2-neckpain.Rmd

---
title: "2-prelim_model"
author: "Bernard"
date: "2021-03-31"
output: workflowr::wflow_html
editor_options:
  chunk_output_type: console
---

# Introduction

```{r}
# Helper
library (tidyverse)

# ML
library (mlr3)
library (mlr3learners)
library (mlr3tuning)
library (mlr3viz)
library (mlr3fselect)
library (mlr3pipelines)

set.seed(7832)
lgr::get_logger("mlr3")$set_threshold("warn")
lgr::get_logger("bbotk")$set_threshold("warn")
```

# Load data

```{r}
dat <- readRDS("output/df.RDS") 

train <- dat$df_list$np$train_imp
test <- dat$df_list$np$test_imp

comb <- bind_rows(train, test)
train_id <- 1: nrow (train)
test_id <- (nrow (train) + 1): nrow (comb)

```

# Set task

```{r}
# Set training task
task<- TaskClassif$new (id = "neckpain", backend = comb, target = "outcome")
task$nrow
task$feature_names
task$set_col_roles("ID", roles = "name")

# # Set test task 
# task_tr <- TaskClassif$new (id = "neckpain", backend = test, target = "imp_np")
# task_tr$set_col_roles("ID", roles = "name")

# Set pre proc sets
poe <- po("encode", method = "one-hot")
poe$train(list(task))[[1]]$data()

poscale <- po("scale", param_vals = list (center = TRUE, scale = TRUE))
poscale$train(list(task))[[1]]$data()


```

# Set tuning

```{r}
evals <- trm("none")
measure <-  msr("classif.auc")
measures <- list (msr("classif.auc"), 
                  msr("classif.acc"),
                  msr("classif.tpr"),
                  msr("classif.fpr"),
                  msr("classif.fnr"),
                  msr("classif.tnr"))
# Set resample
cv_inner <- rsmp("cv", folds = 5)
cv_outer <- rsmp("cv", folds = 3)
```

# Set logistic regression model


```{r}
# Set learner with type proability
lrn_logreg <- lrn("classif.log_reg", id = "log", predict_type = "prob")

# Graph with factor encoding and scaling
grln_logreg <- poscale %>>%
  #poe %>>%
  lrn_logreg 

plot (grln_logreg)
grln_logreg_lnr <- GraphLearner$new(grln_logreg)

# Set autotuner
at_grln_logreg <-  AutoFSelector$new(
  learner = grln_logreg_lnr, 
  resampling = cv_inner, 
  measure = measure,
  terminator = trm("stagnation", iters = 5),
  fselect = fs("sequential", strategy = "sbs"),
  store_models = TRUE)

# Runs the outer loop sequentially and the inner loop in parallel
future::plan(list("sequential", "multisession"))

# Nested resampling for internal validation
rr_logreg <- resample(task, 
                    at_grln_logreg, 
                    cv_outer, 
                    store_models = FALSE)

future::plan("multisession")
# Train learner
at_grln_logreg$train (task, row_ids = train_id)
as.data.table (at_grln_logreg$archive)
at_grln_logreg$fselect_result

# Predict learner
prediction = at_grln_logreg$predict(task, row_ids = test_id)
autoplot(prediction, type = "roc")
prediction$score (measures)


```

# Set kknn model


```{r}
# Set learner with type proability
lrn_kknn <- lrn("classif.kknn", id = "kknn", predict_type = "prob")

# Graph with factor encoding and scaling
grln_kknn <- poscale %>>%
  poe %>>%
  lrn_kknn 

plot (grln_kknn)
grln_kknn_lnr <- GraphLearner$new(grln_kknn)

# Tuning
grln_kknn_lnr$param_set$values$kknn.k <-  to_tune(1, 10)
#grln_kknn_lnr$param_set$values$threshold.thresholds <-  to_tune(p_dbl (0,1))

# Set autotuner
at_grln_kknn <-  AutoTuner$new(
  learner = grln_kknn_lnr,
  resampling = cv_inner,
  measure = measure,
  terminator = evals,
  tuner = tnr("grid_search", resolution = 10),
  store_models = TRUE
)

# Runs the outer loop sequentially and the inner loop in parallel
future::plan(list("sequential", "multisession"))

# Nested resampling for internal validation
rr_kknn <- resample(task, 
                    at_grln_kknn, 
                    cv_outer, 
                    store_models = FALSE)

future::plan("multisession")
# Train learner
at_grln_kknn$train (task, row_ids = train_id)
at_grln_kknn$archive
at_grln_kknn$tuning_result

#grln_kknn_lnr$param_set$values <- at_grln_kknn$tuning_instance$result_learner_param_vals

# Predict learner
prediction = at_grln_kknn$predict(task, row_ids = test_id)
prediction$score (measures)
autoplot(prediction, type = "roc")

