tests/testthat/test-execute_next_setup.R

In Neves-P/utilSIE: Utility Functions for DAISIE

test_that("example run", {

  if (1 == 2) {

    data("pilot_study_parameters")

    project_name = utilSIE::get_project_name()
    account = utilSIE::get_available_accounts()
    download_files = TRUE
    partition = "gelifes"
    time = pilot_study_parameters$time[1] # nolint
    M = pilot_study_parameters$M[1] # nolint
    lac = pilot_study_parameters$lac[1] # nolint
    mu = pilot_study_parameters$mu[1] # nolint
    K = pilot_study_parameters$K[1] # nolint
    gam = pilot_study_parameters$gam[1] # nolint
    laa = pilot_study_parameters$laa[1] # nolint
    divdepmodel = 1
    island_ontogeny = "beta"
    replicates = 1 # nolint
    mu_min = pilot_study_parameters$mu_min[1] # nolint
    mu_max = pilot_study_parameters$mu_max[1] # nolint
    Amax = pilot_study_parameters$Amax[1] # nolint
    Apeak = pilot_study_parameters$Apeak[1] # nolint
    Asharpness = pilot_study_parameters$Asharpness[1] # nolint
    Atotalage = pilot_study_parameters$Atotalage[1] # nolint
    complete_analysis = TRUE
    branch = "@develop"
    force = TRUE


    execute_next_setup(
      project_name = project_name,
      account = account,
      download_files = download_files,
      partition = partition,
      time = time,
      M = M,
      lac = lac,
      mu = mu,
      K = K,
      gam = gam,
      laa = laa,
      divdepmodel = divdepmodel,
      island_ontogeny = island_ontogeny,
      replicates = replicates,
      mu_min = mu_min,
      mu_max = mu_max,
      Amax = Amax,
      Apeak = Apeak,
      Asharpness = Asharpness,
      Atotalage = Atotalage,
      complete_analysis = complete_analysis,
      branch = branch,
      force = force
    )


    # Normal mus
    execute_next_setup(
      project_name = project_name,
      account = account,
      download_files = FALSE,
      partition = partition,
      time = unique(pilot_study_parameters$time),
      M = unique(pilot_study_parameters$M),
      lac = unique(pilot_study_parameters$lac),
      mu = unique(pilot_study_parameters$mu),
      K = unique(pilot_study_parameters$K),
      gam = unique(pilot_study_parameters$gam),
      laa = unique(pilot_study_parameters$laa),
      divdepmodel = divdepmodel,
      island_ontogeny = island_ontogeny,
      replicates = 1,
      mu_min = unique(pilot_study_parameters$mu_min),
      mu_max = unique(pilot_study_parameters$mu_max, 0.2, 5),
      Amax = unique(pilot_study_parameters$Amax),
      Apeak = unique(pilot_study_parameters$Apeak),
      Asharpness = unique(pilot_study_parameters$Asharpness),
      Atotalage = unique(pilot_study_parameters$Atotalage),
      complete_analysis = TRUE,
      branch = branch,
      force = FALSE
    )

    # series of mus
    execute_next_setup(
      project_name = project_name,
      account = account,
      download_files = FALSE,
      partition = partition,
      time = 7,
      M = unique(pilot_study_parameters$M),
      lac = unique(pilot_study_parameters$lac),
      mu = unique(pilot_study_parameters$mu),
      K = unique(pilot_study_parameters$K),
      gam = unique(pilot_study_parameters$gam),
      laa = unique(pilot_study_parameters$laa),
      divdepmodel = divdepmodel,
      island_ontogeny = island_ontogeny,
      replicates = 1000,
      mu_min = c(0.1, 0.4, 0.7),
      mu_max = c(unique(pilot_study_parameters$mu_max), 0.2, 1, 5, 10),
      Amax = unique(pilot_study_parameters$Amax),
      Apeak = unique(pilot_study_parameters$Apeak),
      Asharpness = unique(pilot_study_parameters$Asharpness),
      Atotalage = unique(pilot_study_parameters$Atotalage),
      complete_analysis = TRUE,
      branch = branch,
      force = FALSE
    )




  }

})