Analyze student performance

Source: vignettes/Analyize_student_performance.Rmd

In this article, we use the student performance dataset to demonstrate how to perform subgroup analysis and variable selection simultaneously via the package RSAVS.

NOTE: This article is finished with RSAVS version 0.1.2.

library(ggplot2)
library(dplyr)
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
library(skimr)
remotes::install_github("fenguoerbian/RSAVS", ref = "v0.1.2")
#> Using github PAT from envvar GITHUB_PAT. Use `gitcreds::gitcreds_set()` and unset GITHUB_PAT in .Renviron (or elsewhere) if you want to use the more secure git credential store instead.
#> Downloading GitHub repo fenguoerbian/RSAVS@v0.1.2
#> quantreg (5.98 -> 5.99) [CRAN]
#> Installing 1 packages: quantreg
#> Installing package into '/home/runner/work/_temp/Library'
#> (as 'lib' is unspecified)
#> Running `R CMD build`...
#> * checking for file ‘/tmp/RtmpN2ZKIs/remotes1cea1be277b0/fenguoerbian-RSAVS-fe2e615/DESCRIPTION’ ... OK
#> * preparing ‘RSAVS’:
#> * checking DESCRIPTION meta-information ... OK
#> * cleaning src
#> * checking for LF line-endings in source and make files and shell scripts
#> * checking for empty or unneeded directories
#> * building ‘RSAVS_0.1.2.tar.gz’
#> Installing package into '/home/runner/work/_temp/Library'
#> (as 'lib' is unspecified)
library(RSAVS)

Introduction to the dataset

This student performance dataset is about the grading point of evaluations of 1044 Portuguese students from two core classes(Math and Portuguese). There are 395 observations in the math data frame mat_df and 649 observations in the Portuguese data frame por_df. And the full dataset full_df is just the combination of these two data frames resulting 1044 observations. You can find details about these datasets via ?full_df.

In later analysis, we will use the full dataset full_df. The basic information of this dataset is shown below:

skimr::skim(full_df)
Data summary
Name full_df
Number of rows 1044
Number of columns 33
_______________________
Column type frequency:
character 17
numeric 16
________________________
Group variables None

Variable type: character

skim_variable n_missing complete_rate min max empty n_unique whitespace
school 0 1 2 2 0 2 0
sex 0 1 1 1 0 2 0
address 0 1 1 1 0 2 0
famsize 0 1 3 3 0 2 0
Pstatus 0 1 1 1 0 2 0
Mjob 0 1 5 8 0 5 0
Fjob 0 1 5 8 0 5 0
reason 0 1 4 10 0 4 0
guardian 0 1 5 6 0 3 0
schoolsup 0 1 2 3 0 2 0
famsup 0 1 2 3 0 2 0
paid 0 1 2 3 0 2 0
activities 0 1 2 3 0 2 0
nursery 0 1 2 3 0 2 0
higher 0 1 2 3 0 2 0
internet 0 1 2 3 0 2 0
romantic 0 1 2 3 0 2 0

Variable type: numeric

skim_variable n_missing complete_rate mean sd p0 p25 p50 p75 p100 hist
age 0 1 16.73 1.24 15 16 17 18 22 ▇▅▅▁▁
Medu 0 1 2.60 1.12 0 2 3 4 4 ▁▅▇▆▇
Fedu 0 1 2.39 1.10 0 1 2 3 4 ▁▆▇▆▆
traveltime 0 1 1.52 0.73 1 1 1 2 4 ▇▅▁▁▁
studytime 0 1 1.97 0.83 1 1 2 2 4 ▅▇▁▂▁
failures 0 1 0.26 0.66 0 0 0 0 3 ▇▁▁▁▁
famrel 0 1 3.94 0.93 1 4 4 5 5 ▁▁▂▇▅
freetime 0 1 3.20 1.03 1 3 3 4 5 ▁▃▇▆▂
goout 0 1 3.16 1.15 1 2 3 4 5 ▂▆▇▆▃
Dalc 0 1 1.49 0.91 1 1 1 2 5 ▇▂▁▁▁
Walc 0 1 2.28 1.29 1 1 2 3 5 ▇▅▅▃▂
health 0 1 3.54 1.42 1 3 4 5 5 ▃▂▅▃▇
absences 0 1 4.43 6.21 0 0 2 6 75 ▇▁▁▁▁
G1 0 1 11.21 2.98 0 9 11 13 19 ▁▂▇▇▂
G2 0 1 11.25 3.29 0 9 11 13 19 ▁▂▇▇▂
G3 0 1 11.34 3.86 0 10 11 14 20 ▁▂▇▆▁

Our interest is G3, the final grade. And we want to understand how it’s related to those covariates. Note that although there seems to be several numeric variables in this datasets, most of them are actually binary or nominal coded.

First of all, we project the data on to the space spaned by most of the binary and nominal variables in the dataset. This gives us some basic understanding about how the average final grade is distributed among different observed subgroups.

fit1 <- lm(G3 ~ school + address + Pstatus + famsize + schoolsup + famsup + activities + paid + internet + nursery + higher + romantic + Mjob + Fjob + guardian + reason, data = full_df)
plot(density(fit1$fitted.values))

Looks like most of the grades are centered between 10-14 with some heavy tail at the lower end.

