Unify the structure of testing data

wulingyun · Feb 11, 2014 · 9d72a3e · 9d72a3e
1 parent 6ead2e4
commit 9d72a3e
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diff --git a/.hgignore b/.hgignore
@@ -1,4 +1,7 @@
-glob:src-i386/*
-glob:src-x64/*
-glob:*.bak
-glob:.svn/*
+syntax: glob
+src-i386/*
+src-x64/*
+.svn/*
+*.bak
+*.so
+*.o
diff --git a/R/CRF-package.R b/R/CRF-package.R
@@ -76,9 +76,9 @@
 #' 
 #' library(CRF)
 #' data(Small)
-#' decode.exact(small.crf)
-#' infer.exact(small.crf)
-#' sample.exact(small.crf, 100)
+#' decode.exact(Small$crf)
+#' infer.exact(Small$crf)
+#' sample.exact(Small$crf, 100)
 #' 
 #' @useDynLib CRF, .registration = TRUE
 #' 

diff --git a/R/clamp.R b/R/clamp.R
@@ -22,7 +22,7 @@
 #' 
 #' library(CRF)
 #' data(Small)
-#' crf <- clamp.crf(small.crf, c(0, 0, 1, 1))
+#' crf <- clamp.crf(Small$crf, c(0, 0, 1, 1))
 #' 
 #' 
 #' @export
@@ -80,7 +80,7 @@ clamp.crf <- function(crf, clamped)
 #' 
 #' library(CRF)
 #' data(Small)
-#' crf <- clamp.crf(small.crf, c(0, 0, 1, 1))
+#' crf <- clamp.crf(Small$crf, c(0, 0, 1, 1))
 #' clamp.reset(crf, c(0,0,2,2))
 #' 
 #' 
@@ -123,7 +123,7 @@ clamp.reset <- function(crf, clamped)
 #' 
 #' library(CRF)
 #' data(Small)
-#' crf <- sub.crf(small.crf, c(2, 3))
+#' crf <- sub.crf(Small$crf, c(2, 3))
 #' 
 #' 
 #' @export

