALSE, ... )
object |
Object of class 'probtrans', containing estimated transition probabilities from and to all states in a multi-state model |
times |
Time points at which to evaluate the transition probabilites |
from |
Specifies from which state the transition probabilities are to be printed. Should be subset of 1:S, with S the number of states in the multi-state model. Default is print from state 1 only. User can specify from=0 to print transition probabilities from all states |
to |
Specifies the transition probabilities to which state are to be printed. User can specify to=0 to print transition probabilities to all states. This is also the default |
variance |
Whether or not the standard errors of the estimated
transition probabilities should be printed; default is |
conf.int |
The proportion to be covered by the confidence intervals, default is 0.95 |
conf.type |
The type of confidence interval, one of "log", "none", or "plain". Defaults to "log" |
extend |
logical value: if |
... |
Further arguments to print |
Function summary.probtrans returns an object of class
"summary.probtrans", which is a list (for each from state) of
transition probabilities at the specified (or all) time points. The
print method of a summary.probtrans doesn't return a value.
Hein Putter [email protected]
# First run the example of probtrans tmat <- trans.illdeath() tg <- data.frame(illt=c(1,1,6,6,8,9),ills=c(1,0,1,1,0,1), dt=c(5,1,9,7,8,12),ds=c(1,1,1,1,1,1), x1=c(1,1,1,0,0,0),x2=c(6:1)) tglong <- msprep(time=c(NA,"illt","dt"),status=c(NA,"ills","ds"), data=tg,keep=c("x1","x2"),trans=tmat) tglong <- expand.covs(tglong,c("x1","x2")) cx <- coxph(Surv(Tstart,Tstop,status)~x1.1+x2.2+strata(trans), data=tglong,method="breslow") newdata <- data.frame(trans=1:3,x1.1=c(0,0,0),x2.2=c(0,1,0),strata=1:3) HvH <- msfit(cx,newdata,trans=tmat) pt <- probtrans(HvH,predt=0) # Default, prediction from state 1 summary(pt) # Only from states 1 and 3 summary(pt, from=c(1, 3)) # Use from=0 for prediction from all states summary(pt, from=0) # Only to states 1 and 2 summary(pt, to=1:2) # Default is 95% confidence interval, change here to 90% summary(pt, to=1:2, conf.int=0.90) # Do not show variances (nor confidence intervals) summary(pt, to=1:2, variance=FALSE) # Transition probabilities only at specified time points summary(pt, times=seq(0, 15, by=3)) # Last specified time point is larger than last observed, not printed # Use extend=TRUE as in summary.survfit summary(pt, times=seq(0, 15, by=3), extend=TRUE) # Different types of confidence intervals, default is log summary(pt, times=seq(0, 15, by=3), conf.type="plain") summary(pt, times=seq(0, 15, by=3), conf.type="no") # When the number of time points specified is larger than 12, head and tail is shown x <- summary(pt, times=seq(5, 8, by=0.25)) x# First run the example of probtrans tmat <- trans.illdeath() tg <- data.frame(illt=c(1,1,6,6,8,9),ills=c(1,0,1,1,0,1), dt=c(5,1,9,7,8,12),ds=c(1,1,1,1,1,1), x1=c(1,1,1,0,0,0),x2=c(6:1)) tglong <- msprep(time=c(NA,"illt","dt"),status=c(NA,"ills","ds"), data=tg,keep=c("x1","x2"),trans=tmat) tglong <- expand.covs(tglong,c("x1","x2")) cx <- coxph(Surv(Tstart,Tstop,status)~x1.1+x2.2+strata(trans), data=tglong,method="breslow") newdata <- data.frame(trans=1:3,x1.1=c(0,0,0),x2.2=c(0,1,0),strata=1:3) HvH <- msfit(cx,newdata,trans=tmat) pt <- probtrans(HvH,predt=0) # Default, prediction from state 1 summary(pt) # Only from states 1 and 3 summary(pt, from=c(1, 3)) # Use from=0 for prediction from all states summary(pt, from=0) # Only to states 1 and 2 summary(pt, to=1:2) # Default is 95% confidence interval, change here to 90% summary(pt, to=1:2, conf.int=0.90) # Do not show variances (nor confidence intervals) summary(pt, to=1:2, variance=FALSE) # Transition probabilities only at specified time points summary(pt, times=seq(0, 15, by=3)) # Last specified time point is larger than last observed, not printed # Use extend=TRUE as in summary.survfit summary(pt, times=seq(0, 15, by=3), extend=TRUE) # Different types of confidence intervals, default is log summary(pt, times=seq(0, 15, by=3), conf.type="plain") summary(pt, times=seq(0, 15, by=3), conf.type="no") # When the number of time points specified is larger than 12, head and tail is shown x <- summary(pt, times=seq(5, 8, by=0.25)) x
Convert transition matrix from mstate to etm format
trans2tra(trans)trans2tra(trans)
trans |
Transition matrix in |
Help functions to get insight into the structure of a transition matrix.
