If you are going to drive a car you should learn to drive. Read the
basic intro material for R.
Where does the function "readdata" come from? The syntax you use
(having an assignment inside the function call) is let us say unorthodox
and highly inadvisable.
Since you got an error reading in your data, where did the data that you
are trying to analyse come from?
Don't call your data "data". See fortune(77).
You don't say where the function semiMarkov() comes from; presumably
from the package "semiMarkov". Say so. Do not expect your readers to
be telepathic.
Don't use Excel to do *anything* (except store data, if you *must*).
I certainly can't help you to debug your errors/warnings without seeing
your data. I doubt that anyone else can either. (I *could* be wrong
about that; there are some *very* clever and intuitive people on this list.)
cheers,
Rolf Turner
On 22/07/14 02:04, M.A. Pet wrote:
*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, I’ve 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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--
Rolf Turner
Technical Editor ANZJS
______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
