enable continuous integration via craigcitro/r-travis

.Rbuildignore

@@ -1,3 +1,4 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
-.gitignore
+^\.gitignore$
+^\.travis\.yml$

.travis.yml

@@ -0,0 +1,18 @@
+# Sample .travis.yml for R projects.
+#
+# See README.md for instructions, or for more configuration options,
+# see the wiki:
+#   https://github.com/craigcitro/r-travis/wiki
+
+language: c
+script: ./travis-tool.sh run_tests
+before_install:
+  - curl -OL http://raw.github.com/craigcitro/r-travis/master/scripts/travis-tool.sh
+  - chmod 755 ./travis-tool.sh
+  - ./travis-tool.sh bootstrap
+install:
+  - ./travis-tool.sh install_deps
+notifications:
+  email:
+    on_success: change
+    on_failure: change

DESCRIPTION

@@ -3,7 +3,7 @@ Type: Package
 Title: Miscellaneous functions provided by Dason
 Version: 0.1
 Date: 2012-10-01
-Author@R: c(person("Dason", "Kurkiewicz",
+Authors@R: c(person("Dason", "Kurkiewicz",
     role = c("aut", "ctb", "cre"),
     email = "dasonk@iastate.edu"))
 Author: Dason Kurkiewicz
@@ -22,7 +22,7 @@ Collate:
     'sinkReset.R'
     'permutations.R'
     'getArgs.R'
-    'holtWinters.R'
+    'holtwinters.R'
     'linFinder.R'
     'shadePlot.R'
     'trainTest.R'

NAMESPACE

@@ -1,7 +1,10 @@
 export(getArgs)
-export(goldenRatioRolors)
+export(goldenRatioColors)
+export(holm)
 export(linFinder)
+export(lsos)
 export(permutations)
+export(qvalue)
 export(shadePlot)
 export(sinkReset)
 export(trainTest)

R/goldenRatioColors.R

@@ -17,7 +17,7 @@
 #' xs <- seq(1, n)
 #' plot(c(1, n+1), c(0, 1), type = "n")
 #' rect(xs, 0, xs + 1, 1, col = goldenRatioColors(n))
-goldenRatioRolors <- function(n, s = .5, v = 1, alpha = 1){
+goldenRatioColors <- function(n, s = .5, v = 1, alpha = 1){
     GR <- 2/(1 + sqrt(5))
     hues <- (seq(0, n-1) * GR) %% 1
     cols <- hsv(hues, s, v, alpha)

R/holm.R

@@ -3,6 +3,7 @@
 #' Transform p-values based on Holm's method
 #' 
 #' @param p Numeric. The p-values to adjust
+#' @export
 #' @examples
 #' p <- c(.042, .001, .031, .014, .007)
 #' p.adjust(p, "holm")

R/holtWinters.R → R/holtwinters.R

@@ -5,7 +5,7 @@
 #' @param y Vector. The data to smooth.
 #' @param alpha Numeric.  A smoothing parameter
 #' @param beta Numeric. A smoothing parameter
-holtWinters <- function(y, alpha = .5, beta = .5){
+holtwinters <- function(y, alpha = .5, beta = .5){
     n <- length(y)
     yhat <- numeric(n)
     yhat[1:2] <- NA

