R Under development (unstable) (2024-08-21 r87038 ucrt) -- "Unsuffered Consequences"
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> library(testthat)
>  Sys.setenv('OMP_THREAD_LIMIT'=2)
>  library(rlibkriging)

Attaching package: 'rlibkriging'

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

    load, save

> 
> # pack=list.files(file.path("bindings","R"),pattern = ".tar.gz",full.names = T)
> # install.packages(pack,repos=NULL)
> # #library(rlibkriging)
> ##library(rlibkriging, lib.loc="bindings/R/Rlibs")
> ##library(testthat)
> default_rcond_checked = rlibkriging:::linalg_chol_rcond_checked()
> default_num_nugget = rlibkriging:::linalg_get_num_nugget()
> 
> context("Fit: unstable LL (long range with 1D Gauss kernel)")
> 
> # 1D function, small design, but not stationary
> X <- as.matrix(c(0.0, 0.25, 0.33, 0.45, 0.5, 0.75, 1.0))
> f <- function(x) 1 - 1 / 2 * (sin(4 * x) / (1 + x) + 2 * cos(12 * x) * x^6 + 0.7)
> y <- f(X)  #+ 0.5*rnorm(nrow(X))
> 
> #plot(f)
> #points(X, y)
> 
> rlibkriging:::linalg_check_chol_rcond(FALSE)
> rlibkriging:::linalg_set_num_nugget(1e-15)
> rlibkriging:::linalg_set_chol_warning(TRUE)
> #rlibkriging:::optim_log(4)
> 
> # bad init theta value
> # Build Kriging (https://libkriging.readthedocs.io/en/latest/math/KrigingModels.html)
> k <- Kriging(y, X, kernel="gauss", optim="none", parameters= list(theta=matrix(9.0), sigma2=1e10))
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
> plot(f)
> points(X,y)
> #DiceView::sectionview(k,add=TRUE)
> xx=sort(c(seq(0,1,,101),X))
> lines(xx, k$predict(xx)$mean)
> 
> # Build Kriging (https://libkriging.readthedocs.io/en/latest/math/KrigingModels.html)
> #rlibkriging:::optim_log(4)
> rlibkriging:::linalg_check_chol_rcond(TRUE)
> k <- Kriging(y, X, kernel="gauss", optim="BFGS")
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.3042e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 2.72659e-18 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 5.81821e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 7.45472e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 7.45472e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 7.45472e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 5.31699e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 7.45472e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 7.45472e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.166e-18 is below minimal value.
[WARNING] rcond 7.45472e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 3.17555e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 7.45519e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 7.45472e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 7.45519e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.3042e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
> #DiceView::sectionview(k,add=TRUE,col_surf='orange')
> 
> # plots
> .t=seq(0,10,,101)
> rlibkriging:::linalg_check_chol_rcond(TRUE)
> plot(.t, k$logLikelihoodFun(.t)$logLikelihood)
[WARNING] rcond 5.50322e-18 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 2.13506e-18 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.58973e-18 is below minimal value.
[WARNING] rcond 5.57503e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.09285e-18 is below minimal value.
[WARNING] rcond 2.32291e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 8.19643e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.50694e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.08979e-18 is below minimal value.
[WARNING] rcond 1.82276e-18 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.56941e-18 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 8.87903e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 3.6391e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.53076e-18 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 3.85751e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.99997e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 2.72993e-18 is below minimal value.
[WARNING] rcond 2.77362e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 4.60104e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 2.52173e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.46935e-18 is below minimal value.
[WARNING] rcond 1.06237e-18 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.00597e-18 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 8.92217e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.31411e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.7322e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 2.14247e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.36536e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 2.5548e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.3042e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
> for (t in .t) {
+     arrows(
+         t,     k$logLikelihoodFun(t)$logLikelihood,
+         t-0.2, k$logLikelihoodFun(t)$logLikelihood-0.2*k$logLikelihoodFun(t,return_grad=TRUE)$logLikelihoodGrad, 
+         col='black')
+ }
[WARNING] rcond 5.50322e-18 is below minimal value.
[WARNING] rcond 5.50322e-18 is below minimal value.
[WARNING] rcond 5.50322e-18 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 2.13506e-18 is below minimal value.
[WARNING] rcond 2.13506e-18 is below minimal value.
[WARNING] rcond 2.13506e-18 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.58973e-18 is below minimal value.
[WARNING] rcond 1.58973e-18 is below minimal value.
[WARNING] rcond 1.58973e-18 is below minimal value.
[WARNING] rcond 5.57503e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 5.57503e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 5.57503e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.09285e-18 is below minimal value.
[WARNING] rcond 1.09285e-18 is below minimal value.
[WARNING] rcond 1.09285e-18 is below minimal value.
[WARNING] rcond 2.32291e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 2.32291e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 2.32291e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 8.19643e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 8.19643e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 8.19643e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.50694e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.50694e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.50694e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.08979e-18 is below minimal value.