```

# Set xgboost

```{r}
lrn_xgb <- lrn("classif.xgboost", id = "xgb", predict_type = "prob",  eta = 0.01)

grln_xgb <- poscale %>>%
  poe %>>%
  lrn_xgb

plot (grln_xgb)

grln_xgb_lnr <- GraphLearner$new(grln_xgb)
grln_xgb_lnr$param_set 

ps_xgb <- ParamSet$new(list (
  ParamDbl$new ("xgb.nrounds", lower = 1, upper = 1000),
  ParamDbl$new ("xgb.lambda", lower = 0, upper = 1000),
  ParamDbl$new ("xgb.gamma", lower = 0, upper = 1000),
  ParamDbl$new ("xgb.alpha", lower = 0, upper = 1000)
))

ps_xgb$trafo = function(x, param_set) {
  x$xgb.nrounds = as.integer (x$xgb.nrounds)
  x$xgb.lambda = as.integer (x$xgb.lambda)
  x$xgb.alpha = as.integer (x$xgb.alpha)
  x
}

bind_rows(generate_design_grid(ps_xgb, 3)$transpose())


at_grln_xgb <-  AutoTuner$new (
  learner = grln_xgb_lnr,
  resampling = cv_inner,
  measure = measure,
  search_space = ps_xgb,
  terminator = evals,
  tuner = tnr("gensa"),
  store_models = TRUE
)
# Runs the outer loop sequentially and the inner loop in parallel
future::plan(list("sequential", "multisession"))

# Nested resampling for internal validation
rr_xgb <- resample(task, 
                    at_grln_xgb, 
                    cv_outer, 
                    store_models = FALSE)

future::plan("multisession")
# test learner
at_grln_xgb$train (task, row_ids = train_id)
at_grln_xgb$archive
at_grln_xgb$tuning_result

prediction = at_grln_xgb$predict(task, row_ids = test_id)
prediction$score (measures)
autoplot(prediction, type = "roc")

```

# Set lasso

```{r}
lrn_lasso <- lrn("classif.glmnet", id = "lasso", predict_type = "prob")

grln_lasso <- poscale %>>%
  poe %>>%
  lrn_lasso 

plot (grln_lasso)

grln_lasso_lnr <- GraphLearner$new(grln_lasso)
grln_lasso_lnr$param_set 

grln_lasso_lnr$param_set$values$lasso.s  <-  to_tune(0, 1)

at_grln_lasso <-  AutoTuner$new (
  learner = grln_lasso_lnr,
  resampling = cv_inner,
  measure = measure,
  terminator = evals,
  tuner = tnr("grid_search", resolution = 100),
  store_models = TRUE
)
# Runs the outer loop sequentially and the inner loop in parallel
future::plan(list("sequential", "multisession"))

# Nested resampling for internal validation
rr_lasso <- resample(task, 
                    at_grln_lasso, 
                    cv_outer, 
                    store_models = FALSE)

future::plan("multisession")
# test learner
at_grln_lasso$train (task, row_ids = train_id)
at_grln_lasso$archive
at_grln_lasso$tuning_result

prediction = at_grln_lasso$predict(task, row_ids = test_id)
prediction$score (measures)
autoplot(prediction, type = "roc")
```

# Set random forest

```{r}
lrn_rf <- lrn("classif.ranger", id = "rf", predict_type = "prob")

grln_rf  <- poscale %>>%
  poe %>>%
  lrn_rf 

plot (grln_rf)

grln_rf_lnr <- GraphLearner$new(grln_rf)
grln_rf_lnr$param_set 

ps_rf <- ParamSet$new(list (
  ParamInt$new ("rf.mtry", lower = 5, upper = 15),
  ParamInt$new ("rf.min.node.size", lower = 1, upper = 20),
  ParamDbl$new ("rf.sample.fraction", lower = 0.5, upper = 1)
))

bind_rows(generate_design_grid(ps_rf, 5)$transpose())


at_grln_rf <- AutoTuner$new (
  learner = grln_rf_lnr,
  resampling = cv_inner,
  measure = measure,
  terminator = evals,
  search_space = ps_rf,
  tuner = tnr("grid_search", resolution = 5),
  store_models = TRUE
)
# Runs the outer loop sequentially and the inner loop in parallel
future::plan(list("sequential", "multisession"))

# Nested resampling for internal validation
rr_rf <- resample(task, 
                    at_grln_rf, 
                    cv_outer, 
                    store_models = FALSE)

future::plan("multisession")
# test learner
at_grln_rf$train (task, row_ids = train_id)
at_grln_rf$archive
at_grln_rf$tuning_result

prediction = at_grln_rf$predict(task, row_ids = test_id)
prediction$score (measures)
autoplot(prediction, type = "roc")
```