R/lsos.R

@@ -11,8 +11,10 @@
 #' @param head logical. Use head on the output?
 #' @param n numeric. Number of objects to display is head is TRUE
 #' @author Dirk Eddelbuettel, Tony Breyal
+#' @export
 #' @examples
 #' lsos()
+#' lsos(pos = 2, n = 5)
 #' \dontrun{
 #' a <- rnorm(100000)
 #' b <- matrix(1, 1000, 100)
@@ -23,19 +25,27 @@ lsos <- function (pos = 1, pattern, order.by = "Size",
     napply <- function(names, fn) sapply(names, function(x)
         fn(get(x, pos = pos)))
     names <- ls(pos = pos, pattern = pattern)
-    obj.class <- napply(names, function(x) as.character(class(x))[1])
-    obj.mode <- napply(names, mode)
-    obj.type <- ifelse(is.na(obj.class), obj.mode, obj.class)
-    obj.prettysize <- napply(names, function(x) {
-        capture.output(print(object.size(x), units = "auto")) })
-    obj.size <- napply(names, object.size)
-    obj.dim <- t(napply(names, function(x)
-        as.numeric(dim(x))[1:2]))
-    vec <- is.na(obj.dim)[, 1] & (obj.type != "function")
-    obj.dim[vec, 1] <- napply(names, length)[vec]
+    if (length(names) > 0) {
+        obj.class <- napply(names, function(x) as.character(class(x))[1])
+        obj.mode <- napply(names, mode)
+        obj.prettysize <- napply(names, function(x) {
+            capture.output(print(object.size(x), units = "auto")) })
+        obj.size <- napply(names, object.size)
+        obj.dim <- t(napply(names, function(x) as.numeric(dim(x))[1:2]))
+        obj.type <- ifelse(is.na(obj.class), obj.mode, obj.class)
+        vec <- is.na(obj.dim)[, 1] & (obj.type != "function")
+        obj.dim[vec, 1] <- napply(names, length)[vec]
+    } else {
+        obj.class <- character()
+        obj.mode <- character()
+        obj.prettysize <- character()
+        obj.size <- integer()
+        obj.dim <- data.frame(Rows=integer(), Columns=integer())
+        obj.type <- character()
+    }
     out <- data.frame(obj.type, obj.size, obj.prettysize, obj.dim)
     names(out) <- c("Type", "Size", "PrettySize", "Rows", "Columns")
-    if (!missing(order.by))
+    if (!is.null(order.by) || !is.na(order.by))
         out <- out[order(out[[order.by]], decreasing=decreasing), ]
     if (head)
         out <- head(out, n)

R/qvalue.R

@@ -5,6 +5,7 @@
 #' @param p Numeric. The p-values to adjust
 #' @param m Numeric. The estimated number of true nulls
 #' 
+#' @export
 #' @examples
 #' pval <- rbeta(100, 1, 3)
 #' qvalue(pval)
@@ -15,7 +16,7 @@ qvalue <- function(p, m = length(p)){
     # sort the values
     tmp <- p[id]
     # Do the adjustment
-    qval <- tmp*m/(1:n)
+    qval <- tmp*m/(1:m)
     # Make sure that if p1 < p2 that q1 <= q2
     qval <- rev(cummin(rev(qval)))
     # We could improvate that by doing the sorting in the opposite

man/goldenRatioColors.Rd

@@ -1,8 +1,8 @@
-\name{goldenratiocolors}
-\alias{goldenratiocolors}
+\name{goldenRatioColors}
+\alias{goldenRatioColors}
 \title{Choose n colors using the golden ratio}
 \usage{
-  goldenratiocolors(n, s = 0.5, v = 1, alpha = 1)
+  goldenRatioColors(n, s = 0.5, v = 1, alpha = 1)
 }
 \arguments{
   \item{n}{Integer.  The number of colors you want}
@@ -20,12 +20,12 @@
   ratio.
 }
 \examples{
-cols <- goldenratiocolors(5)
+cols <- goldenRatioColors(5)
 plot(1:5, 1:5, col = cols)
 
 n <- 5
 xs <- seq(1, n)
 plot(c(1, n+1), c(0, 1), type = "n")
-rect(xs, 0, xs + 1, 1, col = goldenratiocolors(n))
+rect(xs, 0, xs + 1, 1, col = goldenRatioColors(n))
 }
 

man/holtwinters.Rd

@@ -4,6 +4,13 @@
 \usage{
   holtwinters(y, alpha = 0.5, beta = 0.5)
 }
+\arguments{
+  \item{y}{Vector. The data to smooth.}
+
+  \item{alpha}{Numeric.  A smoothing parameter}
+
+  \item{beta}{Numeric. A smoothing parameter}
+}
 \description{
   Holt winters smoothing with no seasonality
 }

man/permutations.Rd

@@ -18,7 +18,7 @@
 }
 \examples{
 permutations(1:3)
-permuations(c("a", "b", "c"))
+permutations(c("a", "b", "c"))
 permutations(c("raptors", "are", "horrible"))
 }