[WARNING] rcond 1.08979e-18 is below minimal value.
[WARNING] rcond 1.08979e-18 is below minimal value.
[WARNING] rcond 1.82276e-18 is below minimal value.
[WARNING] rcond 1.82276e-18 is below minimal value.
[WARNING] rcond 1.82276e-18 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.56941e-18 is below minimal value.
[WARNING] rcond 1.56941e-18 is below minimal value.
[WARNING] rcond 1.56941e-18 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 8.87903e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 8.87903e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 8.87903e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 3.6391e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 3.6391e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 3.6391e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.53076e-18 is below minimal value.
[WARNING] rcond 1.53076e-18 is below minimal value.
[WARNING] rcond 1.53076e-18 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 3.85751e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 3.85751e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 3.85751e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.99997e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.99997e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.99997e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 2.72993e-18 is below minimal value.
[WARNING] rcond 2.72993e-18 is below minimal value.
[WARNING] rcond 2.72993e-18 is below minimal value.
[WARNING] rcond 2.77362e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 2.77362e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 2.77362e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 4.60104e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 4.60104e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 4.60104e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 2.52173e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 2.52173e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 2.52173e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.46935e-18 is below minimal value.
[WARNING] rcond 1.46935e-18 is below minimal value.
[WARNING] rcond 1.46935e-18 is below minimal value.
[WARNING] rcond 1.06237e-18 is below minimal value.
[WARNING] rcond 1.06237e-18 is below minimal value.
[WARNING] rcond 1.06237e-18 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.00597e-18 is below minimal value.
[WARNING] rcond 1.00597e-18 is below minimal value.
[WARNING] rcond 1.00597e-18 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 8.92217e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 8.92217e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 8.92217e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.31411e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.31411e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.31411e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.7322e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.7322e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.7322e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 2.14247e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 2.14247e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 2.14247e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.36536e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.36536e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.36536e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 2.5548e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 2.5548e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 2.5548e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.3042e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.3042e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.3042e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
> rlibkriging:::linalg_check_chol_rcond(FALSE)
> lines(.t, k$logLikelihoodFun(.t)$logLikelihood,col='blue')
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
> for (t in .t) {
+     arrows(
+         t,     k$logLikelihoodFun(t)$logLikelihood,
+         t-0.21, k$logLikelihoodFun(t)$logLikelihood-0.21*k$logLikelihoodFun(t,return_grad=TRUE)$logLikelihoodGrad, 
+         col='blue')
+ }
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
> #rlibkriging:::covariance_use_approx_singular(FALSE)
> #rlibkriging:::linalg_set_num_nugget(0)
> 
> abline(v=k$theta())
> abline(h=k$logLikelihood())
> 
> rcond_approx_R = function(theta) {
+     k_tmp = NULL
+     try(k_tmp <- Kriging(y, X, kernel="gauss", optim="none",parameters=list(theta=matrix(theta))))
+     if (is.null(k_tmp)) return(NA)
+     T=k_tmp$T()
+     R = (T) %*% t(T)
+     rlibkriging:::linalg_rcond_approx_chol(T)
+ }
> lines(.t, log(Vectorize(rcond_approx_R)(.t)),col='orange')
[WARNING] rcond_approx 6.63424e-10 is below minimal value.
[WARNING] rcond_approx 4.20693e-10 is below minimal value.
[WARNING] rcond_approx 2.73377e-10 is below minimal value.
[WARNING] rcond_approx 1.81593e-10 is below minimal value.
[WARNING] rcond_approx 1.23044e-10 is below minimal value.
[WARNING] rcond_approx 8.48878e-11 is below minimal value.
[WARNING] rcond_approx 5.95337e-11 is below minimal value.
[WARNING] rcond_approx 4.23849e-11 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 3.06061e-11 is below minimal value.
[WARNING] rcond_approx 1.69149e-11 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 1.65574e-11 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 1.23859e-11 is below minimal value.
[WARNING] rcond_approx 9.3508e-12 is below minimal value.
[WARNING] rcond_approx 4.54058e-12 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 5.4984e-12 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 4.26862e-12 is below minimal value.
[WARNING] rcond_approx 3.33007e-12 is below minimal value.
[WARNING] rcond_approx 1.9744e-12 is below minimal value.
[WARNING] rcond_approx 2.08127e-12 is below minimal value.
[WARNING] rcond_approx 1.25537e-12 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 1.34509e-12 is below minimal value.
[WARNING] rcond_approx 1.0786e-12 is below minimal value.
[WARNING] rcond_approx 8.77273e-13 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 7.26326e-13 is below minimal value.
[WARNING] rcond_approx 5.88233e-13 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 4.95162e-13 is below minimal value.
[WARNING] rcond_approx 4.01433e-13 is below minimal value.
[WARNING] rcond_approx 3.34279e-13 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 2.89291e-13 is below minimal value.
[WARNING] rcond_approx 2.34742e-13 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 2.0781e-13 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 1.77661e-13 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 1.51524e-13 is below minimal value.