Next, we try expolore the relationship between individuals and the average grading point of the observed subgroup via OLS.

fit2 <- lm(fit1$fitted.values ~ sex + age + Medu + Fedu + traveltime + studytime + failures  + famrel + freetime + goout + Dalc + Walc + health + absences, 
           data = full_df)
plot(density(fit2$fitted.values))

The fitted value doesn’t tell much, but the residual plot tells something

ggplot(fit2, aes(fit2$residuals)) + geom_density() + xlab(NULL)

It’s skewed and potentially multimodal, which indicates a robust regression, along with a latent subgroup structure, would be appropriate.Thus, we analyze the dataset by the proposed method of this package with the L1 loss and the SCAD penalty in this study.

Robust subgroup analysis and variable selection

Before the analysis, we randomly sample 100 observations and denote this dataset as D2D_2, and use the remaining 944 observations as the training dataset D1D_1.

# prepare the full dataset
y_vec_full <- fit1$fitted.values
x_mat_full <- stats::model.matrix(fit2)[, -1]    # do not include the intercept term!

# sample 100 observations as test set
test_num <- 100
set.seed(1024)
test_idx <- sample(1 : nrow(full_df), size = test_num, replace = F)

# get the training set
x_mat <- x_mat_full[-test_idx, , drop = FALSE]
y_vec <- y_vec_full[-test_idx]
n <- nrow(x_mat)
p <- ncol(x_mat)

# get the test set
y_vec_test <- y_vec_full[test_idx]
x_mat_test <- x_mat_full[test_idx, , drop = FALSE]

Analysis on the training set

Set some basic variables for the proposed algorithm

lam1_len <- 40    # length of lam1_vec
lam2_len <- 30    # length of lam2_vec
phi <- 5    # constant needed for mBIC

Then we can apply our method at the training set. By default, it will use L1 loss function coupled with the SCAD penalty. You can use ?RSAVS_LargeN to find out more about this function.

# It will take some time!
res <- RSAVS_LargeN(y_vec = y_vec, x_mat = x_mat, 
                    lam1_length = lam1_len, lam2_length = lam2_len,
                    phi = phi, tol = 0.001, max_iter = 100)
#> Basic variables initialized.
#> Beta finished.
#> Mu finished.
#> Z finished.
#> S finished.
#> W finished.
#> q1 finished.
#> q2 finished.
#> q3 finished.
#> D started.
#> D finished.
#> beta left finished.
#> mu left finished.
#> [1] "pamk fail!"

The proposed algorithm can do subgroup analysis and variable selection simultaneously via regularization method. It will search over the grid space spanned by lam1 and lam2. And choose a best one according to a modified BIC criteria.

We can check the covariate effect with

best_ind <- res$best_ind
mu_new <- res$mu_improve_mat[res$best_ind, ]
beta_new <- res$w_mat[res$best_ind, ]
names(beta_new) <- colnames(x_mat)
beta_new
#>        sexM         age        Medu        Fedu  traveltime   studytime 
#>  0.00000000 -0.03657224  0.22212294  0.00000000  0.00000000  0.00000000 
#>    failures      famrel    freetime       goout        Dalc        Walc 
#>  0.00000000  0.00000000  0.00000000  0.00000000  0.00000000  0.00000000 
#>      health    absences 
#>  0.00000000  0.00000000

and the estimated subgroup information with

table(mu_new)
#> mu_new
#> 11.4653382346014 11.4729496143311 
#>              442              502

Also we can visualize the density plot of G3 for these identified subgroups

plot(density(y_vec))
for(i in 1 : length(unique(mu_new))){
  id <- which(mu_new == unique(mu_new)[i])
  abline(v = mean(y_vec[id]))
  abline(v = unique(mu_new)[id], lty = 2)
}

As we can see, the algorithm gives us a reasonable partition of the observations, but the estimation of subgroup effects mu_new is quite indistinguishable due to the presence of the penalty functions.

We can further improve these estimations with an ordinary robust regression without any penalty functions given the estimated parameter structure from the previous results. And we can perform this post-selection estimation over the whole solution plane. (Since there are lam1 and lam2, the regular solution path becomes a solution plane.)

