CODEWITHSUNDEEP
rsegmentation-fault
Andrews
Andrews

Reputation: 335

Package msm: segmentation-fault when introducing covariates

While using the package msm, I am currently getting the error:

* caught segfault * address 0x7f875be5ff48, cause 'memory not mapped'

when I introduce a covariate to my model. Previously, I had resolved a similar error by converting my response variable from a factor to a numeric variable. This however does not resolve my current issue.

The data <- https://www.dropbox.com/s/wx6s4liofaxur0v/data_msm.txt?dl=0

library(msm)

#number of transitions between states
#1: healthy; 2: ill; 3: dead; 4: censor
statetable.msm(state_2, id, data=dat.long)

#setting initial values
q <- rbind(c(0, 0.25, 0.25), c(0.25, 0, 0.25), c(0, 0, 0))
crudeinits <- crudeinits.msm(state_2 ~ time, subject=id, data=dat.long, qmatrix=q, censor = 4, censor.states = c(1,2))

#running model without covariates
(fm1.msm <- msm(state_2 ~ time, subject = id, qmatrix = crudeinits, data = dat.long, death = 3, censor = 4, censor.states = c(1,2)))

#running model with covariates
(fm2.msm <- msm(state_2 ~ time, subject = id, qmatrix = crudeinits, data = dat.long, covariates = ~ gender, death = 3, censor = 4, censor.states = c(1,2)))

Alternatively, I can run the models with covariates if I set the state values dead and censor (3 & 4) to missing. 

#set death and censor to missing    
dat.long$state_2[dat.long$state_2 %in% c(3,4)] <- NA
statetable.msm(state_2, id, data=dat.long)

#setting initial values
q <- rbind(c(0, 0.5), c(0.5, 0))
crudeinits <- crudeinits.msm(state_2 ~ time, subject=id, data=dat.long, qmatrix=q)

#running models with covariates
(fm3.msm <- msm(state_2 ~ time, subject = id, qmatrix = crudeinits, data = dat.long, covariates = ~ gender))
(fm4.msm <- msm(state_2 ~ time, subject = id, qmatrix = crudeinits, data = dat.long, covariates = ~ covar))

Thanks for your help

Upvotes: 0

Views: 305

Answers (1)

Chris Jackson
Chris Jackson

Reputation: 871

In version 1.5 of msm, there's an error in the R code that detects and drops NAs in the data. This is triggered when there are covariates, and the state or time variable contains NAs. Those NAs can then be passed through to the C code that computes the likelihood, causing a crash. I'll fix this for the next version. In the meantime you can work around it by dropping NAs from the data before calling msm.

Upvotes: 1

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