writeup-analyses.Rmd

```{r}
source("lib/function_library.R", echo=F)

# Load other R source files in the lib directory.
load_all_code("lib")

# Load a bunch of required packages, installing missing ones as needed.
load_all_packages(auto_install = T)

# Set some standard settings.
conf = list(data_dir = "data", dir = ".")
```

Dataset

```{r}
load(paste0(conf$data_dir, "/create-dataset.RData"))

# Progression summary.
summary(dataset$outcomes$progression)
sd(dataset$outcomes$progression)
var(dataset$outcomes$progression)
qplot(dataset$outcomes$progression) + theme_bw() + ggtitle("Parkinson's disease progression") + xlab("Progression of UPDRS score: final - baseline") +
  ylab("Count of subjects")
ggsave("visuals/progression-hist.png")
```

# Variable importance

# Prediction
```{r}
load(paste0(conf$data_dir, "/predict_results.RData"))
best_results = results[[length(results)]]
names(best_results)
qplot(best_results$SL.predict)
summary(best_results$SL.predict)

cor = cor(best_results$SL.predict, dataset$outcomes$progression)
cor^2
cor.test(best_results$SL.predict, dataset$outcomes$progression)

reg = lm(dataset$outcomes$progression ~ best_results$SL.predict)
summary(reg)

# Manual R^2.
# Doesn't give the same results as the regression. Formula wrong?
y_bar = mean(dataset$outcomes$progression)
r_sqr = sum((best_results$SL.predict - y_bar)^2) / sum((dataset$outcomes$progression - y_bar)^2)
r_sqr
```