Translate func_MCMC()'s subfunctions to C++

[wleoncio]

Files to be translated

• func_MCMC_graph()
• updateGamma()
• UpdateRPlee11()
• calJpost()

Cleanup

•  Test all valid combinations of model.type, MRF2b and MRF_G (see next section)
•  Print final benchmarks
•  Default all calls to C++ version
•  Remove R code
•  Move all TODOs to issues

Combinations of BayesSurvive() to test

Not all combos are valid, see #11 (comment).

Test number	model.type	MRF_G	MRF_2b
1	Pooled	FALSE	FALSE
2	Pooled	TRUE	FALSE
3	CoxBVSSL	FALSE	FALSE
4	CoxBVSSL	TRUE	FALSE
5	Sub-struct	FALSE	FALSE
6	Sub-struct	FALSE	TRUE
7	Sub-struct	TRUE	FALSE
8	Sub-struct	TRUE	TRUE

•  Test 1
• Test 2
• Test 3
• Test 4
• Test 5
• Test 6
• Test 7
• Test 8

[wleoncio]

Benchmark results for calling BayesSurvive() after translation of func_MCMC_graph():

Unit: seconds
 expr       min        lq     mean    median       uq      max neval cld
    R 48.663260 52.858755 56.45211 54.208202 58.65805 82.42916    30  a 
  C++  7.715861  8.870257 10.02130  9.466554 10.06589 24.06125    30   b

[zhizuio]

Benchmark results for calling BayesSurvive() after translation of func_MCMC_graph():

Unit: seconds
 expr       min        lq     mean    median       uq      max neval cld
    R 48.663260 52.858755 56.45211 54.208202 58.65805 82.42916    30  a 
  C++  7.715861  8.870257 10.02130  9.466554 10.06589 24.06125    30   b

Supert!

[zhizuio]

Hi Waldir,

I have the following error when installing the package from GitHub. One solution is to always keep the folder inst/doc/... with vignettes. Probably you have another better solution?

[wleoncio]

Hi George,

I can reproduce the error and your solution. Keeping track of built files (i.e., anything under /inst/doc) is not ideal, though.

What's the use of that build folder anyway? I tried deleting it and the package still installs with vignettes, you can also try it from the fix-vignettes branch:

remotes::install_github("ocbe-uio/BayesSurvive@fix-vignettes", build_vignettes = TRUE)
browseVignettes("BayesSurvive")

[zhizuio]

Hi George,

I can reproduce the error and your solution. Keeping track of built files (i.e., anything under /inst/doc) is not ideal, though.

What's the use of that build folder anyway? I tried deleting it and the package still installs with vignettes, you can also try it from the fix-vignettes branch:

remotes::install_github("ocbe-uio/BayesSurvive@fix-vignettes", build_vignettes = TRUE)
browseVignettes("BayesSurvive")

This solution works. Do you know if we can set up something, so that the usual installation still works?

[zhizuio]

Thank you very much, Waldir, for updating and testing the package! If I remember correctly, the argument MRF_2b = TRUE is only valid when model.type ="Sub-struct". Then only the following 8 tests are needed, right?

Test number	model.type	MRF_G	MRF_2b
1	Pooled	FALSE	FALSE
2	Pooled	TRUE	FALSE
3	CoxBVSSL	FALSE	FALSE
4	CoxBVSSL	TRUE	FALSE
5	Sub-struct	FALSE	FALSE
6	Sub-struct	FALSE	TRUE
7	Sub-struct	TRUE	FALSE
8	Sub-struct	TRUE	TRUE

It might be also helpful to add the following table in the help file or README.

Model	Fix MRF_G	Infer MRF_G
Pooled	✔	✔
CoxBVSSL	✔	✔
Sub-struct	✔	✔

[wleoncio]

Thanks for checking, will edit accordingly! :)

[wleoncio]

Question: when we have a situation like below (triggered when method != "Pooled" or !MRF_G), is it safe to assume that these objects are the same size across the $g = \{1, \ldots, S\}$ subgroups? For example, sobj$X[[g]] has the same dimensions for all values of g on that loop?

BayesSurvive/R/UpdateRPlee11.R

Lines 48 to 56 in 83698c9

	x <- sobj$X[[g]]
	J <- hyperpar$J[[g]]
	ind.r <- hyperpar$ind.r[[g]]
	ind.d <- hyperpar$ind.d[[g]]
	ind.r_d <- hyperpar$ind.r_d[[g]]
	be.ini <- ini$beta.ini[[g]]
	be.prop.sd.scale <- hyperpar$be.prop.sd.scale[[g]]
	ga.ini <- ini$gamma.ini[[g]]
	h <- ini$h[[g]]

[zhizuio]

Question: when we have a situation like below (triggered when method != "Pooled" or !MRF_G), is it safe to assume that these objects are the same size across the g = { 1 , … , S } subgroups? For example, sobj$X[[g]] has the same dimensions for all values of g on that loop?

BayesSurvive/R/UpdateRPlee11.R

Lines 48 to 56 in 83698c9

	x <- sobj$X[[g]]
	J <- hyperpar$J[[g]]
	ind.r <- hyperpar$ind.r[[g]]
	ind.d <- hyperpar$ind.d[[g]]
	ind.r_d <- hyperpar$ind.r_d[[g]]
	be.ini <- ini$beta.ini[[g]]
	be.prop.sd.scale <- hyperpar$be.prop.sd.scale[[g]]
	ga.ini <- ini$gamma.ini[[g]]
	h <- ini$h[[g]]

Yes, the same dimension across subgroups should be required according to the model setting.

[wleoncio]

Great news, thanks! Then I can just implement those as cubes on C++... :)