v4.0.8 built for ssc

ssc/version_4_0_8/survsim.sthlp

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+{smcl}
+{* *! version 1.0.0}{...}
+{vieweralsosee "survsim parametric" "help survsim parametric"}{...}
+{vieweralsosee "survsim user" "help survsim user"}{...}
+{vieweralsosee "survsim model" "help survsim model"}{...}
+{vieweralsosee "survsim msm" "help survsim msm"}{...}
+{vieweralsosee "merlin" "help merlin"}{...}
+{vieweralsosee "galahad" "help galahad"}{...}
+{title:Title}
+
+{p2colset 5 16 16 2}{...}
+{p2col :{cmd:survsim} {hline 2}}Simulate survival data from a parametric distribution, 
+a user-defined distribution, from a fitted {helpb merlin} model, from a cause-specific 
+hazards competing risks model, or from a general multi-state model{p_end}
+{p2colreset}{...}
+
+
+{title:Description}
+
+{pstd}
+{cmd:survsim} simulates survival data from:
+{p_end}
+
+{phang2}
+{helpb survsim parametric:help survsim parametric} - a parametric distribution including the exponential, Gompertz and Weibull, 
+and 2-component mixtures of them. Baseline covariates can be included, with specified associated log hazard ratios. 
+Non-proportional hazards can also be included with all models; under an exponential or Weibull model covariates are interacted 
+with log time, under a Gompertz model covariates are interacted with time. See {helpb survsim##paper1:Crowther and Lambert (2012)} 
+for more details.
+{p_end}
+
+{phang2}
+{helpb survsim user:help survsim user} - a user-defined distribution. Survival times can be simulated from bespoke, 
+user-defined [log] [cumulative] hazard functions. The function must be specified in Mata code (using colon operators), 
+with survival times generated using a combination of numerical integration and root finding techniques. Time-dependent 
+effects can also be specified with a user-defined function of time. See {helpb survsim##paper2:Crowther and Lambert (2013)} 
+for more details.
+{p_end}
+
+{phang2}
+{helpb survsim model:help survsim model} - a fitted {helpb merlin} model. {helpb merlin} fits a broad class of survival models, 
+including standard parametric models, spline-based survival models, and user-defined survival models. 
+{p_end}
+
+{phang2}
+{helpb survsim msm:help survsim msm} - a competing risks or general multi-state model. Event times can be simulated from 
+transition-specific hazards, where each transition hazard function can be a standard parametric distribution, or a 
+user-defined complex hazard function. Covariates and time-dependent effects can be specified for each transition-specific 
+hazard independently.
+{p_end}
+
+
+{title:Author}
+
+{pstd}{cmd:Michael J. Crowther}{p_end}
+{pstd}Red Door Analytics{p_end}
+{pstd}E-mail: {browse "mailto:[email protected]":[email protected]}{p_end}
+
+{phang}Please report any errors you may find.{p_end}
+
+
+{title:References}
+
+{phang}Bender R, Augustin T and Blettner M. Generating survival times to simulate Cox proportional hazards models. {it:Statistics in Medicine} 2005;24:1713-1723.{p_end}
+
+{phang}Beyersmann J, Latouche A, Buchholz A and Schumacher M. Simulating competing risks data in survival analysis. {it:Statistics in Medicine} 2009;28:956-971.{p_end}
+
+{marker paper1}{...}
+{phang}Crowther MJ and Lambert PC. {browse "http://www.stata-journal.com/article.html?article=st0275":Simulating complex survival data.}{it: The Stata Journal} 2012;12(4):674-687.{p_end}
+
+{marker paper2}{...}
+{phang}Crowther MJ and Lambert PC. {browse "http://onlinelibrary.wiley.com/doi/10.1002/sim.5823/abstract":Simulating biologically plausible complex survival data.} {it:Statistics in Medicine} 2013;32(23):4118-4134.{p_end}
+
+{phang}Jann, B. 2005. moremata: Stata module (Mata) to provide various functions. Available from http://ideas.repec.org/c/boc/bocode/s455001.html.{p_end}
+