diff --git a/R/decode.R b/R/decode.R
@@ -10,7 +10,7 @@
 #' 
 #' library(CRF)
 #' data(Small)
-#' d <- decode.exact(small.crf)
+#' d <- decode.exact(Small$crf)
 #'
 #' @export 
 decode.exact <- function(crf)
@@ -30,7 +30,7 @@ decode.exact <- function(crf)
 #' 
 #' library(CRF)
 #' data(Small)
-#' d <- decode.chain(small.crf)
+#' d <- decode.chain(Small$crf)
 #'
 #' @export 
 decode.chain <- function(crf)
@@ -50,7 +50,7 @@ decode.chain <- function(crf)
 #' 
 #' library(CRF)
 #' data(Small)
-#' d <- decode.tree(small.crf)
+#' d <- decode.tree(Small$crf)
 #'
 #' @export 
 decode.tree <- function(crf)
@@ -73,7 +73,7 @@ decode.tree <- function(crf)
 #' 
 #' library(CRF)
 #' data(Small)
-#' d <- decode.conditional(small.crf, c(0,1,0,0), decode.exact)
+#' d <- decode.conditional(Small$crf, c(0,1,0,0), decode.exact)
 #'
 #' @export 
 decode.conditional <- function(crf, clamped, decode.method, ...)
@@ -101,7 +101,7 @@ decode.conditional <- function(crf, clamped, decode.method, ...)
 #' 
 #' library(CRF)
 #' data(Small)
-#' d <- decode.cutset(small.crf, c(2))
+#' d <- decode.cutset(Small$crf, c(2))
 #'
 #' @export 
 decode.cutset <- function(crf, cutset, engine = "default", start = apply(crf$node.pot, 1, which.max))
@@ -127,7 +127,7 @@ decode.cutset <- function(crf, cutset, engine = "default", start = apply(crf$nod
 #' 
 #' library(CRF)
 #' data(Small)
-#' d <- decode.junction(small.crf)
+#' d <- decode.junction(Small$crf)
 #'
 #' @export 
 decode.junction <- function(crf)
@@ -149,7 +149,7 @@ decode.junction <- function(crf)
 #' 
 #' library(CRF)
 #' data(Small)
-#' d <- decode.sample(small.crf, sample.exact, 10000)
+#' d <- decode.sample(Small$crf, sample.exact, 10000)
 #'
 #' @export 
 decode.sample <- function(crf, sample.method, ...)
@@ -171,7 +171,7 @@ decode.sample <- function(crf, sample.method, ...)
 #' 
 #' library(CRF)
 #' data(Small)
-#' d <- decode.marginal(small.crf, infer.exact)
+#' d <- decode.marginal(Small$crf, infer.exact)
 #'
 #' @export 
 decode.marginal <- function(crf, infer.method, ...)
@@ -194,7 +194,7 @@ decode.marginal <- function(crf, infer.method, ...)
 #' 
 #' library(CRF)
 #' data(Small)
-#' d <- decode.lbp(small.crf)
+#' d <- decode.lbp(Small$crf)
 #'
 #' @export 
 decode.lbp <- function(crf, max.iter = 10000, cutoff = 1e-4, verbose = 0)
@@ -217,7 +217,7 @@ decode.lbp <- function(crf, max.iter = 10000, cutoff = 1e-4, verbose = 0)
 #' 
 #' library(CRF)
 #' data(Small)
-#' d <- decode.trbp(small.crf)
+#' d <- decode.trbp(Small$crf)
 #'
 #' @export 
 decode.trbp <- function(crf, max.iter = 10000, cutoff = 1e-4, verbose = 0)
@@ -239,7 +239,7 @@ decode.trbp <- function(crf, max.iter = 10000, cutoff = 1e-4, verbose = 0)
 #' 
 #' library(CRF)
 #' data(Small)
-#' d <- decode.greedy(small.crf)
+#' d <- decode.greedy(Small$crf)
 #'
 #' @export 
 decode.greedy <- function(crf, restart = 0, start = apply(crf$node.pot, 1, which.max))
@@ -261,7 +261,7 @@ decode.greedy <- function(crf, restart = 0, start = apply(crf$node.pot, 1, which
 #' 
 #' library(CRF)
 #' data(Small)
-#' d <- decode.icm(small.crf)
+#' d <- decode.icm(Small$crf)
 #'
 #' @export 
 decode.icm <- function(crf, restart = 0, start = apply(crf$node.pot, 1, which.max))
@@ -286,7 +286,7 @@ decode.icm <- function(crf, restart = 0, start = apply(crf$node.pot, 1, which.ma
 #' 
 #' library(CRF)
 #' data(Small)
-#' d <- decode.block(small.crf, list(c(1,3), c(2,4)))
+#' d <- decode.block(Small$crf, list(c(1,3), c(2,4)))
 #'
 #' @export 
 decode.block <- function(crf, blocks, decode.method = decode.tree, restart = 0, start = apply(crf$node.pot, 1, which.max), ...)
@@ -356,7 +356,7 @@ decode.block <- function(crf, blocks, decode.method = decode.tree, restart = 0,
 #' 
 #' library(CRF)
 #' data(Small)
-#' d <- decode.ilp(small.crf)
+#' d <- decode.ilp(Small$crf)
 #'
 #' @export 
 decode.ilp <- function(crf, lp.rounding = FALSE)

