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Commit 3e46b8d9 authored by Antoine Lucas's avatar Antoine Lucas
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new modif

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R/dist.R
View file @ 3e46b8d9
Dist <- function(x, method="euclidean", nbproc = 1, diag=FALSE, upper=FALSE)
Dist <- function(x, method="euclidean", nbproc = 2, diag=FALSE, upper=FALSE)
{
if(class(x) == "exprSet")
......
man/dist.Rd
View file @ 3e46b8d9
\name{Dist}
\title{Distance Matrix Computation}
\usage{
Dist(x, method = "euclidean", nbproc = 1, diag = FALSE, upper = FALSE)
Dist(x, method = "euclidean", nbproc = 2, diag = FALSE, upper = FALSE)
}
\alias{Dist}
......@@ -118,6 +118,8 @@ Dist(x, method = "euclidean", nbproc = 1, diag = FALSE, upper = FALSE)
\url{http://en.wikipedia.org/wiki/Kendall_tau_distance}
}
\note{Multi-thread (parallelisation) is disable on Windows.}
\seealso{
\code{\link[cluster]{daisy}} in the \file{cluster} package with more
possibilities in the case of \emph{mixed} (contiuous / categorical)
......
man/hcluster.Rd
View file @ 3e46b8d9
......@@ -31,7 +31,8 @@ hcluster(x, method = "euclidean", diag = FALSE, upper = FALSE,
\code{"average"}, \code{"mcquitty"}, \code{"median"} or
\code{"centroid"}.}
\item{members}{\code{NULL} or a vector with length size of \code{d}.}
\item{nbproc}{integer, number of subprocess for parallelization}
\item{nbproc}{integer, number of subprocess for parallelization [Linux
& Mac only]}
\item{doubleprecision}{True: use of double precision for distance
matrix computation; False: use simple precision}
......@@ -87,6 +88,9 @@ hcluster(x, method = "euclidean", diag = FALSE, upper = FALSE,
For more details, see documentation of \code{hclust} and \code{dist}.
}
\note{Multi-thread (parallelisation) is disable on Windows.}
\author{
The \code{hcluster} function is based on C code adapted from Cran
Fortran routine
......
src/distance_T.cpp
View file @ 3e46b8d9
......@@ -2,7 +2,7 @@
* \brief all functions requiered for R dist function and C hcluster function.
*
* \date Created: probably in 1995
* \date Last modified: Time-stamp: <2005-10-09 13:12:06 antoine>
* \date Last modified: Time-stamp: <2007-10-03 20:05:41 antoine>
*
* \author R core members, and lately: Antoine Lucas
*
......@@ -393,9 +393,38 @@ template<class T> T distance_T<T>::R_correlation(double * x, double * y , int n
return 1 - (num / denum);
}
/** \brief Spearman distance (rank base metric)
* \note Added by A. Lucas
*/
// ---------------------------------------------------------
// Distance Spearman
//
// Spearman distance between 2 vectors a,b is
// d = sum_i (rank(a_i) - rank(b_i) )^2
//
// If one NA found: return NA
//
// This function compute distance between 2 vectors x[i1,] & y[i2,]
// x and y are matrix; we use here only line i1 from x and
// line i2 from y. Number of column (nc) is the same in x and y,
// number of column can differ (nr_x, nr_y).
//
// Flag will be set to 0 if NA value computed in distance
//
// When call by function distance or hclust, x and y are the same; it computes
// distance between vector x[i1,] and x[i2,]
//
// \param x matrix of size nr_x * nc; line i1 is of interest
// \param y matrix of size nr_y * nc; line i1 is of interest
// \param nr_x number of row in matrix x
// \param nr_y number of row in matrix y
// \param nc number of column in matrix x or y
// \param i1 row choosen in matrix x
// \param i2 row choosen in matrix y
// \param flag set to 0 if NA value computed in distance
// \param opt: a set of 6 vectors of size nc, allocated but uninitialised.
// aim of this parameter is to avoid several vector allocation
//
// Return: distance value
//
// ---------------------------------------------------------
template<class T> T distance_T<T>::R_spearman(double * x, double * y , int nr_x, int nr_y, int nc,
int i1, int i2,
int * flag, T_tri & opt)
......@@ -503,11 +532,41 @@ template<class T> T distance_T<T>::R_kendall_corr(double * x, double * y , int
}
*/
/** \brief Kendall distance (rank base metric)
*
*
* \note Added by A. Lucas
*/
// ---------------------------------------------------------
// Distance Kendall
//
// Kendall distance between 2 vectors a,b is
// d = sum_i Kij (x,y)
//
// With Kij(x,y) is 0 if xi,xj in same order as yi,yj;
// 1 if not
//
// If one NA found: return NA
//
// This function compute distance between 2 vectors x[i1,] & y[i2,]
// x and y are matrix; we use here only line i1 from x and
// line i2 from y. Number of column (nc) is the same in x and y,
// number of column can differ (nr_x, nr_y).
