# How to translate a Stan nonlinear fit to brms
**URL:** https://discourse.mc-stan.org/t/how-to-translate-a-stan-nonlinear-fit-to-brms/12764
**Category:** brms
**Created:** [January 22, 2020, 6:33pm UTC](https://discourse.mc-stan.org/t/how-to-translate-a-stan-nonlinear-fit-to-brms/12764 "2020-01-22T18:33:46Z")
**Posts on this page:** 5
**Page:** 1
### Author:  [@denne](https://discourse.mc-stan.org/u/denne)
#### Post date: [January 22, 2020, 6:33pm UTC](https://discourse.mc-stan.org/t/how-to-translate-a-stan-nonlinear-fit-to-brms/12764/1 "2020-01-22T18:33:46Z")
I am trying to demonstrate how a Stan nonlinear fit can be “simplified” by brms, and failed miserably. Data set is from [https://github.com/dmenne/breathtestcore](https://github.com/dmenne/breathtestcore), Stan in [https://github.com/dmenne/breathteststan](https://github.com/dmenne/breathteststan)
```
library(ggplot)
library(breathteststan) # on cran
library(breathtestcore)
library(brms)
data(usz_13c)
# Use a subset
solids = str_detect(usz_13c$patient_id, "00") & str_detect(usz_13c$group, "solid")
bt = usz_13c[solids,]
# cleanup_data standardizes columns
# Stan does not converge when samples are too dense, so do subsampling
bt = cleanup_data(breathtestcore::subsample_data(bt,15))
# Group parameter (patient/normal) is not used here, but that's the subject
# for another day
#plot(null_fit(bt))
# https://github.com/dmenne/breathteststan/blob/master/inst/stan/breath_test_1.stan
# My simple stan model. 1000 iterations, about 30 seeconds on my computer
fit = stan_fit(bt)
plot(fit)
cf = coef(fit)
cf[cf$parameter %in% c("m","k","beta"),c(2,3,5)]
# Simplified model, incorporated constant "dose" parameter into m
fit_model = brm( bf(pdr ~ m*k*beta*(1-exp(-k*minute))^(beta-1)*exp(-k*minute),
m ~ 1 + (1|patient_id),
k ~ 1 + (1|patient_id),
beta ~ 1 + (1|patient_id),
nl = TRUE),
data = bt,
chains = 1,
iter = 1,
family = gaussian(),
control = list(adapt_delta = 0.9, max_treedepth = 20),
inits = list(list(m = 2000, k = 0.02, beta = 2 )),
prior = c(
prior(normal(2000,400), nlpar = "m"),
prior(lognormal(-5, 1), nlpar = "k"),
prior(normal(2, 0.6), nlpar = beta)
))
update(fit_model, iter = 1000)
# No convergence.....
```
---
### Author:  [@denne](https://discourse.mc-stan.org/u/denne)
#### Post date: [January 23, 2020, 9:53am UTC](https://discourse.mc-stan.org/t/how-to-translate-a-stan-nonlinear-fit-to-brms/12764/2 "2020-01-23T09:53:49Z")
Sorry, Paul, with your help some years ago we had already solved this.
See [https://gist.github.com/dmenne/db4bacb7128f2922aaa75bcd9c1f8766](https://gist.github.com/dmenne/db4bacb7128f2922aaa75bcd9c1f8766)
---
### Author:  [@paul.buerkner](https://discourse.mc-stan.org/u/paul.buerkner)
#### Post date: [January 23, 2020, 10:03am UTC](https://discourse.mc-stan.org/t/how-to-translate-a-stan-nonlinear-fit-to-brms/12764/3 "2020-01-23T10:03:41Z")
So no more action required?
---
### Author:  [@denne](https://discourse.mc-stan.org/u/denne)
#### Post date: [January 23, 2020, 10:05am UTC](https://discourse.mc-stan.org/t/how-to-translate-a-stan-nonlinear-fit-to-brms/12764/4 "2020-01-23T10:05:06Z")
No. I still don’t understand why the simple problem does not work, but I am checking.
Closed and thanks.
---
### Author:  [@denne](https://discourse.mc-stan.org/u/denne)
#### Post date: [January 23, 2020, 10:18am UTC](https://discourse.mc-stan.org/t/how-to-translate-a-stan-nonlinear-fit-to-brms/12764/5 "2020-01-23T10:18:50Z")
Krrr… I forgot the dummy ID … Done this before.
```
m ~ 1 + (1|ID|patient_id),
k ~ 1 + (1|ID|patient_id),
beta ~ 1 + (1|ID|patient_id),
```