R Under development (unstable) (2024-09-28 r87201 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
>  Sys.setenv('OMP_THREAD_LIMIT'=2)
>  library(rlibkriging)

Attaching package: 'rlibkriging'

The following objects are masked from 'package:base':

    load, save

> 
> ##library(testthat)
>  Sys.setenv('OMP_THREAD_LIMIT'=2)
> #library(rlibkriging)
> 
> library(RobustGaSP)
#########
##
## Robust Gaussian Stochastic Process, RobustGaSP Package
## Copyright (C) 2016-2024 Mengyang Gu, Jesus Palomo and James O. Berger
#########

Attaching package: 'RobustGaSP'

The following object is masked from 'package:rlibkriging':

    simulate

The following object is masked from 'package:stats':

    simulate

> 
> context("RobustGaSP / Fit: 1D")
> 
> f = function(x) 1-1/2*(sin(12*x)/(1+x)+2*cos(7*x)*x^5+0.7)
> #plot(f)
> n <- 5
> set.seed(123)
> X <- as.matrix(runif(n))
> y = f(X)
> #points(X,y)
> k = RobustGaSP::rgasp(design=X,response=y, trend=cbind(matrix(1,length(y),1),X))
The upper bounds of the range parameters are 184.9743 
The initial values of range parameters are 3.699485 
Start of the optimization  1  : 
The number of iterations is  9 
 The value of the  marginal posterior  function is  3.693599 
 Optimized range parameters are 0.135556 
 Optimized nugget parameter is 0 
 Convergence:  TRUE 
The initial values of range parameters are 0.05223118 
Start of the optimization  2  : 
The number of iterations is  7 
 The value of the  marginal posterior  function is  3.693599 
 Optimized range parameters are 0.135556 
 Optimized nugget parameter is 0 
 Convergence:  TRUE 
> ##library(rlibkriging)
> r <- Kriging(y, X,
+   kernel="matern5_2",
+   regmodel = "linear", normalize = FALSE,
+   optim = "BFGS",
+   objective = "LMP")
> # m = as.list(r)
> 
> # Check lmp function
> 
> lmp_rgasp = function(X, model=k) {if (!is.matrix(X)) X = matrix(X,ncol=1);
+                   # print(dim(X));
+                   apply(X,1,
+                     function(x) {
+                       #y=-logMargPostFun(r,matrix(unlist(x),ncol=2))$logMargPost
+                       y=RobustGaSP:::neg_log_marginal_post_approx_ref(param=(x),nugget=0, nugget.est=model@nugget.est, 
+                                         R0=model@R0,X=model@X, zero_mean=model@zero_mean,output=model@output, 
+                                         CL=model@CL, 
+                                         a=0.2,
+                                         b=1/(length(model@output))^{1/dim(as.matrix(model@input))[2]}*(0.2+dim(as.matrix(model@input))[2]),
+                                         kernel_type=rep(as.integer(3),ncol(X)),alpha=model@alpha
+                                         )
+                       y})}
> lmp_rgasp(1)
[1] -3.173653
> 
> plot(lmp_rgasp,xlim=c(0.01,6))
> abline(v=(log(k@beta_hat)))
> 
> lmp_lk = function(X) {if (!is.matrix(X)) X = matrix(X,ncol=1);
+                   # print(dim(X));
+                   apply(X,1,
+                     function(x) {
+                       y=-logMargPostFun(r,matrix(unlist(exp(-(x))),ncol=1))$logMargPost
+                       y})}
> lmp_lk(1)
[1] -3.173653
> 
> lines(seq(0.1,6,,5),lmp_lk(seq(0.1,6,,5)),col='red')
> abline(v=(log(1/as.list(r)$theta)),col='red')
> 
> precision <- 1e-3
> test_that(desc=paste0("RobustGaSP / Fit: 1D / rgasp/lmp is the same that lk/lmp one"),
+           expect_equal(lmp_rgasp(1),lmp_lk(1),tol = precision))
Test passed 🥳
> test_that(desc=paste0("RobustGaSP / Fit: 1D / fitted theta is the same that RobustGaSP one"),
+           expect_equal(as.list(r)$theta[1],1/k@beta_hat,tol = precision))
Test passed 🥳
> 
> 
> 
> dlmp_rgasp = function(X, model=k) {if (!is.matrix(X)) X = matrix(X,ncol=1);
+                   # print(dim(X));
+                   apply(X,1,
+                     function(x) {
+ 
+ #    print(RobustGaSP:::log_marginal_lik_deriv(param=(x),nugget=0,nugget_est=model@nugget.est, 
+ #                                        R0=model@R0,X=model@X, zero_mean=model@zero_mean,
+ #                                        output=model@output, 
+ #                                        kernel_type=rep(as.integer(3),ncol(X)),alpha=model@alpha))
+ #
+ #    print(RobustGaSP:::log_approx_ref_prior_deriv(param=(x),nugget=0, nugget_est=model@nugget.est, 
+ #                                        CL=model@CL, 
+ #                                        a=0.2,
+ #                                        b=1/(length(model@output))^{1/dim(as.matrix(model@input))[2]}*(0.2+dim(as.matrix(model@input))[2])))
+ 
+ 
+                       #y=-logMargPostFun(r,matrix(unlist(x),ncol=2))$logMargPost
+                       y=RobustGaSP:::neg_log_marginal_post_approx_ref_deriv(param=(x),nugget=0, nugget.est=model@nugget.est, 
+                                         R0=model@R0,X=model@X, zero_mean=model@zero_mean,output=model@output, 
+                                         CL=model@CL, 
+                                         a=0.2,
+                                         b=1/(length(model@output))^{1/dim(as.matrix(model@input))[2]}*(0.2+dim(as.matrix(model@input))[2]),
+                                         kernel_type=rep(as.integer(3),ncol(X)),alpha=model@alpha
+                                         )
+                       y})}
> dlmp_rgasp(1)
[1] -0.9422739
> 
> dlmp_lk = function(X) {if (!is.matrix(X)) X = matrix(X,ncol=1);
+                   apply(X,1,
+                     function(x) {
+                       y=-logMargPostFun(r,matrix(unlist(exp(-(x))),ncol=1),TRUE)$logMargPostGrad
+                       y})}
> -exp(-1)*dlmp_lk(1)
[1] -0.9422739
> 
> precision <- 1e-3
> test_that(desc=paste0("RobustGaSP / Fit: 1D / rgasp/lmp deriv is the same that lk/lmp deriv"),
+           expect_equal(dlmp_rgasp(1),-exp(-1)*dlmp_lk(1),tol = precision))
Test passed 🎉
> 
> proc.time()
   user  system elapsed 
   1.82    0.28    2.10