clean_parameters and smooth terms or other special cases

[strengejacke]

What would you suggest, how to deal with "special" terms like smooth terms? I have indicated the SD in the component-column. But should we also mark the smooth-terms themselves, because not always are these of interest, so we might want to filter them out easily...

But how to indicate? They are fixed (or maybe even random?) effects, they can belong to count or zero-inflated part...

library(insight)
m <- download_model("brms_smooth_2")
clean_parameters(m)
#>       parameter effects   component cleaned_parameter
#> 1   b_Intercept   fixed conditional       (Intercept)
#> 2   bs_t2x0x1_1   fixed conditional          t2x0x1_1
#> 3   bs_t2x0x1_2   fixed conditional          t2x0x1_2
#> 4   bs_t2x0x1_3   fixed conditional          t2x0x1_3
#> 5   bs_sx2.x3_1   fixed conditional          sx2.x3_1
#> 6   bs_sx2.x3_2   fixed conditional          sx2.x3_2
#> 7  sds_t2x0x1_1   fixed   smooth_sd          t2x0x1_1
#> 8  sds_t2x0x1_2   fixed   smooth_sd          t2x0x1_2
#> 9  sds_t2x0x1_3   fixed   smooth_sd          t2x0x1_3
#> 10  sds_sx2x3_1   fixed   smooth_sd           sx2x3_1

^{Created on 2019-05-21 by the reprex package (v0.2.1)}

[DominiqueMakowski]

🙉 that's a good question. Mmh I think I would tend to see the smooth term as neither fixed nor random (i.e., as a third category)... but maybe I am miconceptualising things here.

[strengejacke]

It seems to complicated.. (possibly related to #42)

[strengejacke]

library(insight)
library(mgcv)
dat <- gamSim(1, n = 400, dist = "normal", scale = 2)
m1 <- mgcv::gam(y ~ s(x0) + s(x1) + s(x2) + s(x3), data = dat)
m2 <- download_model("brms_smooth_1")
m3 <- download_model("stanreg_gamm4_3")


clean_parameters(m1)
#>     parameter effects   component    fun
#> 1 (Intercept)   fixed conditional       
#> 2       s(x0)   fixed conditional smooth
#> 3       s(x1)   fixed conditional smooth
#> 4       s(x2)   fixed conditional smooth
#> 5       s(x3)   fixed conditional smooth

clean_parameters(m2)
#>     parameter effects   component    fun cleaned_parameter
#> 1 b_Intercept   fixed conditional              (Intercept)
#> 2    bs_sx0_1   fixed conditional smooth             sx0_1
#> 3    bs_sx1_1   fixed conditional smooth             sx1_1
#> 4    bs_sx2_1   fixed conditional smooth             sx2_1
#> 5    bs_sx3_1   fixed conditional smooth             sx3_1
#> 6   sds_sx0_1   fixed   smooth_sd smooth             sx0_1
#> 7   sds_sx1_1   fixed   smooth_sd smooth             sx1_1
#> 8   sds_sx2_1   fixed   smooth_sd smooth             sx2_1
#> 9   sds_sx3_1   fixed   smooth_sd smooth             sx3_1

clean_parameters(m3)
#>                     parameter effects   component  group    fun cleaned_parameter
#> 1                 (Intercept)   fixed conditional                     (Intercept)
#> 2           Speciesversicolor   fixed conditional               Speciesversicolor
#> 3            Speciesvirginica   fixed conditional                Speciesvirginica
#> 4       b[(Intercept) Cat1:X]  random conditional Cat1:X              (Intercept)
#> 5       b[(Intercept) Cat1:Y]  random conditional Cat1:Y              (Intercept)
#> 6 smooth_sd[s(Petal.Length)1]   fixed   smooth_sd        smooth  s(Petal.Length)1
#> 7 smooth_sd[s(Petal.Length)2]   fixed   smooth_sd        smooth  s(Petal.Length)2

^{Created on 2019-05-21 by the reprex package (v0.3.0)}

[strengejacke]

maybe a fun (=function) column, to indicate parameters that stem from special functions?

[DominiqueMakowski]

good idea, and maybe call it function? :)

[strengejacke]

That's a reserved word, which is turned into function. when printing... Any way to avoid this?

[DominiqueMakowski]

or right! hum maybe "special" in that case? a bit vague though

[strengejacke]

a bit vague though

Indeed. Let us stick to fun until we agree on a better name (though I'm very bad at finding names).

[DominiqueMakowski]

type? group? subtype? subcomponent? link ? transformation ?

[strengejacke]

Ok, and now I would through a dart and let it decide...

[strengejacke]

type?

Not sure if a function that is applied to parameters is a "type"...

group?

We already have "group" (random effects).

subtype?

See type

subcomponent?

See type :-D

link?

Is it a link? I think this connotation is reserved for link-functions, somehow...

transformation?

This sounds quite good, but then we would have to do this for other transformations (log(), poly(), ...) as well - I think this is too much, especially since you can nest such transformations.

[DominiqueMakowski]

🙉

class? category? form?

maybe a composite word, type_function?

[strengejacke]

To keep this link in mind:
https://noamross.github.io/gams-in-r-course/

Maybe, in bette understanding the nature of smooth-terms, we find an appropriate name ;-) I'll get back to the above link the next days...

[strengejacke]

library(insight)
m <- download_model("brms_smooth_2")
clean_parameters(m)
#>       Parameter Effects   Component Function Cleaned_Parameter
#> 1   b_Intercept   fixed conditional                (Intercept)
#> 2   bs_t2x0x1_1   fixed conditional   smooth          t2x0x1_1
#> 3   bs_t2x0x1_2   fixed conditional   smooth          t2x0x1_2
#> 4   bs_t2x0x1_3   fixed conditional   smooth          t2x0x1_3
#> 5   bs_sx2.x3_1   fixed conditional   smooth          sx2.x3_1
#> 6   bs_sx2.x3_2   fixed conditional   smooth          sx2.x3_2
#> 7  sds_t2x0x1_1   fixed   smooth_sd   smooth          t2x0x1_1
#> 8  sds_t2x0x1_2   fixed   smooth_sd   smooth          t2x0x1_2
#> 9  sds_t2x0x1_3   fixed   smooth_sd   smooth          t2x0x1_3
#> 10  sds_sx2x3_1   fixed   smooth_sd   smooth           sx2x3_1

^{Created on 2019-06-26 by the reprex package (v0.3.0)}

I leave this issue open, because we might revise the handling of smooth-terms in the future.