trans |
Transition matrix, for instance produced by |
Function to.trans2 simply lists the transitions in trans in a
data frame; function trans2Q converts trans to a Q
matrix, the (j,k)th element of which contains the (shortest) number of
transitions needed to travel from the jth to the kth state; function
absorbing returns a vector (named if trans contains row or
columnc names) with the state numbers that are absorbing; function
is.circular returns (a Boolean) whether the transition matrix
specified in trans is circular or not.
See details.
Hein Putter <[email protected]>
# Irreversible illness-death model tmat <- trans.illdeath(c("Healthy", "Illness", "Death")) tmat to.trans2(tmat) trans2Q(tmat) absorbing(tmat) is.circular(tmat) # Reversible illness-death model tmat <- transMat(x = list( c(2, 3), c(1, 3), c() ), names = c("Healthy", "Illness", "Death")) tmat to.trans2(tmat) trans2Q(tmat) absorbing(tmat) is.circular(tmat)# Irreversible illness-death model tmat <- trans.illdeath(c("Healthy", "Illness", "Death")) tmat to.trans2(tmat) trans2Q(tmat) absorbing(tmat) is.circular(tmat) # Reversible illness-death model tmat <- transMat(x = list( c(2, 3), c(1, 3), c() ), names = c("Healthy", "Illness", "Death")) tmat to.trans2(tmat) trans2Q(tmat) absorbing(tmat) is.circular(tmat)
Define transition matrices for multi-state model. Specific functions for defining such transition matrices are pre-defined for common multi-state models like the competing risks model and the illness-death model.
transMat(x, names)transMat(x, names)
x |
List of possible transitions; x[[i]] consists of a vector of state numbers reachable from state i |
names |
A character vector containing the names of either the competing
risks or the states in the multi-state model specified by the competing
risks or illness-death model. |
If names is missing, the names "eventfree", "cause1",
etcetera are assigned in trans.comprisk, or "healthy",
"illness", "death" in trans.illdeath.
A transition matrix describing the states and transitions in the multi-state model.
Steven McKinney <[email protected]>; Hein Putter <[email protected]>
transMat(list(c(2, 3), c(), c(1, 2)), names = c("Disease-free", "Death", "Relapsed")) tmat <- transMat(x = list( c(2, 3), c(1, 3), c() ), names = c("Normal", "Low", "Death")) tmat transListn <- list("Normal" = c(2, 3), "Low" = c(1, 3), "Death" = c()) transMat(transListn) trans.comprisk(3) trans.comprisk(3,c("c1","c2","c3")) trans.comprisk(3,c("nothing","c1","c2","c3")) trans.illdeath() trans.illdeath(c("nothing","ill","death"))transMat(list(c(2, 3), c(), c(1, 2)), names = c("Disease-free", "Death", "Relapsed")) tmat <- transMat(x = list( c(2, 3), c(1, 3), c() ), names = c("Normal", "Low", "Death")) tmat transListn <- list("Normal" = c(2, 3), "Low" = c(1, 3), "Death" = c()) transMat(transListn) trans.comprisk(3) trans.comprisk(3,c("c1","c2","c3")) trans.comprisk(3,c("nothing","c1","c2","c3")) trans.illdeath() trans.illdeath(c("nothing","ill","death"))
A function that upgrades varHaz from the msfit object where the variances are estimated using the Greenwood estimator; it is further assumed that variances for the population hazards are equal to zero.
