R Under development (unstable) (2026-01-22 r89323 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2026 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.

> # test.ISOpureS2.model_optimize.theta_functions.R #################################################
> # Testing script for functions needed in the optimilzation of mm in Step 2
> # Test theta separately since it takes a while...
> #
> # The functions are of the form ISOpureS2.model_optimize.---
> # (theta)
> #   theta_loglikelihood
> #   theta_deriv_loglikelihood
> 
> # LOAD DATA #######################################################################################
> # load library 
> library(ISOpureR);
> 
> # load the data from that path
> data.path <-  paste0(file.path(system.file(package = "ISOpureR"), 'extdata', 'Beer'));  
> load(file.path(data.path , 'beer.tumordata.250.transcripts.30.patients.RData'));
> load(file.path(data.path, 'beer.ISOpureS2model.250.transcripts.30.patients.RData'));
> 
> # the normaldata and tumourdata should be matrices
> beer.tumordata <- as.matrix(beer.tumordata);
> 
> # TEST THETA FUNCTIONS ############################################################################
> 
> # inputs needed for theta functions
> # initial value of theta (this is testing just patient 1)
> ww <- t(ISOpureS2model$theta_weights[1, ,drop=F])
> 
> # test theta functions (just for patient 1, that's the third entry)
> ISOpureS2.model_optimize.theta.theta_loglikelihood(ww, beer.tumordata, 1, ISOpureS2model);
[1] 1499714
> ISOpureS2.model_optimize.theta.theta_deriv_loglikelihood(ww, beer.tumordata, 1, ISOpureS2model);
               [,1]
 [1,]  0.000000e+00
 [2,]  2.926387e-05
 [3,]  1.753981e-04
 [4,] -1.280010e-04
 [5,]  2.499281e-05
 [6,]  1.827424e-04
 [7,] -9.476450e-05
 [8,] -1.622017e-04
 [9,]  3.293253e-05
[10,]  3.286415e-05
> 
> # remove parameters used in the test
> rm(K, ww);
Warning message:
In rm(K, ww) : object 'K' not found
> 
> proc.time()
   user  system elapsed 
   0.23    0.04    0.28