---
title: "Getting Started with splineplot"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Getting Started with splineplot}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width = 7,
  fig.height = 5,
  dpi = 100
)
```

```{r setup}
library(splineplot)
library(mgcv)
library(survival)
library(splines)
library(ggplot2)
```

## Introduction

The `splineplot` package provides a unified interface for visualizing spline effects from various regression models. This vignette will guide you through the basic usage of the package.

## Preparing Your Data

First, let's create some sample data to work with:

```{r data}
set.seed(42)
n <- 500

# Continuous predictor
age <- rnorm(n, mean = 50, sd = 10)

# Non-linear effect
true_effect <- -0.05*(age - 50) + 0.001*(age - 50)^3/100

# Various outcomes
time_to_event <- rexp(n, rate = exp(true_effect))
event_status <- rbinom(n, 1, 0.8)
binary_outcome <- rbinom(n, 1, plogis(true_effect))
count_outcome <- rpois(n, lambda = exp(true_effect/2))
continuous_outcome <- true_effect + rnorm(n, 0, 0.5)

# Create data frame
data <- data.frame(
  age = age,
  time = time_to_event,
  status = event_status,
  binary = binary_outcome,
  count = count_outcome,
  continuous = continuous_outcome
)
```

## GAM Models

### Cox Proportional Hazards

GAM with Cox family is useful for flexible modeling of survival data:

```{r gam-cox}
# Fit GAM Cox model using weights
gam_cox <- gam(time ~ s(age),
               family = cox.ph(),
               weights = status,
               data = data)

# Create spline plot
splineplot(gam_cox, data,
          ylim = c(0.5, 2.0),
          xlab = "Age (years)",
          ylab = "Hazard Ratio")
```

The plot shows:
- The smooth effect of age on hazard
- 95% confidence intervals (dotted lines)
- A reference point (diamond) where HR = 1
- Histogram showing the distribution of data

### Logistic Regression

For binary outcomes:

```{r gam-logistic}
gam_logit <- gam(binary ~ s(age),
                 family = binomial(),
                 data = data)

splineplot(gam_logit, data,
          ylim = c(0.5, 2.0),
          ylab = "Odds Ratio")
```

### Poisson Regression

For count data:

```{r gam-poisson}
gam_poisson <- gam(count ~ s(age),
                   family = poisson(),
                   data = data)

splineplot(gam_poisson, data,
          ylab = "Rate Ratio")
```

## GLM with Splines

When you prefer parametric splines over GAM smooths:

### Natural Splines (ns)

```{r glm-ns}
glm_ns <- glm(binary ~ ns(age, df = 4),
              family = binomial(),
              data = data)

splineplot(glm_ns, data,
          ylim = c(0.5, 2.0))
```

### B-splines (bs)

```{r glm-bs}
glm_bs <- glm(count ~ bs(age, df = 4),
              family = poisson(),
              data = data)

splineplot(glm_bs, data)
```

## Cox Models with Splines

For survival analysis without GAM:

```{r cox-ns}
cox_ns <- coxph(Surv(time, status) ~ ns(age, df = 4),
                data = data)

splineplot(cox_ns, data,
          ylim = c(0.5, 2.0))
```

## Customizing Your Plots

### Reference Values

By default, the reference value is the median. You can change this:

```{r custom-ref}
splineplot(gam_cox, data,
          refx = 45,  # Set reference at age 45
          ylim = c(0.5, 2.0))
```

### Confidence Interval Styles

Choose between dotted lines (default) or ribbon style:

```{r ci-styles}
# Ribbon style confidence intervals
splineplot(gam_logit, data,
          ribbon_ci = TRUE,
          ylim = c(0.5, 2.0))
```

### Histogram Options

You can toggle the histogram display:

```{r histogram}
splineplot(gam_cox, data,
          show_hist = FALSE,
          ylim = c(0.5, 2.0))
```

### Log Scale

For odds ratios, rate ratios, or hazard ratios, you might prefer log scale:

```{r log-scale}
splineplot(gam_logit, data,
          log_scale = TRUE)
```

## Interaction Terms

The package automatically detects and visualizes interaction terms:

```{r interaction}
# Add a grouping variable
data$group <- factor(sample(c("Male", "Female"), n, replace = TRUE))

# Fit model with interaction
gam_interact <- gam(time ~ s(age, by = group),
                   family = cox.ph(),
                   weights = status,
                   data = data)

# Plot shows separate curves for each group
splineplot(gam_interact, data,
          ylim = c(0.5, 2.0))
```

## Tips for Best Results

1. **Model Choice**: Use GAM for maximum flexibility, GLM with splines for parametric approach
2. **Degrees of Freedom**: Higher df allows more flexibility but may overfit
3. **Reference Point**: Choose a meaningful reference value for interpretation
4. **Confidence Intervals**: Ribbon style is visually appealing, dotted lines show precision better
5. **Sample Size**: Ensure adequate sample size for stable spline estimates

## Conclusion

The `splineplot` package simplifies the visualization of non-linear effects across different model types. It handles the complexity of extracting and transforming model predictions while providing a consistent, publication-ready output.
.