varHaz.fixed(varHaz, link_trans, varHaz_original)varHaz.fixed(varHaz, link_trans, varHaz_original)
varHaz |
The varHaz object (present in a msfit object). |
link_trans |
A list that gives the linkage between the original and upgraded transition matrix. |
varHaz_original |
The original varHaz object from msfit (without the eventual time conversion). |
Return the upgraded varHaz object containing variances for the split transitions.
Damjan Manevski [email protected]
A mirror plot for comparing two different "probtrans" objects. Useful
for comparing predicted probabilities for different levels of a covariate,
or for different subgroups at some prediction time horizon.
vis.mirror.pt( x, titles, size_titles = 5, horizon = NULL, breaks_x_left, breaks_x_right, from = 1, cols, ord, xlab = "Time", ylab = "Probability", legend.pos = "right" )vis.mirror.pt( x, titles, size_titles = 5, horizon = NULL, breaks_x_left, breaks_x_right, from = 1, cols, ord, xlab = "Time", ylab = "Probability", legend.pos = "right" )
x |
A list of two |
titles |
A character vector c("Title for left", "Title for right") |
size_titles |
Numeric, size of the title text |
horizon |
Numeric, position denoting (in time) where to symmetrically mirror the plots. Default is maximum follow-up of from both plots. |
breaks_x_left |
Numeric vector specifying axis breaks on the left plot |
breaks_x_right |
Numeric vector specifying axis breaks on the right plot |
from |
The starting state from which the probabilities are used to plot |
cols |
A vector specifying colors for the different transitions;
default is a palette from green to red, when type= |
ord |
A vector of length equal to the number of states, specifying the
order of plotting in case type= |
xlab |
A title for the x-axis, default is "Time" |
ylab |
A title for the y-axis, default is "Probability" |
legend.pos |
Position of the legend, default is "right" |
A ggplot2 object.
Edouard F. Bonneville [email protected]
library(ggplot2) data("aidssi") head(aidssi) si <- aidssi # Prepare transition matrix tmat <- trans.comprisk(2, names = c("event-free", "AIDS", "SI")) # Run msprep si$stat1 <- as.numeric(si$status == 1) si$stat2 <- as.numeric(si$status == 2) silong <- msprep( time = c(NA, "time", "time"), status = c(NA, "stat1", "stat2"), data = si, keep = "ccr5", trans = tmat ) # Run cox model silong <- expand.covs(silong, "ccr5") c1 <- coxph(Surv(time, status) ~ ccr5WM.1 + ccr5WM.2 + strata(trans), data = silong) # 1. Prepare reference patient data - both CCR5 genotypes WW <- data.frame( ccr5WM.1 = c(0, 0), ccr5WM.2 = c(0, 0), trans = c(1, 2), strata = c(1, 2) ) WM <- data.frame( ccr5WM.1 = c(1, 0), ccr5WM.2 = c(0, 1), trans = c(1, 2), strata = c(1, 2) ) # 2. Make msfit objects msf.WW <- msfit(c1, WW, trans = tmat) msf.WM <- msfit(c1, WM, trans = tmat) # 3. Make probtrans