inst/schizo.R

In dustinfife/flexforest: Estimate Structural Equation Models with Bagging

require(tidyverse)
d = read.csv("~/Downloads/defense formatted2.csv") %>%
  mutate(sfs_ic1 = as.numeric(sfs_ic1))

source("~/Downloads/Defense Full Initial Model - sembag ready 3.R")

# check variables are in dataset
#parse_model_code(full.model)
#observed = parse_model_code(full.model)$observed %>% trimws


parcels = read.csv("~/Downloads/parcels.csv")
for (i in 1:2) {
results = sembag:::sembag(data=d, iterations = 100,
                          formula = full.model,
                          fit_function = sembag:::fit_rf_sem,
                          variable_sampler = sembag:::variable_sampler_sem,
                          validation_function = sembag:::loss_sem,
                          spearman_brown=TRUE, parcel_sizes=parcels,
                          mtry=20)
  save(results, file=paste0("~/Downloads/parcel_test_nosb-", i, ".rdata"))
}


files = list.files(path = "~/Downloads", pattern="parcel_test_nosb-", full.names = T)
for (i in 1:length(files)) {
  load(files[i])
  results
  if (i==1) {
    importance_measures = data.frame(matrix(nrow=length(files), ncol=length(results)))
    names(importance_measures) = names(results)
  }
  importance_measures[i,] = results
}

sort(colMeans(importance_measures))


full_model2 = '
  pdi =~ pdi_think+pdi_true+pdi_dis
  spq.pos =~ spq_suspic+spq_ideas_ref+spq_unus_percep
    pos.schiz =~ pqb_posdis_sum+olife_ue_sum+mssb_pos_sum + spq.pos + pdi


  spq.neg =~ spq_constricted_affect+spq_noclosefriends+spq_social_anx

  spq.dis =~ spq_eccentric_behavior+spq_odd_speech
    dis.schiz =~ olife_cd_sum+mssb_dis_sum+pqb_disdis_sum + spq.dis

  family =~ ctq_ea+ctq_en+fesfs_family

  mh_history =~ mommh_diagnosis+dadmh_diagnosis+mom_treat

  dep =~ dass_2110+dass_2116+dass_2117

  sf =~ fesfs_friends+fesfs_independent+fesfs_interacting

  qol =~qol_daily_activities_sat+qol_health_sat+qol_family_sat

    qol ~ mh_history + dep + sf + spq.neg + dis.schiz + pos.schiz + family
'
require(lavaan)
fit = cfa(full_model2, data=d, missing = "ML")




# some of these items are not numeric: psqi4, psqi15, psqi1-4, psqi26
# these items do not exist:
  # pdi_think17, pdi_true3, pdi_true21, pdi_dis19, pdi_dis17 pdi_true11 pdi_end10 pdi_dis8 pdi_dis4 pqb_dis29 pdi_end8
  # pdi_end11 pdi_true15 pqb_dis33 pqb_dis39 pdi_end2 pdi_dis5 pqb_dis23 pqb_dis3 pdi_think6 pdi_think2 pdi_think10 pdi_true9 pdi_dis3
  # pqb_dis1 pqb_dis5 pqb_dis7 pqb_dis9 pqb_dis13 pqb_dis15 pqb_dis17 pqb_dis21 pqb_dis25 pqb_dis27 pqb_dis31 pqb_dis35 pqb_dis37
  # pdi_end3 pdi_end4 pdi_end6 pdi_end7 pdi_end12 pdi_end14 pdi_end15 pdi_end16 pdi_end18 pdi_end19 pdi_end20
  # pdi_dis1 pdi_dis7 pdi_dis9 pdi_dis11 pdi_dis12 pdi_dis13 pdi_dis15 pdi_dis16 pdi_dis20 pdi_dis21
  # pdi_think1 pdi_think4 pdi_think5 pdi_think8 pdi_think9 pdi_think12 pdi_think13 pdi_think14 pdi_think16 pdi_think18 pdi_think20 pdi_think21 pdi_true1 pdi_true2 pdi_true5 pdi_true6 pdi_true7 pdi_true10 pdi_true13 pdi_true14 pdi_true17 pdi_true18
  # pdi_true19

names(results)


save(results, file="inst/schizo_sembag_results.Rdat")
results$varimp# sembag_inloop(data=d, formula=full.model, iterations = 10,
#                                fit_function = fit_rf_sem, variable_sampler = variable_sampler_sem,
#                                validation_function = loss_sem,
#                                mtry = 10)
# start = Sys.time()
# results
# end = Sys.time()
# end - start