# Set neural net

```{r}
lrn_net <- lrn("classif.nnet", id = "nnet", predict_type = "prob")

grln_net <- poscale %>>%
  poe %>>%
  lrn_net 

plot (grln_net)

grln_net_lnr <- GraphLearner$new(grln_net)
grln_net_lnr$param_set 

ps_net <- ParamSet$new(list (
  ParamInt$new ("nnet.size", lower = 1, upper = 10),
  ParamDbl$new ("nnet.decay", lower = 0.1, upper = 0.5)
))

bind_rows(generate_design_grid(ps_net, 5)$transpose())


at_grln_net <- AutoTuner$new (
  learner = grln_net_lnr,
  resampling = cv_inner,
  measure = measure,
  terminator = evals,
  search_space = ps_net,
  tuner = tnr("grid_search", resolution = 10),
  store_models = TRUE
)
# Runs the outer loop sequentially and the inner loop in parallel
future::plan(list("sequential", "multisession"))

# Nested resampling for internal validation
rr_net <- resample(task, 
                    at_grln_net, 
                    cv_outer, 
                    store_models = FALSE)

future::plan("multisession")
# test learner
at_grln_net$train (task, row_ids = train_id)
at_grln_net$archive
at_grln_net$tuning_result

prediction = at_grln_net$predict(task, row_ids = test_id)
prediction$score (measures)
autoplot(prediction, type = "roc")
```

# Set support vector machine

```{r}
lrn_svm <- lrn("classif.svm", id = "svm", type = "C-classification", kernel = "radial", predict_type = "prob")

grln_svm <- poscale %>>%
  poe %>>%
  lrn_svm 

plot (grln_svm)

grln_svm_lnr <- GraphLearner$new(grln_svm)
grln_svm_lnr$param_set 

ps_svm <- ParamSet$new(list (
  ParamDbl$new ("svm.cost", lower = 0.1, upper = 10),
  ParamDbl$new ("svm.gamma", lower = 0, upper = 5)
))

bind_rows(generate_design_grid(ps_svm, 5)$transpose())


at_grln_svm <- AutoTuner$new (
  learner = grln_svm_lnr,
  resampling = resampling,
  measure = measure,
  terminator = evals,
  search_space = ps_svm,
  tuner = tnr("grid_search", resolution = 10),
  store_models = TRUE
)
# Runs the outer loop sequentially and the inner loop in parallel
future::plan(list("sequential", "multisession"))

# Nested resampling for internal validation
rr_svm <- resample(task, 
                    at_grln_svm, 
                    cv_outer, 
                    store_models = FALSE)

future::plan("multisession")
# test learner
at_grln_svm$train (task, row_ids = train_id)
at_grln_svm$archive
at_grln_svm$tuning_result

prediction = at_grln_svm$predict(task, row_ids = test_id)
prediction$score (measures)
autoplot(prediction, type = "roc")
```


# Save files
```{r}
rsmp_list <- list (rr_logreg = rr_logreg,
                   rr_kknn = rr_kkn,
                   rr_xgb = rr_xgb,
                   rr_lasso = rr_lasso,
                   rr_rf = rr_rf,
                   rr_net = rr_net,
                   rr_svm = rr_svm)

model_list <- list (at_grln_logreg = at_grln_logreg,
                   at_grln_kknn = at_grln_kkn,
                   at_grln_xgb = at_grln_xgb,
                   at_grln_lasso = at_grln_lasso,
                   at_grln_rf = at_grln_rf,
                   at_grln_net = at_grln_net,
                   at_grln_svm = at_grln_svm)

saveRDS (list (rsmp_list = rsmp_list,
               model_list = model_list),
         "output/np_result.RDS")

```