objects pt.WW <- probtrans(msf.WW, predt = 0) pt.WM <- probtrans(msf.WM, predt = 0) # Mirror plot split at 10 years - see vignette for more details vis.mirror.pt( x = list(pt.WW, pt.WM), titles = c("WW", "WM"), horizon = 10 )library(ggplot2) data("aidssi") head(aidssi) si <- aidssi # Prepare transition matrix tmat <- trans.comprisk(2, names = c("event-free", "AIDS", "SI")) # Run msprep si$stat1 <- as.numeric(si$status == 1) si$stat2 <- as.numeric(si$status == 2) silong <- msprep( time = c(NA, "time", "time"), status = c(NA, "stat1", "stat2"), data = si, keep = "ccr5", trans = tmat ) # Run cox model silong <- expand.covs(silong, "ccr5") c1 <- coxph(Surv(time, status) ~ ccr5WM.1 + ccr5WM.2 + strata(trans), data = silong) # 1. Prepare reference patient data - both CCR5 genotypes WW <- data.frame( ccr5WM.1 = c(0, 0), ccr5WM.2 = c(0, 0), trans = c(1, 2), strata = c(1, 2) ) WM <- data.frame( ccr5WM.1 = c(1, 0), ccr5WM.2 = c(0, 1), trans = c(1, 2), strata = c(1, 2) ) # 2. Make msfit objects msf.WW <- msfit(c1, WW, trans = tmat) msf.WM <- msfit(c1, WM, trans = tmat) # 3. Make probtrans objects pt.WW <- probtrans(msf.WW, predt = 0) pt.WM <- probtrans(msf.WM, predt = 0) # Mirror plot split at 10 years - see vignette for more details vis.mirror.pt( x = list(pt.WW, pt.WM), titles = c("WW", "WM"), horizon = 10 )
Helper function allowing to visualise state probabilities for
different reference patients/covariates. Multiple "probtrans" objects
are thus needed.
vis.multiple.pt( x, from = 1, to, xlab = "Time", ylab = "Probability", xlim = NULL, ylim = NULL, cols, lwd, labels, conf.int = 0.95, conf.type = c("log", "plain", "none"), legend.title )vis.multiple.pt( x, from = 1, to, xlab = "Time", ylab = "Probability", xlim = NULL, ylim = NULL, cols, lwd, labels, conf.int = 0.95, conf.type = c("log", "plain", "none"), legend.title )
x |
A list of |
from |
The starting state from which the probabilities are used to plot
Numeric, as in |
to |
(Numeric) destination state |
xlab |
A title for the x-axis; default is |
ylab |
A title for the y-axis; default is |
xlim |
The x limits of the plot(s), default is range of time |
ylim |
The y limits of the plot(s); if ylim is specified for type="separate", then all plots use the same ylim for y limits |
cols |
A vector specifying colors for the different transitions;
default is a palette from green to red, when type= |
lwd |
The line width, see |
labels |
Character vector labelling each element of x (e.g. label for a reference patient) - so labels = c("Patient 1", "Patient 2") |
conf.int |
Confidence level (%) from 0-1 for probabilities, default is 0.95 (95% CI). Setting to 0 removes the CIs. |
conf.type |
Type of confidence interval - either "log" or "plain" . See function details for details. |
legend.title |
Character - title of legend |
A ggplot object.
