Updated readme

Author: CollinErickson

README.Rmd

@@ -15,7 +15,7 @@ knitr::opts_chunk$set(
 
 # ContourFunctions
 
-[![Travis-CI Build Status](https://travis-ci.org/CollinErickson/contour.svg?branch=master)](https://travis-ci.org/CollinErickson/contour)
+[![Travis-CI Build Status](https://travis-ci.org/CollinErickson/ContourFunctions.svg?branch=master)](https://travis-ci.org/CollinErickson/ContourFunctions)
 [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/ContourFunctions)](https://cran.r-project.org/package=ContourFunctions)
 [![Codecov test coverage](https://codecov.io/gh/CollinErickson/ContourFunctions/branch/master/graph/badge.svg)](https://codecov.io/gh/CollinErickson/ContourFunctions?branch=master)
 
@@ -33,6 +33,21 @@ The main functions are:
 
 * `cf`: Passes arguments to `cf_function` or `cf_data` depending on whether the first argument is a function or numeric.
 
+All of these functions make the plot using base graphics by default.
+To make plots using ggplot2, add the argument `gg=TRUE`,
+or put g in front of the function name.
+E.g., `gcf_data(...)` is the same as `cf_data(..., gg=TRUE)`,
+and makes a similar plot to `cf_data` but using ggplot2.
+
+There are two functions for making plots in higher dimensions:
+
+* `cf_4dim`: Plots functions with four inputs by making a series
+of contour plots.
+
+* `cf_highdim`: Plots for higher dimensional inputs by making a
+contour plot for each pair of input dimensions and holding the other
+inputs constant or averaging over them.
+
 
 ## Installation
 
@@ -47,21 +62,26 @@ devtools::install_github("CollinErickson/contour")
 
 ## Usage
 
-```{r cf_grid}
+Plot a grid of data:
 
+```{r cf_grid}
 library(ContourFunctions)
 a <- b <- seq(-4*pi, 4*pi, len = 27)
 r <- sqrt(outer(a^2, b^2, "+"))
 cf_grid(a, b, cos(r^2)*exp(-r/(2*pi)))
 ```
 
-
+Plot a function with two input dimensions:
 
 ```{r cf_func}
 f1 <- function(r) cos(r[1]^2 + r[2]^2)*exp(-sqrt(r[1]^2 + r[2]^2)/(2*pi))
 cf_func(f1, xlim = c(-4*pi, 4*pi), ylim = c(-4*pi, 4*pi))
 ```
 
+Using data with two inputs and an output,
+fit a Gaussian process model and show the
+contour surface with dots where the points are:
+
 ```{r cf_data}
 set.seed(0)
 x <- runif(20)
@@ -70,13 +90,17 @@ z <- exp(-(x-.5)^2-5*(y-.5)^2)
 cf_data(x,y,z)
 ```
 
+For more than two input dimensions:
+
 ```{r cf_highdim}
 friedman <- function(x) {
   10*sin(pi*x[1]*x[2]) + 20*(x[3]-.5)^2 + 10*x[4] + 5*x[5]
 }
 cf_highdim(friedman, 5, color.palette=topo.colors)
 ```
 
+For (three or) four inputs dimensions:
+
 ```{r cf_4dim}
 cf_4dim(function(x) {x[1] + x[2]^2 + sin(2*pi*x[3])})
 ```

README.md

@@ -4,7 +4,7 @@
 # ContourFunctions
 
 [![Travis-CI Build
-Status](https://travis-ci.org/CollinErickson/contour.svg?branch=master)](https://travis-ci.org/CollinErickson/contour)
+Status](https://travis-ci.org/CollinErickson/ContourFunctions.svg?branch=master)](https://travis-ci.org/CollinErickson/ContourFunctions)
 [![CRAN\_Status\_Badge](https://www.r-pkg.org/badges/version/ContourFunctions)](https://cran.r-project.org/package=ContourFunctions)
 [![Codecov test
 coverage](https://codecov.io/gh/CollinErickson/ContourFunctions/branch/master/graph/badge.svg)](https://codecov.io/gh/CollinErickson/ContourFunctions?branch=master)
@@ -26,6 +26,20 @@ The main functions are:
   - `cf`: Passes arguments to `cf_function` or `cf_data` depending on
     whether the first argument is a function or numeric.
 
+All of these functions make the plot using base graphics by default. To
+make plots using ggplot2, add the argument `gg=TRUE`, or put g in front
+of the function name. E.g., `gcf_data(...)` is the same as `cf_data(...,
+gg=TRUE)`, and makes a similar plot to `cf_data` but using ggplot2.
+
+There are two functions for making plots in higher dimensions:
+
+  - `cf_4dim`: Plots functions with four inputs by making a series of
+    contour plots.
+
+  - `cf_highdim`: Plots for higher dimensional inputs by making a
+    contour plot for each pair of input dimensions and holding the other
+    inputs constant or averaging over them.
+
 ## Installation
 
     # It can be installed like any other package
@@ -37,8 +51,9 @@ The main functions are:
 
 ## Usage
 
-``` r
+Plot a grid of data:
 
+``` r
 library(ContourFunctions)
 a <- b <- seq(-4*pi, 4*pi, len = 27)
 r <- sqrt(outer(a^2, b^2, "+"))
@@ -47,13 +62,18 @@ cf_grid(a, b, cos(r^2)*exp(-r/(2*pi)))
 
 ![](tools/README-cf_grid-1.png)<!-- -->
 
+Plot a function with two input dimensions:
+
 ``` r
 f1 <- function(r) cos(r[1]^2 + r[2]^2)*exp(-sqrt(r[1]^2 + r[2]^2)/(2*pi))
 cf_func(f1, xlim = c(-4*pi, 4*pi), ylim = c(-4*pi, 4*pi))
 ```
 
 ![](tools/README-cf_func-1.png)<!-- -->
 
+Using data with two inputs and an output, fit a Gaussian process model
+and show the contour surface with dots where the points are:
+
 ``` r
 set.seed(0)
 x <- runif(20)
@@ -64,6 +84,8 @@ cf_data(x,y,z)
 
 ![](tools/README-cf_data-1.png)<!-- -->
 
+For more than two input dimensions:
+
 ``` r
 friedman <- function(x) {
   10*sin(pi*x[1]*x[2]) + 20*(x[3]-.5)^2 + 10*x[4] + 5*x[5]
@@ -73,6 +95,8 @@ cf_highdim(friedman, 5, color.palette=topo.colors)
 
 ![](tools/README-cf_highdim-1.png)<!-- -->
 
+For (three or) four inputs dimensions:
+
 ``` r
 cf_4dim(function(x) {x[1] + x[2]^2 + sin(2*pi*x[3])})
 ```