ssc/version_4_0_8/survsim_details.txt

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+TITLE: `SURVSIM' : module to simulate survival/time-to-event data
+
+DESCRIPTION/AUTHOR: survsim simulates survival data from a parametric distribution, 
+a user-defined distribution, a cause-specific hazards competing risks model, a general 
+multi-state model, or from an estimated -merlin- model. Baseline covariates and 
+time-dependent effects can be specified when defining a data-generating model. 
+Delayed entry/left truncation is allowed.
+
+Author: Michael J. Crowther, Red Door Analytics
+Support: email [email protected]
+
+Requires: Stata version 14.2

ssc/version_4_0_8/survsim_model.ado

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+
+program define survsim_model
+ version 14.2
+
+ syntax newvarname(min=1 max=2), ///
+ ///
+ Model(string) ///
+ MAXTime(string) /// -Maximum simulated time-
+ //
+
+ local nvars : word count `varlist'
+ local stime : word 1 of `varlist'
+ local event : word 2 of `varlist'
+
+ cap which merlin
+ if _rc {
+ display in yellow "You need to install the merlin package. This can be installed using,"
+ display in yellow ". {stata ssc install merlin}"
+ exit 198
+ }
+ cap which predictms
+ if _rc {
+ display in yellow "You need to install the multistate package. This can be installed using,"
+ display in yellow ". {stata ssc install multistate}"
+ exit 198
+ }
+
+ //====================================================================================================================//
+
+ quietly {
+
+ qui gen double `stime' = .
+ cap drop _survsim_rc
+ qui gen _survsim_rc = 0
+ tempvar modtouse
+ gen byte `modtouse' = 1
+ local N = _N
+
+ //make sure right censoring handled
+ //-> gets replaced if less than row specific maxtime() afterwards
+ tempvar tvar
+ su `maxtime'
+ gen `tvar' = `r(max)' in 1
+
+ predictms , models(`model') ///
+ singleevent ///
+ survsim(`stime') ///
+ survsimtouse(`modtouse') ///
+ n(`N') ///
+ timevar(`tvar') ///
+ probability ///
+ simulate //
+
+ }
+
+end

