index.Rmd

---
title: Generalized Additive Models
author:  |
  <span class="noem">Michael Clark</span> <br>
  [m-clark.github.io](https://m-clark.github.io/)
# date: "`r Sys.Date()`"
site: bookdown::bookdown_site
output:
  bookdown::gitbook:
    anchor_sections: FALSE
always_allow_html: yes
documentclass: book
# bibliography: refs.bib
font-import: http://fonts.googleapis.com/css?family=Roboto|Open+Sans|Stalemate|Alex+Brush
biblio-style: apalike
link-citations: yes
description: "An introduction to generalized additive models (GAMs) is provided, with an emphasis on generalization from familiar linear models. It makes extensive use of the mgcv package in R.  Discussion includes common approaches, standard extensions, and relations to other techniques.  More technical modeling details are described and demonstrated as well."
cover-image: 'img/nineteeneightyR.png'
url: 'https\://m-clark.github.io/generalized-additive-models/' 
favicon: 'img/favicon.ico'
github-repo:  'm-clark/generalized-additive-models/'
bibliography: refs.bib
nocite: | 
  @wood_generalized_2006,  @wood_generalized_2017, @venables_modern_2002, @rosscourse, @rasmussen_gaussian_2006, @hardin_generalized_2012, 
  @rigby_generalized_2005, @hastie_generalized_1990, @fox_multiple_2000, @fox_nonparametric_2000,
  @breiman_statistical_2001, @bybee_pisa_2009, @hastie_elements_2009, @ruppert_semiparametric_2003,
  @wasserman_all_2006, @fahrmeir2013regression, @friedman2000additive, @shalizi2016
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(
  # code
  echo    = TRUE,
  message = FALSE,
  warning = FALSE,
  error   = FALSE,
  comment = NA,
  R.options = list(width = 120),
  # viz
  # out.width = '40%',
  fig.asp = .5,
  fig.width = 8,
  fig.align = 'center',
  dev.args = list(bg = 'transparent'),
  dev = 'svglite',
  #cache
  cache.rebuild = FALSE,
  cache = TRUE
)

library(tidyverse)

# create a theme
theme_clean <- function (
  font_size = 12,
  font_family = "",
  center_axis_labels = FALSE
) {
  
  if (center_axis_labels) {
    haxis_just_x <- 0.5
    vaxis_just_y <- 0.5
    v_rotation_x <- 0
    v_rotation_y <- 0
  }
  else {
    haxis_just_x <- 0
    vaxis_just_y <- 1
    v_rotation_x <- 0
    v_rotation_y <- 0
  }
  
  ggplot2::theme(
    text = ggplot2::element_text(
      family = font_family,
      face   = "plain",
      color  = "gray30",
      size   = font_size,
      hjust  = 0.5,
      vjust  = 0.5,
      angle  = 0,
      lineheight = 0.9,
      margin = ggplot2::margin(),
      debug  = FALSE
    ),
    axis.title.x = ggplot2::element_text(
      hjust = haxis_just_x,
      angle = v_rotation_x,
      size  = 0.8 * font_size
    ),
    axis.title.y = ggplot2::element_text(
      vjust = vaxis_just_y,
      hjust = 0,
      angle = v_rotation_y,
      size  = 0.8 * font_size
    ),
    axis.ticks        = ggplot2::element_line(color = "gray30"),
    title             = ggplot2::element_text(color = "gray30", size = font_size * 1.25),
    plot.subtitle     = ggplot2::element_text(color = "gray30", size = font_size * .75, hjust = 0),
    plot.caption      = ggplot2::element_text(color = "gray30", size = font_size * .5, hjust = 0),
    legend.position   = 'bottom', 
    legend.key        = ggplot2::element_rect(fill = "transparent", color = NA),
    legend.background = ggplot2::element_rect(fill = "transparent", color = NA),
    legend.title      = ggplot2::element_blank(), 
    panel.background  = ggplot2::element_blank(),
    panel.grid        = ggplot2::element_blank(),
    strip.background  = ggplot2::element_blank(),
    plot.background   = ggplot2::element_rect(fill = "transparent", color = NA),
  )
}

# set the theme as default
theme_set(theme_clean())

# set other point/line default colors; in most cases, we can use the color from
# default discrete scale for more consistency across plots.
# paletteer::palettes_d$colorblindr$OkabeIto
update_geom_defaults('vline',   list(color = 'gray25',  alpha = .25))  # vlines and hlines are typically not attention grabbers so set alpha
update_geom_defaults('hline',   list(color = 'gray25',  alpha = .25))  # usually a zero marker
update_geom_defaults('point',   list(color = '#D55E00', alpha = .5))   # alpha as usually there are many points
update_geom_defaults('smooth',  list(color = '#56B4E9', alpha = .15))
update_geom_defaults('line',    list(color = '#56B4E9', alpha = .5))
update_geom_defaults('bar',     list(color = '#D55E00', fill = '#D55E00'))  
update_geom_defaults('col',     list(color = '#D55E00', fill = '#D55E00'))
update_geom_defaults('dotplot', list(color = '#D55E00', fill = '#D55E00'))

# use colorblind safe colors for categories; if you supply a continuous value to
# color you'll get an error, but you just have to use `myplot +
# scale_color_continous()` or whatever to override this; likewise you can always
# override this scale for categorical schemes if desired also. Note that this
# will apply for both color and fill, which is usually what we want.

okabe_ito = c(
  '#D55E00',
  '#56B4E9',
  '#009E73',
  '#F0E442',
  '#0072B2',
  '#D55E00',
  '#CC79A7',
  '#999999'
)

ggplot <- function(...) ggplot2::ggplot(...) + 
  # okabe ito colorblind safe scheme
  scale_color_manual(
    values = okabe_ito,
    drop = FALSE,
    aesthetics = c('color', 'fill')
  )

gt <- function(..., decimals = 2, title = NULL, subtitle = NULL) {
  gt::gt(...) %>% 
    gt::fmt_number(
      columns = where(is.numeric),
      decimals = decimals
    ) %>% 
    gt::tab_header(title = title, subtitle = subtitle) %>% 
    gtExtras::gt_theme_nytimes()
}

gt_theme <-   
  list(
    # report median (IQR) and n (percent) as default stats in `tbl_summary()`
    "tbl_summary-str:continuous_stat" = "{mean} ({sd})",
    "tbl_summary-str:categorical_stat" = "{n} ({p})"
  )


gtsummary::set_gtsummary_theme(gt_theme)

tbl_summary <- function(..., title = '', butcher = TRUE) {
  tbl_out <- gtsummary::tbl_summary(
    ..., 
    digits = list(
    all_continuous() ~ c(1, 1),
    all_categorical() ~ c(0, 1)
    )
  ) %>% 
    modify_caption(caption = title)
  # 
  # # trim dataset etc from table; may lose other functionality
  if (butcher)
    tbl_out <- tbl_out %>% 
      gtsummary::tbl_butcher()
  # 
  tbl_out
}
```

```{r loadpacks, include=FALSE, cache=FALSE, results='hide'}
library(gt)
library(tidyverse)
library(broom)
library(mgcv)
library(gratia)
library(modelr)
library(purrr)

library(htmltools)
library(lazerhawk)
library(visibly)
library(plotly)
library(scico)
library(ggborderline)
```


```{r cover_image, fig.align='center', out.width=200, echo=FALSE}
knitr::include_graphics('img/198R.png', dpi = NA)
```


```{r ccimg, fig.align='center',  out.width=0, fig.show='hide', echo=FALSE}
knitr::include_graphics('img/mc_logo.png', dpi = NA)
```