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updated package was returning wrong variable

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1 parent fe901d6 commit c36454331a14dac721fe87c7430bb9d8377d1606 @anasrana committed Nov 24, 2013
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+* State Transitions using Aggregate Markov Models
+
+** Installation
+Please download the *stamm_[version].tar.gz* and install package in R.
+
+** Load Package anad Data
+Once installed you can load the package with
+#+BEGIN_SRC R
+library(stamm)
+#+END_SRC
+
+There is a demo data set included in the package you can load them as follows:
+#+BEGIN_SRC R
+data(gdat) # simulated expression data
+data(tdat) # time points
+data(sim_data) # full simulation data
+#+END_SRC
+
+** Example code
+Also included is an example code file to obain main results
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+library(stamm)
+
+data(gdat)
+data(tdat)
+data(sim_data)
+
+
+fit.km <- StammKmeans(g.dat, m.v=2:30, iter.max=1000, nstart=500)
+print(fit.km$kmeans.plot)
+
+StammMSEcv.K(g.dat, t.dat, k.states=1:5, hat.m=13, n.core=50, l.pen=0, return.all=FALSE)
+StammMSEcv.m(g.dat, t.dat, m.cl=12:20, k.states=1:5, n.core=50, l.pen=0)
+
+StammMSEcvK.plot(mse, k.states)
+StammStab.plot(fit.k, m.v, m.init=2)
+StammStabPen.plot(fit, fit.m, t.dat)
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-Package: stamm
-Type: Package
-Title: State Transitions using Aggregated Markov Models
-Version: 0.8
-Date: 2013-11-23
-Author: Anas A Rana
-Maintainer: Anas A Rana<anas.rana@gmail.com>
-Description: More about what it does (maybe more than one line)
-Depends: ggplot2, grid, stats, expm, msm, tmvtnorm, multicore
-License: What license is it under?
-Built: R 3.0.1; ; 2013-11-24 19:19:28 UTC; unix
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-exportPattern("^[[:alpha:]]+")
@@ -1,27 +0,0 @@
-# File share/R/nspackloader.R
-# Part of the R package, http://www.R-project.org
-#
-# Copyright (C) 1995-2012 The R Core Team
-#
-# This program is free software; you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 2 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# A copy of the GNU General Public License is available at
-# http://www.r-project.org/Licenses/
-
-local({
- info <- loadingNamespaceInfo()
- pkg <- info$pkgname
- ns <- .getNamespace(as.name(pkg))
- if (is.null(ns))
- stop("cannot find namespace environment for ", pkg, domain = NA);
- dbbase <- file.path(info$libname, pkg, "R", pkg)
- lazyLoad(dbbase, ns, filter = function(n) n != ".__NAMESPACE__.")
-})
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@@ -1,22 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html><head><title>R: State Transitions using Aggregated Markov Models</title>
-<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
-<link rel="stylesheet" type="text/css" href="R.css">
-</head><body>
-<h1> State Transitions using Aggregated Markov Models
-<img class="toplogo" src="../../../doc/html/logo.jpg" alt="[R logo]">
-</h1>
-<hr>
-<div align="center">
-<a href="../../../doc/html/packages.html"><img src="../../../doc/html/left.jpg" alt="[Up]" width="30" height="30" border="0"></a>
-<a href="../../../doc/html/index.html"><img src="../../../doc/html/up.jpg" alt="[Top]" width="30" height="30" border="0"></a>
-</div><h2>Documentation for package &lsquo;stamm&rsquo; version 0.8</h2>
-
-<ul><li><a href="../DESCRIPTION">DESCRIPTION file</a>.</li>
-</ul>
-
-<h2>Help Pages</h2>
-
-
-There are no help pages in this package
-</body></html>
@@ -1,57 +0,0 @@
-BODY{ background: white;
- color: black }
-
-A:link{ background: white;
- color: blue }
-A:visited{ background: white;
- color: rgb(50%, 0%, 50%) }
-
-H1{ background: white;
- color: rgb(55%, 55%, 55%);
- font-family: monospace;
- font-size: x-large;
- text-align: center }
-
-H2{ background: white;
- color: rgb(40%, 40%, 40%);
- font-family: monospace;
- font-size: large;
- text-align: center }
-
-H3{ background: white;
- color: rgb(40%, 40%, 40%);
- font-family: monospace;
- font-size: large }
-
-H4{ background: white;
- color: rgb(40%, 40%, 40%);
- font-family: monospace;
- font-style: italic;
- font-size: large }
-
-H5{ background: white;
- color: rgb(40%, 40%, 40%);
- font-family: monospace }
-
-H6{ background: white;
- color: rgb(40%, 40%, 40%);
- font-family: monospace;
- font-style: italic }
-
-IMG.toplogo{ vertical-align: middle }
-
-IMG.arrow{ width: 30px;
- height: 30px;
- border: 0 }
-
-span.acronym{font-size: small}
-span.env{font-family: monospace}
-span.file{font-family: monospace}
-span.option{font-family: monospace}
-span.pkg{font-weight: bold}
-span.samp{font-family: monospace}
-
-div.vignettes a:hover {
- background: rgb(85%, 85%, 85%);
-}
-
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@@ -63,14 +63,14 @@ DLmse <- function(fit, loop.var, t.dat, g.dat) {
StammKmeans.plot <- function(DeltaJ, m.vec, x.lab='No. of clusters, m', y.lab=expression(paste(Delta, "J")), p.title=" ") {
km.cl <- data.frame(m=m.vec, within.ss=DeltaJ)
- ggplot(km.cl, aes(x=m, y=within.ss)) +
+ km.plot <- ggplot(km.cl, aes(x=m, y=within.ss)) +
geom_hline(aes(yintercept=0.1), col='gray', size=1.5, linetype='dashed') +
geom_point(size=4) +
geom_line() +
xlab(x.lab) +
ylab(y.lab) +
ggtitle(p.title)
- return(km.cl)
+ return(km.plot)
}
## ********************************************************************************
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