load .Rmd files with system.file from inst/examples instead

cboettig · May 13, 2014 · 6a38ce0 · 6a38ce0
1 parent 67cad00
commit 6a38ce0
Show file tree

Hide file tree

Showing 6 changed files with 14 additions and 526 deletions.
diff --git a/R/gp_mcmc.R b/R/gp_mcmc.R
@@ -119,7 +119,7 @@ summary_gp_mcmc <- function(gp, burnin=0, thin=1){
   df <- melt(postdist, id="index")
   traces_plot <- 
     ggplot(df) + geom_line(aes(index, value)) + 
-    facet_wrap(~ variable, scale="free", ncol=1)
+    facet_wrap(~ variable, scales="free", ncol=1)
 
   s2.p <- gp$s2.p
   d.p <- gp$d.p
@@ -136,7 +136,7 @@ summary_gp_mcmc <- function(gp, burnin=0, thin=1){
   posteriors_plot <- ggplot(df, aes(value)) + 
     stat_density(geom="path", position="identity", alpha=0.7) +
     geom_line(data=prior_curves, aes(x=value, y=density), col="red") + 
-    facet_wrap(~ variable, scale="free", ncol=2)
+    facet_wrap(~ variable, scales="free", ncol=2)
 
  # print(traces_plot)
 #  print(posteriors_plot)

diff --git a/R/gp_plot.R b/R/gp_plot.R
@@ -2,12 +2,13 @@
 #' Plot a Gaussian Process
 #' 
 #' Plot the mean (line) and 2 standard deviations (ribbon)
-#' @param gp a gpfit object from \code{\link{gp_fit}}
+#' @param x a gpfit object from \code{\link{gp_fit}}
 #' @param true an optional data.frame with columns "x" and "y" containing target curve.  
+#' @param ... additional arguments (not implemented) 
 #' @return a ggplot object of the plot
 #' @export
-plot.gpfit <- function(gp, ...){
-  dat <- data.frame(x=gp$X, y=(gp$Ef), ymin=(gp$Ef-2*sqrt(diag(gp$Cf))), ymax=(gp$Ef+2*sqrt(diag(gp$Cf))))
+plot.gpfit <- function(x, true, ...){
+  dat <- data.frame(x=x$X, y=(x$Ef), ymin=(x$Ef-2*sqrt(diag(x$Cf))), ymax=(x$Ef+2*sqrt(diag(x$Cf))))
   p <- ggplot(dat) +
     geom_ribbon(aes(x=x,y=y, ymin=ymin, ymax=ymax), fill="grey80") + # Var
     geom_line(aes(x=x,y=y), size=1) + #MEAN

diff --git a/man/plot.gpfit.Rd b/man/plot.gpfit.Rd
@@ -3,12 +3,14 @@
 \alias{plot.gpfit}
 \title{Plot a Gaussian Process}
 \usage{
-\method{plot}{gpfit}(gp, ...)
+\method{plot}{gpfit}(x, true, ...)
 }
 \arguments{
-\item{gp}{a gpfit object from \code{\link{gp_fit}}}
+\item{x}{a gpfit object from \code{\link{gp_fit}}}
 
 \item{true}{an optional data.frame with columns "x" and "y" containing target curve.}
+
+\item{...}{additional arguments (not implemented)}
 }
 \value{
 a ggplot object of the plot

diff --git a/tests/testthat/gaussian-process-basics.Rmd b/tests/testthat/gaussian-process-basics.Rmd