diff --git a/R/infer.R b/R/infer.R
@@ -14,7 +14,7 @@
 #' 
 #' library(CRF)
 #' data(Small)
-#' i <- infer.exact(small.crf)
+#' i <- infer.exact(Small$crf)
 #' 
 #' @export
 infer.exact <- function(crf)
@@ -38,7 +38,7 @@ infer.exact <- function(crf)
 #' 
 #' library(CRF)
 #' data(Small)
-#' i <- infer.chain(small.crf)
+#' i <- infer.chain(Small$crf)
 #' 
 #' @export
 infer.chain <- function(crf)
@@ -62,7 +62,7 @@ infer.chain <- function(crf)
 #' 
 #' library(CRF)
 #' data(Small)
-#' i <- infer.tree(small.crf)
+#' i <- infer.tree(Small$crf)
 #' 
 #' @export
 infer.tree <- function(crf)
@@ -89,7 +89,7 @@ infer.tree <- function(crf)
 #' 
 #' library(CRF)
 #' data(Small)
-#' i <- infer.conditional(small.crf, c(0,1,0,0), infer.exact)
+#' i <- infer.conditional(Small$crf, c(0,1,0,0), infer.exact)
 #' 
 #' @export
 infer.conditional <- function(crf, clamped, infer.method, ...)
@@ -133,7 +133,7 @@ infer.conditional <- function(crf, clamped, infer.method, ...)
 #' 
 #' library(CRF)
 #' data(Small)
-#' i <- infer.cutset(small.crf, c(2))
+#' i <- infer.cutset(Small$crf, c(2))
 #' 
 #' @export
 infer.cutset <- function(crf, cutset, engine = "default")
@@ -163,7 +163,7 @@ infer.cutset <- function(crf, cutset, engine = "default")
 #' 
 #' library(CRF)
 #' data(Small)
-#' i <- infer.junction(small.crf)
+#' i <- infer.junction(Small$crf)
 #' 
 #' @export
 infer.junction <- function(crf)
@@ -189,7 +189,7 @@ infer.junction <- function(crf)
 #' 
 #' library(CRF)
 #' data(Small)
-#' i <- infer.sample(small.crf, sample.exact, 10000)
+#' i <- infer.sample(Small$crf, sample.exact, 10000)
 #' 
 #' @export
 infer.sample <- function(crf, sample.method, ...)
@@ -216,7 +216,7 @@ infer.sample <- function(crf, sample.method, ...)
 #' 
 #' library(CRF)
 #' data(Small)
-#' i <- infer.lbp(small.crf)
+#' i <- infer.lbp(Small$crf)
 #' 
 #' @export
 infer.lbp <- function(crf, max.iter = 10000, cutoff = 1e-4, verbose = 0)
@@ -243,7 +243,7 @@ infer.lbp <- function(crf, max.iter = 10000, cutoff = 1e-4, verbose = 0)
 #' 
 #' library(CRF)
 #' data(Small)
-#' i <- infer.trbp(small.crf)
+#' i <- infer.trbp(Small$crf)
 #' 
 #' @export
 infer.trbp <- function(crf, max.iter = 10000, cutoff = 1e-4, verbose = 0)

diff --git a/R/sample.R b/R/sample.R
@@ -12,7 +12,7 @@
 #' 
 #' library(CRF)
 #' data(Small)
-#' s <- sample.exact(small.crf, 100)
+#' s <- sample.exact(Small$crf, 100)
 #' 
 #' @export
 sample.exact <- function(crf, size)
@@ -34,7 +34,7 @@ sample.exact <- function(crf, size)
 #' 
 #' library(CRF)
 #' data(Small)
-#' s <- sample.chain(small.crf, 100)
+#' s <- sample.chain(Small$crf, 100)
 #' 
 #' @export
 sample.chain <- function(crf, size)
@@ -56,7 +56,7 @@ sample.chain <- function(crf, size)
 #' 
 #' library(CRF)
 #' data(Small)
-#' s <- sample.tree(small.crf, 100)
+#' s <- sample.tree(Small$crf, 100)
 #' 
 #' @export
 sample.tree <- function(crf, size)
@@ -81,7 +81,7 @@ sample.tree <- function(crf, size)
 #' 
 #' library(CRF)
 #' data(Small)
-#' s <- sample.conditional(small.crf, 100, c(0,1,0,0), sample.exact)
+#' s <- sample.conditional(Small$crf, 100, c(0,1,0,0), sample.exact)
 #' 
 #' @export
 sample.conditional <- function(crf, size, clamped, sample.method, ...)
@@ -111,7 +111,7 @@ sample.conditional <- function(crf, size, clamped, sample.method, ...)
 #' 
 #' library(CRF)
 #' data(Small)
-#' s <- sample.cutset(small.crf, 100, c(2))
+#' s <- sample.cutset(Small$crf, 100, c(2))
 #' 
 #' @export
 sample.cutset <- function(crf, size, cutset, engine = "default")
@@ -139,7 +139,7 @@ sample.cutset <- function(crf, size, cutset, engine = "default")
 #' 
 #' library(CRF)
 #' data(Small)
-#' s <- sample.junction(small.crf, 100)
+#' s <- sample.junction(Small$crf, 100)
 #' 
 #' @export
 sample.junction <- function(crf, size)
@@ -163,7 +163,7 @@ sample.junction <- function(crf, size)
 #' 
 #' library(CRF)
 #' data(Small)
-#' s <- sample.gibbs(small.crf, 100)
+#' s <- sample.gibbs(Small$crf, 100)
 #' 
 #' @export
 sample.gibbs <- function(crf, size, burn.in = 1000, start = apply(crf$node.pot, 1, which.max))

