.right[] ggResidpanel

.title[
# .right[<img src="figures/logo.png" />] ggResidpanel
]
.subtitle[
## Easy Creation of Panels of Diagnostics Plots
]
.author[
### Katherine Goode
]
.date[
### October 4, 2019
]

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# Overview

1. Introduction: background and motivation

2. ggResidpanel Functionality

3. Current Development

4. Resources

<br>

For following along...

```r
# Installs package
install.packages("ggResidpanel")

# Loads package
library(ggResidpanel)
```

---

# Example Data: Trees

`trees` data available in base R

"This data set provides measurements of the diameter, height and volume of timber in 31 felled black cherry trees." - R documentation

```r
str(trees)
```

```
## 'data.frame':	31 obs. of  3 variables:
##  $ Girth : num  8.3 8.6 8.8 10.5 10.7 10.8 11 11 11.1 11.2 ...
##  $ Height: num  70 65 63 72 81 83 66 75 80 75 ...
##  $ Volume: num  10.3 10.3 10.2 16.4 18.8 19.7 15.6 18.2 22.6 19.9 ...
```

*Linear Model*

```r
# Example linear model
tree_model <- lm(Volume ~ Height + Girth, data = trees)
```

---

# Example Data: Penguins

`penguins` data available in ggResidpanel

Data from a study on how the heart rate of the emperor penguins relates to the depth and duration during a dive. Multiple observations taken from 9 penguins.

```r
str(ggResidpanel::penguins)
```

```
## 'data.frame':	125 obs. of  4 variables:
##  $ heartrate: num  88.8 103.4 97.4 85.3 60.6 ...
##  $ depth    : num  5 9 22 25.5 30.5 32.5 38 32 6 10.5 ...
##  $ duration : num  1.05 1.18 1.92 3.47 7.08 ...
##  $ bird     : Factor w/ 9 levels "1","2","3","4",..: 1 1 1 1 1 1 1 1 1 1 ...
```

*Mixed effects model*

```r
penguin_model <- lme4::lmer(heartrate ~ depth + duration + (1|bird), 
                            data = penguins)
```

---

# Introduction

---

# Example of Model Assumptions

### Linear Model

For `$i=1,...,n$`:

`$$y_i=\beta_0+\beta_1x_{1,i}+\cdots+\beta_px_{p,i}+\epsilon_i$$`

where

`$$\epsilon_i\overset{iid}{\sim}N(0,\sigma^2)$$`

### Assumptions (in words)

- independence of residuals
- linearity
- constant variance of residuals
- normality of residuals

---

# Examples of Diagnostic Plots

.center[
<img src="slides_files/figure-html/unnamed-chunk-6-1.png" style="display: block; margin: auto;" />
]

---

# Examples of Diagnostic Plots

.center[
<img src="slides_files/figure-html/unnamed-chunk-7-1.png" style="display: block; margin: auto;" />
]

---

# What is ggResidpanel?

R package for the easy creation of panels of diagnostics plots using ggplot2 (joint work with Katie Rey)

```r
resid_panel(tree_model)
```

---

# Motivation

- Katie Rey and I worked as stats consultants

- Encourage checking of model assumptions

- Annoyed by the base R plotting option

`> plot(model)`  
    `Hit <Return> to see next plot:`  
    `Hit <Return> to see next plot:`  
    .  
    .  
    .
    
- Wanted to develop a tool for easy creation of residual plots using ggplot

---

# Other Tools: plot.lm

```r
par(mfrow = c(2, 2)) # specifies the layout
plot(tree_model) # plots 'lm' default diagnostic plots
```

---

# Other Tools: plot.merMod

```r
plot(penguin_model)
```

---

# Other Tools: ggfortify

```r
library(ggfortify)
autoplot(tree_model)
```

---

# Other Tools: ggfortify

```r
autoplot(penguin_model)
```

```
## Error in `autoplot()`:
## ! Objects of class <lmerMod> are not supported by autoplot.
## ℹ have you loaded the required package?
```

