R Under development (unstable) (2025-11-26 r89066 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2025 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 code example 1 from 
> ## Gjuvsland AB, Wang Y, Plahte E, Omholt SW (2013) Monotonicity is a key feature of genotype-phenotype maps. Submitted to Frontiers in Genetics
> 
> library(gpmap)
Loading required package: isotone
Loading required package: plyr
Loading required package: ggplot2
Loading required package: foreach
> data(GPmaps)
> gp <- mouseweight
> 
> ## Tabulate genotypic values
> cbind(gp$genotype,gp$values)
  Locus_B Locus_A LG_JxSM_J
1    B1B1    A1A1    36.839
2    B1B2    A1A1    36.527
3    B2B2    A1A1    33.824
4    B1B1    A1A2    37.951
5    B1B2    A1A2    35.898
6    B2B2    A1A2    34.125
7    B1B1    A2A2    34.118
8    B1B2    A2A2    34.894
9    B2B2    A2A2    31.234
> 
> ## Plot the GP map
> plot(gp)		
[[1]]

> 
> ## Compute degree of monotonicity
> gp <- degree_of_monotonicity(gp)
> gp$degree.monotonicity.locus
        LG_JxSM_J
Locus_B 0.8623747
Locus_A 0.7107472
> print(gp)
1 GP map: 
	 LG_JxSM_J 

2 loci: 
	 Locus_B Locus_A 

Summary of genotypic values:
   LG_JxSM_J    
 Min.   :31.23  
 1st Qu.:34.12  
 Median :34.89  
 Mean   :35.05  
 3rd Qu.:36.53  
 Max.   :37.95  


Degree of monotonicity (m):
     LG_JxSM_J
[1,] 0.7919894

> 
> ## Quantify monotonicity by isotonic regression
> gp <- decompose_monotone(gp)
Warning message:
executing %dopar% sequentially: no parallel backend registered 
> print(gp)
1 GP map: 
	 LG_JxSM_J 

2 loci: 
	 Locus_B Locus_A 

Summary of genotypic values:
   LG_JxSM_J    
 Min.   :31.23  
 1st Qu.:34.12  
 Median :34.89  
 Mean   :35.05  
 3rd Qu.:36.53  
 Max.   :37.95  


Degree of monotonicity (m):
     LG_JxSM_J
[1,] 0.7919894

R-square from isotone regression:
          LG_JxSM_J
LG_JxSM_J 0.9701623

> 
> ## Plot decomposed GP map
> plot(gp,decomposed=TRUE) 
[[1]]

> 
> 
> proc.time()
   user  system elapsed 
   1.73    0.25    1.96