rearrange files into package

Author: SimonVaughanDataAndCode

.Rbuildignore

@@ -0,0 +1,2 @@
+^.*\.Rproj$
+^\.Rproj\.user$

.gitignore

@@ -1,3 +1,4 @@
 .Rproj.user
 .Rhistory
 .RData
+gin.Rproj

DESCRIPTION

@@ -0,0 +1,10 @@
+Package: gin
+Title: Gaussian Processes for time series inference
+Version: 0.0.0.9000
+Authors@R: person("Simon", "Vaughan", email = "[email protected]", role = c("aut", "cre"))
+Description: A set of functions for analysing and generating time series using 
+             Gaussian Process (GP) models.
+Depends: R (>= 3.2.2)
+License: MIT + file LICENSE
+Encoding: UTF-8
+LazyData: true

NAMESPACE

@@ -0,0 +1,2 @@
+# Generated by roxygen2: fake comment so roxygen2 overwrites silently.
+exportPattern("^[^\\.]")

gin.Rproj

@@ -1,13 +1,16 @@
 Version: 1.0
 
-RestoreWorkspace: Default
-SaveWorkspace: Default
+RestoreWorkspace: No
+SaveWorkspace: No
 AlwaysSaveHistory: Default
 
 EnableCodeIndexing: Yes
-UseSpacesForTab: Yes
-NumSpacesForTab: 2
 Encoding: UTF-8
 
-RnwWeave: knitr
-LaTeX: pdfLaTeX
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace

gp_functions.R

@@ -89,6 +89,7 @@ LogLike <- function(theta,
   if (!("dy" %in% colnames(dat))) { 
     dat$dy <- array(0, n) 
   }
+  dy <- dat$dy
 
   # if n * n array tau is not present then make one
   if (is.null(tau)) {
@@ -108,7 +109,7 @@ LogLike <- function(theta,
   mu <- theta[1]
   nu <- abs(theta[2])
   theta <- theta[c(-1, -2)]
-  
+
   # now subtract the mean from the data: y <- (y - mu)
   y <- dat$y - mu