R Under development (unstable) (2026-01-22 r89323 ucrt) -- "Unsuffered Consequences"
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> # test.ISOpureS1.model_optimize.theta_functions.R #################################################
> # Testing script for functions needed in the optimilzation of mm in Step 1
> # Test theta separately since it takes a while...
> #
> # The functions are of the form ISOpureS1.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.ISOpureS1model.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(ISOpureS1model$theta_weights[1, ,drop=F])
> 
> # test theta functions (just for patient 1, that's the third entry)
> ISOpureS1.model_optimize.theta.theta_loglikelihood(ww, beer.tumordata, 1, ISOpureS1model);
[1] 1501574
> ISOpureS1.model_optimize.theta.theta_deriv_loglikelihood(ww, beer.tumordata, 1, ISOpureS1model);
              [,1]
 [1,]  0.000000000
 [2,]  0.001229955
 [3,]  0.023485554
 [4,]  0.026567605
 [5,]  0.001675811
 [6,]  0.023433361
 [7,]  0.033343157
 [8,]  0.006817121
 [9,]  0.001705219
[10,]  0.001674340
[11,] -0.117255813
> 
> # remove parameters used in the test
> rm(K, ww);
Warning message:
In rm(K, ww) : object 'K' not found
> 
> proc.time()
   user  system elapsed 
   0.26    0.09    0.31