diff --git a/data/Chain.RData b/data/Chain.RData
diff --git a/data/Clique.RData b/data/Clique.RData
diff --git a/data/Loop.RData b/data/Loop.RData
diff --git a/data/Rain.RData b/data/Rain.RData
diff --git a/data/Small.RData b/data/Small.RData
diff --git a/data/Tree.RData b/data/Tree.RData
diff --git a/man/CRF-package.Rd b/man/CRF-package.Rd
@@ -95,9 +95,9 @@ model }
 \examples{
 library(CRF)
 data(Small)
-decode.exact(small.crf)
-infer.exact(small.crf)
-sample.exact(small.crf, 100)
+decode.exact(Small$crf)
+infer.exact(Small$crf)
+sample.exact(Small$crf, 100)
 }
 \author{
 Ling-Yun Wu \email{wulingyun@gmail.com}

diff --git a/man/clamp.crf.Rd b/man/clamp.crf.Rd
@@ -34,7 +34,7 @@ on the clamped vector.
 \examples{
 library(CRF)
 data(Small)
-crf <- clamp.crf(small.crf, c(0, 0, 1, 1))
+crf <- clamp.crf(Small$crf, c(0, 0, 1, 1))
 }
 \seealso{
 \code{\link{make.crf}}, \code{\link{sub.crf}},

diff --git a/man/clamp.reset.Rd b/man/clamp.reset.Rd
@@ -26,7 +26,7 @@ the conditional potentials based on the clamped vector.
 \examples{
 library(CRF)
 data(Small)
-crf <- clamp.crf(small.crf, c(0, 0, 1, 1))
+crf <- clamp.crf(Small$crf, c(0, 0, 1, 1))
 clamp.reset(crf, c(0,0,2,2))
 }
 \seealso{

diff --git a/man/decode.block.Rd b/man/decode.block.Rd
@@ -32,6 +32,6 @@ modes algorithm
 \examples{
 library(CRF)
 data(Small)
-d <- decode.block(small.crf, list(c(1,3), c(2,4)))
+d <- decode.block(Small$crf, list(c(1,3), c(2,4)))
 }
 
diff --git a/man/decode.chain.Rd b/man/decode.chain.Rd
@@ -21,6 +21,6 @@ algorithm.
 \examples{
 library(CRF)
 data(Small)
-d <- decode.chain(small.crf)
+d <- decode.chain(Small$crf)
 }
 
diff --git a/man/decode.conditional.Rd b/man/decode.conditional.Rd
@@ -27,6 +27,6 @@ input)
 \examples{
 library(CRF)
 data(Small)
-d <- decode.conditional(small.crf, c(0,1,0,0), decode.exact)
+d <- decode.conditional(Small$crf, c(0,1,0,0), decode.exact)
 }
 
diff --git a/man/decode.cutset.Rd b/man/decode.cutset.Rd
@@ -30,6 +30,6 @@ conditioning
 \examples{
 library(CRF)
 data(Small)
-d <- decode.cutset(small.crf, c(2))
+d <- decode.cutset(Small$crf, c(2))
 }
 
diff --git a/man/decode.exact.Rd b/man/decode.exact.Rd
@@ -20,6 +20,6 @@ Exact decoding for small graphs with brute-force search
 \examples{
 library(CRF)
 data(Small)
-d <- decode.exact(small.crf)
+d <- decode.exact(Small$crf)
 }