---

# Other Tools: broom + ggplot2

```r
library(broom)

# extracts model info in a dataframe
tree_model_values <- augment(tree_model) 
head(tree_model_values)
```

```
## # A tibble: 6 × 9
##   Volume Height Girth .fitted .resid   .hat .sigma  .cooksd .std.resid
##    <dbl>  <dbl> <dbl>   <dbl>  <dbl>  <dbl>  <dbl>    <dbl>      <dbl>
## 1   10.3     70   8.3    4.84  5.46  0.116    3.79 0.0978        1.50 
## 2   10.3     65   8.6    4.55  5.75  0.147    3.77 0.148         1.60 
## 3   10.2     63   8.8    4.82  5.38  0.177    3.78 0.167         1.53 
## 4   16.4     72  10.5   15.9   0.526 0.0592   3.95 0.000409      0.140
## 5   18.8     81  10.7   19.9  -1.07  0.121    3.95 0.00394      -0.294
## 6   19.7     83  10.8   21.0  -1.32  0.156    3.94 0.00840      -0.370
```

---

# Other Tools: broom + ggplot2

```r
ggplot(tree_model_values, aes(x = .fitted, y = .resid)) + 
  geom_point()
```

---

# Other Tools: SAS residual panels

### Residual Panels from SAS Procedures

---

# Goals for ggResidpanel

- simple creation of panels of diagnostic plots

- ggplot2 framework

- functionality for linear and mixed models

- more plot options and choice of plots

- additional features:

- interactive
    - comparison of models
    - more residual choices

---

# ggResidpanel Functionality

---

# Functions Available

**Models of type**: “lm”, “glm”, “lme”, “lmer”, “glmer”, and “lmerTest”

- `resid_panel`: panel of diagnostic plots 
- `resid_interact`: interactive panel of diagnostic plots
- `resid_xpanel`: panel of diagnostic plots of the predictor variables
- `resid_compare`: panel of diagnostic plots from multiple models

**Any model type**

- `resid_auxpanel`: mimics (to a certain extent) `resid_panel` for any model type

---

# resid_panel

```r
resid_panel(penguin_model)
```

---

# resid_panel: plot options

*Note: cookd, ls, lev only available for "lm" and "glm" models*

---

# resid_panel: plot options

**Additional Options**

- `bins` = number of bins for the histogram
- `qqbands` = include 95% confidence bands line on qq plot?
- `qqline` = include 1-1 line on qq plot?
- `smoother` = include a smoother on index, ls, lev, and resid plots?

---

# resid_panel: individual plot

```r
resid_panel(penguin_model, plots = "yvp")
```

---

# resid_panel: vector of plots

```r
resid_panel(penguin_model, plots = c("resid", "qq", "yvp"), nrow = 1)
```

---

# resid_panel: prespecified panels

```r
resid_panel(penguin_model, plots = "SAS")
```

---

# resid_panel: prespecified panels

```r
resid_panel(penguin_model, plots = "all")
```

---

# resid_panel: prespecified panels

```r
resid_panel(tree_model, plots = "all", 
            smoother = TRUE, qqbands = TRUE)
```

---

# resid_panel: prespecified panels

```r
resid_panel(tree_model, plots = "R", smoother = TRUE) # for lm and glm models only
```

---

# resid_panel: residual types

- pearson
- response*
- standardized

**“glm” model:**

- pearson
- deviance*
- response
- stand.deviance
- stand.pearson

]

- pearson*
- response

**“glmer” model:**

- pearson
- deviance*
- response

*Note: plots of ls and lev only accept standardized residuals*
]

*** Denotes default residual type

---

# resid_panel: residual types

```r
resid_panel(tree_model, type = "standardized")
```

---

# resid_panel: residual types

```r
resid_panel(penguin_model, type = "response")
```

---

# resid_panel: panel formatting

**Format Options**

- `axis.text.size` = adjust axis text size

- `title.text.size` = adjust title text size

- `nrow` = number of rows in the panel

- `scale` = adjusts the size of the graphics

- `theme` = “bw”, “classic”, and “grey” (or “gray”)