mu_further_improve_mat <- matrix(0, nrow = lam1_len * lam2_len, ncol = n)
beta_further_improve_mat <- matrix(0, nrow = lam1_len * lam2_len, ncol = p)
bic_vec <- rep(0, lam1_len * lam2_len)
max_bic <- max(res$bic_mat)
for(i in 1 : (lam1_len * lam2_len)){
  tmp <- RSAVS_Further_Improve(y_vec = y_vec, x_mat = x_mat, mu_vec = res$mu_improve_mat[i, ], beta_vec = res$w_mat[i, ])
  mu_new <- as.vector(tmp$mu_vec)
  beta_new <- tmp$beta_vec
  mu_further_improve_mat[i, ] <- mu_new
  beta_further_improve_mat[i, ] <- beta_new
  bic_vec[i] <- RSAVS:::RSAVS_Compute_BIC(y_vec, x_mat, beta_new, mu_new, loss_type = "1", phi = phi)
  # update bic according to complexsity upper bound
  current_group_num <- length(unique(mu_new))
  current_active_num <- sum(beta_new != 0)
  if((current_active_num + current_group_num) >= 11){
    bic_vec[i] <- max_bic
  }
}

best_id <- which.min(bic_vec)
if(best_id == 1){
  best_id <- which.min(bic_vec[-1]) + 1
}
mu_new <- mu_further_improve_mat[best_id, ]
beta_new <- beta_further_improve_mat[best_id, ]
names(beta_new) <- colnames(x_mat)

After this further improving procedure, the estimated covariate effects are

beta_new
#>       sexM        age       Medu       Fedu traveltime  studytime   failures 
#>  0.0000000 -0.1164212  0.3768496  0.0000000  0.0000000  0.0000000  0.0000000 
#>     famrel   freetime      goout       Dalc       Walc     health   absences 
#>  0.0000000  0.0000000  0.0000000  0.0000000  0.0000000  0.0000000  0.0000000

and the identified subgroups are

table(mu_new)
#> mu_new
#> 11.5671844210441 13.1302268201393 
#>              439              505

We can visualize the estimated subgroups. First we just need to prepare a data.frame for ggplot.

Mu_to_ID <- function(mu_vec, mu_unique){
  # This function converts the original mu vector to a resulting vector, with the same length.
  # But the entries is replaced with the index of this entry in unique(mu_vec), or the provided variable mu_unique

  if(missing(mu_unique)){
    mu_unique <- unique(mu_vec)
  }
  mu_vec <- sapply(mu_vec, FUN = function(x, unique_vec){
    return(which(unique_vec == x))
  }, unique_vec = mu_unique)
  return(mu_vec)
}

rsavs_res <- data.frame(target = y_vec, 
                        fitted = mu_new + x_mat %*% beta_new, 
                        residual = y_vec - mu_new - x_mat %*% beta_new, 
                        mu_new = mu_new, 
                        mu_id = as.factor(Mu_to_ID(mu_new, unique(mu_new))), 
                        course = c(rep("por", nrow(por_df)), rep("mat", nrow(mat_df)))[-test_idx])

Now we can show the density plot of the G3 given the estimated latent subgroups with the dashed line being the median of each group.

rsavs_res %>% group_by(mu_id) %>% 
  mutate(subgroup_median = median(fitted)) %>%
  ggplot(aes(target, fill = mu_id, color = mu_id, group = mu_id)) + 
  geom_density(alpha = 0.2) + 
  geom_vline(aes(xintercept = subgroup_median, color = mu_id), linetype = "dashed") + 
  xlab("Response") + labs(color = "Subgroup", fill = "Subgroup")

Some inference on the test set

Based on the results from training set, we can propose a model as yi=α+δdi+Medui×β1+Agei×β2+εi y_i = \alpha + \delta d_i + \text{Medu}_i \times \beta_1 + \text{Age}_i \times \beta_2 + \varepsilon_i where yiy_i refers to the G3 of the i-th subject and di=0d_i = 0 if the i-th subject belongs to the subgroup 1 and otherwise di=0d_i = 0. δ\delta is the difference between these 2 subgroups.

We use regular K-medoids method to partition the dataset D2D_2 into two clusters with respect to the adjusted response with the covariate effects removed with the coefficients given by our method based on Dataset D1D_1

# residual_test is the adjusted response with the covariate effects removed
residual_test <- y_vec_test - x_mat_test %*% beta_new

# cluster residual_test into 2 groups with regular kmeans
tmp_kmeans <- stats::kmeans(residual_test, centers = 2)
group_indicator <- tmp_kmeans$cluster - 1

# form the simplified covariate matrix with only active covariates
x_mat_test_active <- x_mat_test[, which(beta_new != 0), drop = FALSE]

We can make inference about these parameters in the models with the simplified robust regression

rqfit <- quantreg::rq(y_vec_test ~ group_indicator + x_mat_test_active)
#> Warning in rq.fit.br(x, y, tau = tau, ...): Solution may be nonunique
summary(rqfit, alpha = 0.05)
#> Warning in rq.fit.br(x, y, tau = tau, ci = TRUE, ...): Solution may be
#> nonunique
#> 
#> Call: quantreg::rq(formula = y_vec_test ~ group_indicator + x_mat_test_active)
#> 
#> tau: [1] 0.5
#> 
#> Coefficients:
#>                       coefficients lower bd upper bd
#> (Intercept)           14.52525     11.00448 17.76657
#> group_indicator       -1.32816     -2.13047 -1.11966
#> x_mat_test_activeage  -0.20520     -0.39711 -0.02019
#> x_mat_test_activeMedu  0.35623      0.22410  0.62545

At 95% confidence level, the results implies that younger students may outperform older ones, and higher G3 scores can alos be expected for those children whose mothers have been given higher level education.