R/tests/EM_test.R

In weidewind/evolikelihood: What the package does (short line)

if (!(prot == "h1" && !is.null(splitted) && length(splitted) == 539)){
    prot <- "h1"
    inpath <- paste(c(getwd(), "/data/"),collapse= "")
    prot_data <-  read.csv(paste(c(inpath, prot,"_for_LRT.csv"), collapse=""),stringsAsFactors=FALSE)  
    splitted <- split(prot_data, list(prot_data$site, prot_data$ancestor_node), drop=TRUE)
}
if (is.null(params) || nrow(params) != 142){
    params <- parameters(splitted, mutation_position = "middle", filter = TRUE, jack = FALSE, pack = "rootsolve", verbose = FALSE)
}


## too time-consuming
#test_initialize_by_clustering <- function (){
#  #arrange
#  cluster.number = 3
#  #act
#  init_values <- initialize_by_clustering(data = splitted, params = params, cluster.number = cluster.number)
#  #assert
#  checkEquals(class(init_values) == "list")
  
#  checkEquals(class(init_values$iparameters) == "matrix")
#  checkEquals(nrow(init_values$iparameters) == cluster.number)
#  checkEquals(ncol(init_values$iparameters) == 2)
  
#  checkEquals(length(init_values$iweights) == cluster.number)
#  checkEquals(sum(init_values$iweights) == 1)
  
#  checkTrue(all(!is.na(init_values$iparameters)))
#  checkTrue(all(!is.na(init_values$iweights)))

#}

#test_initialize_random <- function (){
#  cluster.number = 3
#  
#  init_values <- initialize_by_random(data = splitted, params = parameters, cluster.number = cluster.number)
#  #list(iparameters = iparameters, iweights = iweights, irkvector = irkvector)
#  checkEquals(class(init_values) == "list")
#  
#  checkEquals(class(init_values$iparameters) == "matrix")
#  checkEquals(nrow(init_values$iparameters) == cluster.number)
#  checkEquals(ncol(init_values$iparameters) == 2)
#  
#  checkEquals(length(init_values$iweights) == cluster.number)
#  checkEquals(length(init_values$irkvector) == cluster.number)
#  
#  checkTrue(all(!is.na(init_values$iparameters)))
#  checkTrue(all(!is.na(init_values$iweights)))
#  checkTrue(all(!is.na(init_values$irkvector)))
#  
#  
#}



test_initialize_by <-function (){
  cluster.number = 3
  init_params = c(9,1,1,1,2,3) #incorrect number of parameters
  init_weights = c(0.5, 0.4, 0.1)
  model = "exponential"
  
  checkException(initialize_by(init_params =init_params, init_weights= init_weights,model = model, cluster.number = cluster.number),silent = TRUE)

  cluster.number = 3
  init_params = c(9,1,1) #incorrect number of parameters
  init_weights = c(0.5, 0.4, 0.1)
  model = "weibull"
  
  checkException(initialize_by(init_params =init_params, init_weights= init_weights,model = model, cluster.number = cluster.number),silent = TRUE)
  
  
  cluster.number = 3
  init_params = c(9,1,1)
  init_weights = c(0.5, 0.4, 0.6) #incorrect sum of weights
  model = "exponential"
  
  checkException(initialize_by(init_params =init_params, init_weights= init_weights,model = model, cluster.number = cluster.number),silent = TRUE)
  
}