stan_nlmer formula and fixed effects
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Description
Summary:
Problem in specifying fixed effects in stan_nlmer formula.
Description:
Following the documentation of stan_nlmer the formula needs to be in the same form as the nlmer one: a three-part “nonlinear mixed model” formula, of the form resp ~ Nonlin(...) ~ fixed + random (from the nlmer help page).
I can't find a way to specify the fixed effect variable. When I do it, after a long list of rejected values I get:
Chain 1:
Chain 1: Initialization between (-2, 2) failed after 100 attempts.
Chain 1: Try specifying initial values, reducing ranges of constrained values, or reparameterizing the model.
[1] "Error in sampler$call_sampler(args_list[[i]]) : Initialization failed."
error occurred during calling the sampler; sampling not done
Error in check_stanfit(stanfit) :
Invalid stanfit object produced please report bug
Also if I try to specify my own function with the suggested deriv option (check example 3 of the nlmer help page), I'm not able to fit the model with stan_nlmer.
I suspect is a long standing problem of nlmer..
Reproducible Steps:
Here an example of the problem with the code you have in your help page
data("Orange", package = "datasets")
Orange$circumference <- Orange$circumference / 100
Orange$age <- Orange$age / 100
#define a new to use as fixed effect:
Orange$fixed.eff <- ifelse(Orange$Tree=="3"|Orange$Tree=="5",1,2)
#try to include it following the formula definition:
fit <- stan_nlmer(
circumference ~ SSlogis(age, Asym, xmid, scal) ~ fixed.eff + (Asym|Tree),
data = Orange,
#for speed only
chains = 1,
iter = 1000
)
RStanARM Version:
packageVersion("rstanarm")
[1] ‘2.21.2’
packageVersion("lme4")
[1] ‘1.1.23’
packageVersion("rstan")
[1] ‘2.21.2’
R Version:
[1] ‘4.0.2’
Operating System:
OS X 10.15.6
Contributor guide
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the reproducible Orange example in the issue and the stan_nlmer documentation, then compare its three-part formula handling with the nlmer help example and deriv option. The issue names no source files or tests; done means establishing whether fixed.eff and a user-supplied deriv function are supported and clearly characterizing the observed behavior.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- r
- Domain
- data
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100