[WARNING] rcond_approx 1.2038e-13 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 1.1293e-13 is below minimal value.
[WARNING] rcond_approx 8.77578e-14 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 8.59612e-14 is below minimal value.
[WARNING] rcond_approx 6.5476e-14 is below minimal value.
[WARNING] rcond_approx 5.65888e-14 is below minimal value.
[WARNING] rcond_approx 4.89143e-14 is below minimal value.
[WARNING] rcond_approx 4.24029e-14 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 4.73308e-14 is below minimal value.
[WARNING] rcond_approx 3.32565e-14 is below minimal value.
[WARNING] rcond_approx 2.85043e-14 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 3.52154e-14 is below minimal value.
[WARNING] rcond_approx 2.25163e-14 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 3.00767e-14 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 2.83017e-14 is below minimal value.
[WARNING] rcond_approx 1.52849e-14 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 2.44587e-14 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 2.26598e-14 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 2.10257e-14 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 2.0201e-14 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 1.84965e-14 is below minimal value.
[WARNING] rcond_approx 7.51119e-15 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 1.71419e-14 is below minimal value.
[WARNING] rcond_approx 6.04772e-15 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 1.57766e-14 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 1.59086e-14 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 1.61058e-14 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 1.4511e-14 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 1.35154e-14 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 1.43733e-14 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 1.32008e-14 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 1.30386e-14 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 1.35448e-14 is below minimal value.
[WARNING] rcond_approx 2.65779e-15 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 1.27221e-14 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 1.20813e-14 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 1.32691e-14 is below minimal value.
[WARNING] rcond_approx 1.51623e-15 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 1.15726e-14 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 1.27848e-14 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 1.2407e-14 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 1.17498e-14 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 1.09655e-14 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 1.13648e-14 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 1.15861e-14 is below minimal value.
[WARNING] rcond_approx 1.12638e-15 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 1.14567e-14 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 1.19422e-14 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 1.03312e-14 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond_approx 1.23473e-14 is below minimal value.
[WARNING] rcond_approx 8.71993e-16 is below minimal value.
> abline(h=log(1e-10),col='orange')
> rcond_R = function(theta) {
+     k_tmp = NULL
+     try(k_tmp <- Kriging(y, X, kernel="gauss", optim="none",parameters=list(theta=matrix(theta))))
+     if (is.null(k_tmp)) return(NA)
+     T=k_tmp$T()
+     R = (T) %*% t(T)
+     rlibkriging:::linalg_rcond_chol(T)
+ }
> lines(.t, log(Vectorize(rcond_R)(.t)),col='red')
[WARNING] rcond 5.50322e-18 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 2.13506e-18 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.58973e-18 is below minimal value.
[WARNING] rcond 5.57503e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.09285e-18 is below minimal value.
[WARNING] rcond 2.32291e-19 is below minimal value.
[WARNING] rcond 8.19643e-19 is below minimal value.
[WARNING] rcond 1.50694e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.08979e-18 is below minimal value.
[WARNING] rcond 1.82276e-18 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.56941e-18 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 8.87903e-19 is below minimal value.
[WARNING] rcond 3.6391e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.53076e-18 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 3.85751e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.99997e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 2.72993e-18 is below minimal value.
[WARNING] rcond 2.77362e-19 is below minimal value.
[WARNING] rcond 4.60104e-19 is below minimal value.
[WARNING] rcond 2.52173e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.46935e-18 is below minimal value.
[WARNING] rcond 1.06237e-18 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.00597e-18 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 8.92217e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.31411e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.7322e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 2.14247e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.36536e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 2.5548e-19 is below minimal value.
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] rcond 1.3042e-19 is below minimal value.
> abline(h=log(1e-18),col='red')
> # rcond = function(theta) {
> #     k_tmp = NULL
> #     try(k_tmp <- Kriging(y, X, kernel="gauss", optim="none",parameters=list(theta=matrix(theta))))
> #     if (is.null(k_tmp)) return(NA)
> #     T=k_tmp$T()
> #     R = (T) %*% t(T)
> #     1/kappa(R,norm='2')
> # }
> # lines(.t, log(Vectorize(rcond)(.t)),col='pink')
> 
> k10 <- Kriging(y, X, kernel="gauss", optim="BFGS10")
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
[WARNING] Added 1 numerical nugget to force Cholesky decomposition
> 
> abline(v=k10$theta(), col='red')
> abline(h=k10$logLikelihood(), col='red')
> 
> test_that(desc=paste0("LL / Fit: unstable LL fixed using rcond failover (linalg_get_num_nugget:", rlibkriging:::linalg_get_num_nugget(), ")"),
+           expect_equal(k$theta(), k10$theta(), tol=1e-4))
Test passed 🎉
> 
> 
> rlibkriging:::linalg_check_chol_rcond(default_rcond_checked)
> rlibkriging:::linalg_set_num_nugget(default_num_nugget)
> 
> proc.time()
   user  system elapsed 
   1.73    0.21    1.93