.gitignore

@@ -3,3 +3,4 @@
 .RData
 .Ruserdata
 *.Rproj
+inst/doc

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: tidymv
 Type: Package
 Title: Tidy Model Visualisation
-Version: 1.0.0
+Version: 1.1.0
 Authors@R: person("Stefano", "Coretta", email = paste0("stefano.coretta", "@", "gmail.com"),
                   role = c("aut", "cre"))
 Description: This package provides functions for model visualisation using tidy
@@ -10,8 +10,12 @@ License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 6.0.1
-Imports: cowplot,
+Imports: tidyverse,
+    cowplot,
     dplyr,
     itsadug,
     ggplot2,
     magrittr
+Suggests: knitr,
+    rmarkdown
+VignetteBuilder: knitr

NEWS.md

@@ -1,5 +1,13 @@
 # Change Log
 
+## [1.1.0] - 2017-10-31
+### Added
+- black and white option for `plot_gamsd()`
+
+### Changed
+- `gam` model in the vignette now has a reference smooth `s(x2)`
+- updated vignette
+
 ## [1.0.0] - 2017-10-21
 ### Added
 - documentation of package
@@ -15,4 +23,5 @@
 - `create_start_event` function
 - `plot_gamsd` function
 
-[1.0.0]: https://github.com/stefanocoretta/tidymv/compare/v0.1.0...v1.0.0
+[1.1.0]: https://github.com/stefanocoretta/tidymv/compare/v1.0.0...v1.1.0
+[1.0.0]: https://github.com/stefanocoretta/tidymv/compare/v0.1.0...v1.0.0

R/functions.R

@@ -29,10 +29,11 @@ create_event_start <- function(tibble, event.col) {
 #' @param view The predictor determining the time series.
 #' @param comparison The levels for the comparison as a named list.
 #' @param conditions The values to use for other predictors as a named list.
+#' @param bw Whether to plot in black and white (the default is \code{FALSE}).
 #'
 #' @importFrom magrittr "%>%"
 #' @export
-plot_gamsd <- function(model, view, comparison, conditions = NULL) {
+plot_gamsd <- function(model, view, comparison, conditions = NULL, bw = FALSE) {
     diff.df <- itsadug::plot_diff(
         model,
         view = view,
@@ -65,8 +66,9 @@ plot_gamsd <- function(model, view, comparison, conditions = NULL) {
 
     annotate <- ggplot2::annotate(
         "rect",
-        xmin=sig.diff$start, xmax=sig.diff$end,
-        ymin=-Inf, ymax=Inf, alpha=0.1, fill="red"
+        xmin = sig.diff$start, xmax = sig.diff$end,
+        ymin = -Inf, ymax = Inf, alpha = 0.1,
+        fill = ifelse(bw == FALSE, "red", "black")
     )
 
     is.sig <- is.null(sig.diff) == FALSE
@@ -79,13 +81,25 @@ plot_gamsd <- function(model, view, comparison, conditions = NULL) {
         ggplot2::geom_ribbon(
             ggplot2::aes(ymin = ymin.sm,
                          ymax = ymax.sm,
-                         fill = smooth.df[[comp.column]]),
+                         group = smooth.df[[comp.column]]
+                        ),
             alpha = 0.2,
             colour = "NA"
         ) +
-        ggplot2::geom_line(
-            ggplot2::aes(colour = smooth.df[[comp.column]])
-        ) +
+        {if (bw == FALSE) {
+            ggplot2::aes(fill = smooth.df[[comp.column]])}
+        } +
+        {if (bw == FALSE) {
+            ggplot2::geom_line(
+                ggplot2::aes(colour = smooth.df[[comp.column]])
+            )
+            }
+            else {
+                ggplot2::geom_line(
+                ggplot2::aes(linetype = smooth.df[[comp.column]])
+                )
+            }
+        } +
         ggplot2::theme_bw() +
         ggplot2::theme(
             axis.title.x = ggplot2::element_blank(),
@@ -94,8 +108,14 @@ plot_gamsd <- function(model, view, comparison, conditions = NULL) {
             legend.position = "top"
         ) +
         ggplot2::xlim(min(diff.df[[view]]), max(diff.df[[view]])) +
-        ggplot2::scale_colour_discrete(name = names(comparison)) +
-        ggplot2::scale_fill_discrete(name = names(comparison))
+        {if (bw == FALSE) {
+            ggplot2::scale_colour_discrete(name = names(comparison))
+            }
+            else {
+                ggplot2::scale_linetype_discrete(name = names(comparison))
+                }
+        } +
+        {if (bw == FALSE) {ggplot2::scale_fill_discrete(name = names(comparison))}}
 
