*Hello,*
I never worked with R before my supervisor asks me to run a semiMarkov
analysis a month ago. After a long struggle, to date, the code works, but I
still get some warnings. However, because of my lack of knowledge in R I am
not possible to figure out the problems or say anything about the influence
of these warnings on my outcome. Hopefully, someone would help me with
these ( I think basic) questions.
What is the case? I want to do a semiMarkov analysis with 3 states (state
n, state s and state e). Wherefore I want to run the analysis to see
whether there is a difference in Hazard Ratio between transitions nà e and sà e.
Therefore, Iâve got data of nearly 60 persons. In excel, every worksheet
reflects a person. To answer my research question I tried to run the
script for one person.
Unfortunately, I get the following error:
> # read data and convert to correct format (and print tail).
> data <- readdata( input <- 'E1_tijd_stress.csv' )
Error in `$<-.data.frame`(`*tmp*`, "state", value = "s") :
replacement has 1 row, data has 0
Called from: `$<-`(`*tmp*`, "state", value = "s")
Furthermore, I used a macro in excel to merge these worksheets into one
worksheet ( all persons in one file) . However, after running the script I
saw the following warnings:
> # semi-Markov model without covariates.
> fit.semi.markov <- semiMarkov( data = data, states = states.semi.markov,
> mtrans = mtrans.semi.markov )
Iter: 1 fn: 11224.5658 Pars: 1000.00000 412.24725 261.14293
66.30789 1.67507 5.59420 0.55746 1.37715 0.59734 0.48604
0.73281 0.74205
Iter: 2 fn: 11224.5658 Pars: 1000.00000 412.24425 261.14508
66.30635 1.67506 5.59420 0.55746 1.37716 0.59734 0.48604
0.73281 0.74206
solnp--> Completed in 2 iterations
Warning messages:
1: In .safefunx(tmpv, .solnp_fun, .env, ...) :
solnp-->warning: Inf detected in function call...check your function
These repeated for 7 times. Or the following warning:
> fit.semi.markov <- semiMarkov( data = data, states = states.semi.markov,
> mtrans = mtrans.semi.markov )
Iter: 1 fn: 444562.8860 Pars: 1.00000 1.00000 1.00000 1.00000
1.00000 1.00000 1.00000 1.00000 1.00000 0.47882 0.72691 0.74627
solnp--> Completed in 1 iterations
Error in svd(X) : infinite or missing values in 'x'
In addition: There were 29 warnings (use warnings() to see them)
29: In .safefunx(tmpv, .solnp_fun, .env, ...) :
solnp-->warning: NaN detected in function call...check your function
Furthermore, I want to control the analysis for some covariates.
> # semi-Markov model with covariates
> fit2 <- semiMarkov( data = data,cov= as.data.frame(data$stress.score), states
> = states, mtrans = mtrans )
Error in mtrans[as.numeric(substring(trans.hh[i], first = 1, last = 1)), :
subscript out of bounds
Is someone able to tell me what these warnings exactly mean? Or someone I
can contact to discuss about this? I understand inf and NaN for example but
I am not able to figure out what to change in my data format of script (
the problem is, some of my data run without problems, some does not).
Hopefully I give enough information, otherwise let me know.
Thank you!
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