- `title.opt` = whether to include a title

---

# resid_panel: formatting options

```r
formatted <- resid_panel(
  penguin_model,
  plots = c("yvp", "index"),
  axis.text.size = 24,
  title.text.size = 30,
  nrow = 2, 
  scale = 0.9,
  theme = "grey"
)
```
]

```r
formatted
```

<img src="slides_files/figure-html/unnamed-chunk-25-1.png" style="display: block; margin: auto;" />
]

---

# resid_interact

```r
resid_interact(penguin_model)
```

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---

# resid_interact: options

Same options as `resid_panel` <small> (except `qqbands` is not available) </small>

```r
resid_interact(penguin_model, plots = c("resid", "yvp"), 
               theme = "classic", smoother = TRUE)
```

<div id="htmlwidget-b8c5ab2b3011e9de1e20" style="width:100%;height:504px;" class="widgetframe html-widget "></div>
<script type="application/json" data-for="htmlwidget-b8c5ab2b3011e9de1e20">{"x":{"url":"slides_files/figure-html//widgets/widget_unnamed-chunk-29.html","options":{"xdomain":"*","allowfullscreen":false,"lazyload":false}},"evals":[],"jsHooks":[]}</script>

---

# resid_xpanel

```r
resid_xpanel(penguin_model)
```

---

# resid_xpanel: options

- `yvar`: "residual" (default) or "response"
- `smoother`: indicates whether to add a smoother or not
- `type`: residual types (same as `resid_panel`)
- format options: same as `resid_panel`

```r
resid_xpanel(penguin_model, yvar = "response", 
             smoother = TRUE, nrow = 1)
```

---

# resid_compare

```r
# Fit a new model to the 
# penguin data
penguin_model_log2 <- 
  lme4::lmer(
    log(heartrate) ~ 
      depth + 
      duration +
      I(duration^2) + 
      (1|bird), 
    data = penguins)

# Compare the residuals from 
# the two penguin models
compare_panel <- 
  resid_compare(
    list(penguin_model, 
         penguin_model_log2))
```
]

```r
compare_panel
```

<img src="slides_files/figure-html/unnamed-chunk-33-1.png" style="display: block; margin: auto;" />
]

---

# resid_compare: options

Same options as resid_panel <small> (expect no `nrow`) </small>

```r
resid_compare(models = list(penguin_model, penguin_model_log2), 
              plots = c("resid", "yvp"), smoother = TRUE, 
              theme = "gray")
```

---

# resid_auxpanel

```r
# Fit a regression tree
penguin_tree <- rpart::rpart(
  heartrate ~ depth + duration, 
  data = penguins)

# Obtain the predicted values
tree_pred <- 
  predict(penguin_tree)

# Obtain the residuals
tree_resid <- 
  penguins$heartrate - 
  tree_pred

# Create default panel
tree_panel <- resid_auxpanel(
  residuals = tree_resid,
  predicted = tree_pred)
```
]

```r
tree_panel
```

<img src="slides_files/figure-html/unnamed-chunk-36-1.png" style="display: block; margin: auto;" />
]

---

# resid_auxpanel: options

Same as `resid_panel` (except for available plots)

**Plots Options**: boxplot, hist, index, qq, resid  
**Prespecified Panels**: all, default, SAS

```r
resid_auxpanel(residuals = tree_resid, predicted = tree_pred,
               plots = c("resid", "index"), smoother = TRUE)
```

---

# Current Development

---

# In progress...

- Additional residual types 
    - such as standardized residuals for mixed models  
    
- Interactions in resid_xpanel

- Option to color by a variable

---

# Resources

---

# Helpful Links

- [Website](https://goodekat.github.io/ggResidpanel/)
- [Introduction Vignette](https://cran.r-project.org/web/packages/ggResidpanel/vignettes/introduction.html)
- [Tutorial and User Manual](https://goodekat.github.io/ggResidpanel-tutorial/tutorial.html)
- [GitHub Repository](https://github.com/goodekat/ggResidpanel)