ssc/version_4_0_8/survsim_model.sthlp

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+{smcl}
+{* *! version 1.0.0}{...}
+{vieweralsosee "survsim" "help survsim"}{...}
+{vieweralsosee "survsim parametric" "help survsim parametric"}{...}
+{vieweralsosee "survsim user" "help survsim user"}{...}
+{vieweralsosee "survsim msm" "help survsim msm"}{...}
+{vieweralsosee "merlin" "help merlin"}{...}
+{vieweralsosee "galahad" "help galahad"}{...}
+{viewerjumpto "Syntax" "survsim model##syntax"}{...}
+{viewerjumpto "Description" "survsim model##description"}{...}
+{viewerjumpto "Options" "survsim model##options"}{...}
+{viewerjumpto "Examples" "survsim model##examples"}{...}
+{title:Title}
+
+{p2colset 5 16 16 2}{...}
+{p2col :{cmd:survsim} {hline 2}}Simulate survival data from a parametric distribution, 
+a user-defined distribution, from a fitted {helpb merlin} model, from a cause-specific 
+hazards competing risks model, or from a general multi-state model{p_end}
+{p2colreset}{...}
+
+
+{marker syntax}{...}
+{title:Syntax}
+
+{phang}
+Syntax for simulating survival times from a fitted {helpb merlin} survival model:
+
+{phang2}
+{cmd: survsim} {it:newvarname1} {it:newvarname2} {cmd:,} {opt mod:el(name)} {opt maxt:ime(#|varname)}
+
+
+{synoptset 36 tabbed}{...}
+{synopthdr:Options}
+{synoptline}
+{synopt:{opt mod:el(name)}}the {helpb estimates store} {it:name} of the fitted {helpb merlin} model; see details{p_end}
+{synopt:{opt maxt:ime(#|varname)}}right censoring time(s); either a common number or a {varname}{p_end}
+{synoptline}
+{p2colreset}{...}
+
+
+{marker description}{...}
+{title:Description}
+
+{pstd}
+{helpb survsim} simulates survival data from a parametric distribution, a user-defined distribution, from a fitted 
+{helpb merlin} model, from a cause-specific hazards competing risks model, or from a Markov multi-state model. 
+This help file centres on simulating from a fitted {helpb merlin} model.
+{p_end} 
+{pstd}
+Survival times can be simulated from the estimated model, using the variables in your current dataset. The variables can simply 
+be altered, to provide a flexible framework to simulate using the estimated parameter vector.
+{p_end}
+
+{pstd}
+{it:newvarname1} specifies the new variable name to contain the generated survival times. {it:newvarname2} specifies the 
+new variable name to contain the generated event indicator. 
+{p_end}
+
+
+{marker options}{...}
+{title:Options}
+
+{phang}{opt model(name)} specifies the name of the {helpb estimates store} object containing the estimates of the model 
+fitted. The survival must be estimated using the {helpb merlin} command. For example,{p_end}
+
+{phang2}{cmd:. merlin (_t trt , family(weibull, failure(_d)))}{p_end}
+{phang2}{cmd:. estimates store m1}{p_end}
+{phang2}{cmd:. survsim stime died, model(m1) maxtime(10)}{p_end}
+
+{phang2}{cmd:survsim} will simulate from the fitted model, using covariate values that are in your current dataset.{p_end}
+
+{phang}{opt maxtime(#|varname)} specifies the right censoring time(s). Either a common maximum follow-up time {cmd:#} can be 
+specified for all observations, or observation specific censoring times can be specified by using a {varname}. {p_end}
+
+
+{title:Remarks}
+
+{pstd}Always {helpb set seed}, to ensure reproducibility.{p_end}
+
+
+{marker examples}{...}
+{title:Examples}
+
+{phang}Simulate from a fitted Weibull survival model:{p_end}
+{phang2}{cmd:. webuse brcancer}{p_end}
+{phang2}{cmd:. stset rectime, failure(censrec) scale(365)}{p_end}
+{phang2}{cmd:. merlin (_t hormon , family(weibull, failure(_d)))}{p_end}
+{phang2}{cmd:. estimates store m1}{p_end}
+{phang2}{cmd:. survsim stime died, model(m1) maxtime(10)}{p_end}
+
+{phang}Simulate from a fitted Royston-Parmar spline-based survival model:{p_end}
+{phang2}{cmd:. webuse brcancer}{p_end}
+{phang2}{cmd:. stset rectime, failure(censrec) scale(365)}{p_end}
+{phang2}{cmd:. merlin (_t hormon , family(rp, failure(_d) df(3)))}{p_end}
+{phang2}{cmd:. estimates store m2}{p_end}
+{phang2}{cmd:. survsim stime died, model(m2) maxtime(10)}{p_end}
+
+
+{title:Author}
+
+{pstd}{cmd:Michael J. Crowther}{p_end}
+{pstd}Red Door Analytics{p_end}
+{pstd}E-mail: {browse "mailto:[email protected]":[email protected]}{p_end}
+
+{phang}Please report any errors you may find.{p_end}
+
+
+{title:References}
+
+{phang}Bender R, Augustin T and Blettner M. Generating survival times to simulate Cox proportional hazards models. {it:Statistics in Medicine} 2005;24:1713-1723.{p_end}
+
+{marker paper1}{...}
+{phang}Crowther MJ and Lambert PC. {browse "http://www.stata-journal.com/article.html?article=st0275":Simulating complex survival data.}{it: The Stata Journal} 2012;12(4):674-687.{p_end}
+
+{marker paper2}{...}
+{phang}Crowther MJ and Lambert PC. {browse "http://onlinelibrary.wiley.com/doi/10.1002/sim.5823/abstract":Simulating biologically plausible complex survival data.} {it:Statistics in Medicine} 2013;32(23):4118-4134.{p_end}
+
+{phang}Jann, B. 2005. moremata: Stata module (Mata) to provide various functions. Available from http://ideas.repec.org/c/boc/bocode/s455001.html.{p_end}
+