tests/testthat/make.test.data.R

In AnacletoLAB/HEMDAG: Hierarchical Ensemble Methods for Directed Acyclic Graphs

## create data for testing
check.graph <- function(){
  if(requireNamespace("graph", quietly=TRUE)){
    TRUE
  }else{
    FALSE
  }
}

make.graph <- function(){
  if (!check.graph()){ skip("graph package cannot be loaded"); }
  V <- LETTERS[1:10];
  edL <- vector("list", length=length(V));
  names(edL) <- V;
  edL[[1]] <- list(edges=c(2,3,7,5));
  edL[[2]] <- list(edges=c(4,6));
  edL[[3]] <- list(edges=c(6,8));
  edL[[4]] <- list(edges=c(6,9));
  edL[[5]] <- list(edges=c(8));
  edL[[6]] <- list(edges=c(8,9,10));
  edL[[7]] <- list(edges=c(8,5));
  edL[[8]] <- list(edges=c());
  edL[[9]] <- list(edges=c());
  g <- graph::graphNEL(nodes=V, edgeL=edL, edgemode="directed");
  return(g);
}

make.scores <- function(){
  set.seed(12345);
  S <- matrix(round(runif(40),2), nrow=4);
  dimnames(S) <- list(paste0("pr",1:4), LETTERS[1:ncol(S)]);
  return(S);
}

make.spec.ann <- function(){
  pr1 <- c(1,0,0);
  pr2 <- c(0,1,0);
  pr3 <- c(0,0,1);
  pr4 <- c(1,0,0);
  spec.ann <- rbind(pr1,pr2,pr3,pr4);
  colnames(spec.ann) <- c("I","H","J");
  return(spec.ann);
}

make.ann <- function(){
  g <- make.graph();
  spec.ann <- make.spec.ann();
  anc <- build.ancestors(g);
  ann <- transitive.closure.annotations(spec.ann, anc);
  return(ann);
}