Edouard F. Bonneville [email protected]
library(ggplot2) data("aidssi") head(aidssi) si <- aidssi # Prepare transition matrix tmat <- trans.comprisk(2, names = c("event-free", "AIDS", "SI")) # Run msprep si$stat1 <- as.numeric(si$status == 1) si$stat2 <- as.numeric(si$status == 2) silong <- msprep( time = c(NA, "time", "time"), status = c(NA, "stat1", "stat2"), data = si, keep = "ccr5", trans = tmat ) # Run cox model silong <- expand.covs(silong, "ccr5") c1 <- coxph(Surv(time, status) ~ ccr5WM.1 + ccr5WM.2 + strata(trans), data = silong) # 1. Prepare patient data - both CCR5 genotypes WW <- data.frame( ccr5WM.1 = c(0, 0), ccr5WM.2 = c(0, 0), trans = c(1, 2), strata = c(1, 2) ) WM <- data.frame( ccr5WM.1 = c(1, 0), ccr5WM.2 = c(0, 1), trans = c(1, 2), strata = c(1, 2) ) # 2. Make msfit objects msf.WW <- msfit(c1, WW, trans = tmat) msf.WM <- msfit(c1, WM, trans = tmat) # 3. Make probtrans objects pt.WW <- probtrans(msf.WW, predt = 0) pt.WM <- probtrans(msf.WM, predt = 0) # Plot - see vignette for more details vis.multiple.pt( x = list(pt.WW, pt.WM), from = 1, to = 2, conf.type = "log", cols = c(1, 2), labels = c("Pat WW", "Pat WM"), legend.title = "Ref patients" )library(ggplot2) data("aidssi") head(aidssi) si <- aidssi # Prepare transition matrix tmat <- trans.comprisk(2, names = c("event-free", "AIDS", "SI")) # Run msprep si$stat1 <- as.numeric(si$status == 1) si$stat2 <- as.numeric(si$status == 2) silong <- msprep( time = c(NA, "time", "time"), status = c(NA, "stat1", "stat2"), data = si, keep = "ccr5", trans = tmat ) # Run cox model silong <- expand.covs(silong, "ccr5") c1 <- coxph(Surv(time, status) ~ ccr5WM.1 + ccr5WM.2 + strata(trans), data = silong) # 1. Prepare patient data - both CCR5 genotypes WW <- data.frame( ccr5WM.1 = c(0, 0), ccr5WM.2 = c(0, 0), trans = c(1, 2), strata = c(1, 2) ) WM <- data.frame( ccr5WM.1 = c(1, 0), ccr5WM.2 = c(0, 1), trans = c(1, 2), strata = c(1, 2) ) # 2. Make msfit objects msf.WW <- msfit(c1, WW, trans = tmat) msf.WM <- msfit(c1, WM, trans = tmat) # 3. Make probtrans objects pt.WW <- probtrans(msf.WW, predt = 0) pt.WM <- probtrans(msf.WM, predt = 0) # Plot - see vignette for more details vis.multiple.pt( x = list(pt.WW, pt.WM), from = 1, to = 2, conf.type = "log", cols = c(1, 2), labels = c("Pat WW", "Pat WM"), legend.title = "Ref patients" )
Given a dataset in long format, for instance generated by
msprep, this function takes a cross-section at a given time
point, to list the subjects under observation (at risk) at that time point
and the states currently occupied.
xsect(msdata, xtime = 0)xsect(msdata, xtime = 0)
msdata |
An object of class |
xtime |
The time point at which the intersection is to be made |
It is possible that subjects have moved to one of the absorbing states prior
to xtime; this is NOT taken into account. The function xsect
only concerns subjects currently (at time) at risk.
A list containing idstate, a data frame containing
id's and state, the number of the state currently occupied;
atrisk, the number at risk, and prop, a table counting how
many of those at risk occupy which state.
Hein Putter [email protected]
tmat <- trans.illdeath(names=c("Tx","PR","RelDeath")) data(ebmt3) # data from Section 4 of Putter, Fiocco & Geskus (2007) msebmt <- msprep(time=c(NA,"prtime","rfstime"),status=c(NA,"prstat","rfsstat"), data=ebmt3,trans=tmat) # At the start everyone is in state 1 (default xtime=0 is used) xsect(msebmt) # At 5 years xsect(msebmt, xtime=1826)tmat <- trans.illdeath(names=c("Tx","PR","RelDeath")) data(ebmt3) # data from Section 4 of Putter, Fiocco & Geskus (2007) msebmt <- msprep(time=c(NA,"prtime","rfstime"),status=c(NA,"prstat","rfsstat"), data=ebmt3,trans=tmat) # At the start everyone is in state 1 (default xtime=0 is used) xsect(msebmt) # At 5 years xsect(msebmt, xtime=1826)