     ymin.di <- diff.df$est - diff.df$CI
     ymax.di <- diff.df$est + diff.df$CI

README.md

@@ -1 +1,7 @@
-# `tidymv`
+# `tidymv`: Tidy Model Visualisation
+
+This is the repository of the `R` package `tidymv`. This package provides functions for the visualisation of GAM(M)s using tidy tools from the `tidyverse`. `tidymv` is based on the `itsadug` package, and indeed it uses some of its functions under the hood.
+
+## Installation
+
+To install the package, use devtools::install_github("stefanocoretta/tidymv@v1.1.0", build_vignettes = TRUE). To learn how to use the package, do vignette("plot-gamms", package = "tidymv") after the installation.

vignettes/plot-gamms.R

@@ -0,0 +1,34 @@
+## ----setup, echo=FALSE, include=FALSE------------------------------------
+knitr::opts_chunk$set(out.width = "300px", fig.align = "center", dpi = 300)
+library(tidyverse)
+theme_set(theme_bw())
+library(itsadug)
+library(tidymv)
+
+## ----gam-----------------------------------------------------------------
+set.seed(10)
+data <- gamSim(4)
+model <- gam(
+    y ~
+        fac +
+        s(x2) +
+        s(x2, by = fac) +
+        s(x0),
+    data = data
+)
+
+## ----plot-1-2------------------------------------------------------------
+plot_gamsd(
+    model = model,
+    view = "x2",
+    comparison = list(fac = c("1", "2"))
+)
+
+## ----plot-1-3------------------------------------------------------------
+plot_gamsd(
+    model = model,
+    view = "x2",
+    comparison = list(fac = c("1", "3")),
+    bw = TRUE
+)
+

vignettes/plot-gamms.Rmd

@@ -0,0 +1,58 @@
+---
+title: "Plot GAM(M)s reference and difference smooths"
+author: "Stefano Coretta"
+date: "`r Sys.Date()`"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{Vignette Title}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+```{r setup, echo=FALSE, include=FALSE}
+knitr::opts_chunk$set(out.width = "300px", fig.align = "center", dpi = 300)
+library(tidyverse)
+theme_set(theme_bw())
+library(itsadug)
+library(tidymv)
+```
+
+Reference and difference smooths of factor predictos from a `gam` model can be plotted with `plot_gamsd()`.
+To illustrate how to use `plot_gamsd()`, let's first prepare some dummy data with a factor variable and run `gam()` on this data. The `gam` model includes a reference smooth `s(x2)`, a by-factor difference smooth `s(x2, by = fac)`, and a smooth `s(x0)`.
+
+```{r gam}
+set.seed(10)
+data <- gamSim(4)
+model <- gam(
+    y ~
+        fac +
+        s(x2) +
+        s(x2, by = fac) +
+        s(x0),
+    data = data
+)
+```
+
+We can now plot the estimated smooths for the two levels of `fac`, and the difference smooth.
+It is only possible to compare two levels at once, so here we plot `1` and `2`.
+Portions of the estimated smooths that are significantly different are indicated by a shaded red area both in the estimated smooths panel (top) and the difference smooth panel (bottom).
+Significance is based on the difference smooth: at any point, if the confidence interval of the difference smooth does not include 0, the difference between the estimated smooths is significant.
+
+```{r plot-1-2}
+plot_gamsd(
+    model = model,
+    view = "x2",
+    comparison = list(fac = c("1", "2"))
+)
+```
+
+Here we compare `1` with `3`, and we plot in black and white (gray scale).
+
+```{r plot-1-3}
+plot_gamsd(
+    model = model,
+    view = "x2",
+    comparison = list(fac = c("1", "3")),
+    bw = TRUE
+)
+```