Skip to content

as.matrix.projection() for GAMs: SDs for smoothing terms missing #151

Open
@fweber144

Description

@fweber144

On branch develop (commit 96d8e11), this reprex:

options(mc.cores = parallel::detectCores(logical = FALSE))
data("kidiq", package = "rstanarm")
kidiq <- head(kidiq, 45)
fit_gauss <- rstanarm::stan_gamm4(
  kid_score ~ s(mom_iq),
  data = kidiq,
  iter = 500,
  seed = 734572
)

library(projpred)
prj <- project(fit_gauss, solution_terms = c("s(mom_iq)"),
               ndraws = 25)
colnames(as.matrix(prj))

gives

 [1] "b_Intercept"   "b_s(mom_iq).1" "b_s(mom_iq).2" "b_s(mom_iq).3"
 [5] "b_s(mom_iq).4" "b_s(mom_iq).5" "b_s(mom_iq).6" "b_s(mom_iq).7"
 [9] "b_s(mom_iq).8" "b_s(mom_iq).9" "sigma"

(so the output matrix does not include the SD(s) for the smoothing term) whereas

colnames(as.matrix(fit_gauss))

(correctly) gives

 [1] "(Intercept)"           "s(mom_iq).1"          
 [3] "s(mom_iq).2"           "s(mom_iq).3"          
 [5] "s(mom_iq).4"           "s(mom_iq).5"          
 [7] "s(mom_iq).6"           "s(mom_iq).7"          
 [9] "s(mom_iq).8"           "s(mom_iq).9"          
[11] "sigma"                 "smooth_sd[s(mom_iq)1]"
[13] "smooth_sd[s(mom_iq)2]"

Metadata

Metadata

Assignees

No one assigned

    Labels

    additiveIssues concerning additive models (GAMs and GAMMs).bugBugs.

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions