easystats / easystats/parameters

`model_parameters` not displaying smooth parameter for brms additive model when `bs` is supplied to the smooth

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3 investigators :grey_question::question: Bug :bug:
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R
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Merged PRs (30d)
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Description

Everything works fine for model fitted withmgcv but not with brms

library("brms")
library("parameters")
library("ordPens")
library("mgcv")

data("ChickWeight")

fit <- gam(
    weight ~ s(as.ordered(Time), bs = "ordinal") + s(Chick, bs = "re"), 
    data = ChickWeight
)
model_parameters(fit)

# # Fixed Effects 

# Parameter   | Coefficient |   SE |           95% CI | t(525.77) |      p
# ------------------------------------------------------------------------
# (Intercept) |      121.27 | 3.85 | [113.70, 128.84] |     31.47 | < .001

# # Smooth Terms 

# Parameter           |      F |    df |      p
# ---------------------------------------------
# Smooth term (Time)  | 256.86 |  6.88 | < .001
# Smooth term (Chick) |  10.90 | 44.35 | < .001
brmsfit <- brm(
    bf(weight ~ s(as.ordered(Time), bs = "ordinal") + s(Chick, bs = "re")),
    data = ChickWeight
)
model_parameters(brmsfit, effects = "full", component = "all")

# # Fixed Effects 

# Parameter   | Median |           95% CI |   pd |  Rhat | ESS
# ------------------------------------------------------------
# (Intercept) | 121.24 | [113.10, 129.45] | 100% | 1.006 | 361

# # sigma Parameters 

# Parameter | Median |         95% CI |   pd |  Rhat |  ESS
# ---------------------------------------------------------
# sigma     |  27.75 | [26.17, 29.54] | 100% | 0.999 | 6027

# Uncertainty intervals (equal-tailed) computed using a MCMC
#   distribution approximation.

The parameter would reappear if bs is removed

brmsfit2 <- brm(
    bf(weight ~ s(Time) + s(Chick, bs = "re")),
    data = ChickWeight
)
model_parameters(brmsfit2, effects = "full", component = "all")

# # Fixed Effects 

# Parameter   | Median |           95% CI |   pd |  Rhat |  ESS
# -------------------------------------------------------------
# (Intercept) | 121.31 | [113.46, 128.53] | 100% | 1.010 |  338
# sTime_1     | 237.81 | [159.69, 307.29] | 100% | 1.002 | 1418

# # sigma Parameters 

# Parameter | Median |         95% CI |   pd |  Rhat |  ESS
# ---------------------------------------------------------
# sigma     |  27.64 | [26.03, 29.37] | 100% | 1.000 | 3027

# Uncertainty intervals (equal-tailed) computed using a MCMC
#   distribution approximation.

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by running the ChickWeight reproductions for mgcv and brms, comparing model_parameters() output with and without bs on the smooth. Trace how brms smooth terms are identified and displayed; done means the ordinal smooth parameter appears for the brms model while existing output remains correct.

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
Mostly clear
Newbie friendliness
45/100

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