//
// Flag will be set to 0 if NA value computed in distance
//
// When call by function distance or hclust, x and y are the same; it computes
// distance between vector x[i1,] and x[i2,]
//
// \param x matrix of size nr_x * nc; line i1 is of interest
// \param y matrix of size nr_y * nc; line i1 is of interest
// \param nr_x number of row in matrix x
// \param nr_y number of row in matrix y
// \param nc number of column in matrix x or y
// \param i1 row choosen in matrix x
// \param i2 row choosen in matrix y
// \param flag set to 0 if NA value computed in distance
// \param opt: a set of 6 vectors of size nc, allocated but uninitialised.
// aim of this parameter is to avoid several vector allocation
//
// Return: distance value
//
// ---------------------------------------------------------
template<class T> T distance_T<T>::R_kendall(double * x, double * y , int nr_x, int nr_y, int nc,
int i1, int i2,
int * flag, T_tri & opt)
......@@ -562,19 +621,21 @@ template<class T> T distance_T<T>::R_kendall(double * x, double * y , int nr_x,
}
/**
* R_distance: compute parallelized distance. Function called direclty by R
* \brief compute distance and call function thread_dist
* that call one of function R_euclidean or R_...
* \param x input matrix
* \param nr,nc number of row and columns
* nr individuals with nc values.
* \param d distance half matrix.
* \param diag if we compute diagonal of dist matrix (usualy: no).
* \param method 1, 2,... method used
* \param nbprocess: number of threads to create
* \param ierr error return; 1 good; 0 missing values
*/
// ---------------------------------------------------------
//
// R_distance: compute parallelized distance. Function called direclty by R
// \brief compute distance and call function thread_dist
// that call one of function R_euclidean or R_...
// \param x input matrix
// \param nr,nc number of row and columns
// nr individuals with nc values.
// \param d distance half matrix.
// \param diag if we compute diagonal of dist matrix (usualy: no).
// \param method 1, 2,... method used
// \param nbprocess: number of threads to create
// \param ierr error return; 1 good; 0 missing values
//
// ---------------------------------------------------------
template<class T> void distance_T<T>::distance(double *x, int *nr,
int *nc, T *d, int *diag,
int *method,int *nbprocess,
......@@ -777,24 +838,24 @@ template <class T> void* distance_T<T>::thread_dist(void* arguments_void)
/**
* R_distance_kms: compute distance between individual i1 and
* centroid i2
* \brief compute distance and call one of function R_euclidean or R_...
* \brief This function is called by kmeans_Lloyd2
* \param x input matrix (individuals)
* \param y input matrix (centroids)
* \param nr1,nr2,nc number of row (nr1:x, nr2:y) and columns
* nr individuals with nc values.
* \param i1, i2: indice of individuals (individual i1, centroid i2)
* \param method 1, 2,... method used
* \param ierr for NA 0 if no value can be comuted due to NA
* \param opt optional parameter send to spearman dist.
*/
// ---------------------------------------------------------
//
// R_distance_kms: compute distance between individual i1 and
// centroid i2
//
// compute distance and call one of function R_euclidean or R_...
// This function is called by kmeans_Lloyd2
//
// \param x input matrix (individuals)
// \param y input matrix (centroids)
// \param nr1,nr2,nc number of row (nr1:x, nr2:y) and columns
// nr individuals with nc values.
// \param i1, i2: indice of individuals (individual i1, centroid i2)
// \param method 1, 2,... method used
// \param ierr for NA 0 if no value can be comuted due to NA
// \param opt optional parameter send to spearman dist.
//
// ---------------------------------------------------------
template <class T> T distance_T<T>::distance_kms(double *x,double *y, int nr1,int nr2, int nc,int i1,int i2, int *method,
int * ierr, T_tri & opt)
{
......@@ -809,7 +870,7 @@ template <class T> T distance_T<T>::distance_kms(double *x,double *y, int nr1,in
T (*distfun)(double*,double*,int, int, int, int, int, int *, T_tri &) = NULL;
// choice of distance
switch(*method) {
case EUCLIDEAN:
distfun = R_euclidean;
......@@ -842,7 +903,8 @@ template <class T> T distance_T<T>::distance_kms(double *x,double *y, int nr1,in
default:
error("distance(): invalid distance");
}
// here: distance computation
res = distfun(x,y, nr1,nr2, nc, i1, i2,ierr, opt);
return( res);
}
src/distance_T.h
View file @ 3e46b8d9
......@@ -50,6 +50,20 @@ template<class T> class distance_T
public:
/** \brief R_distance compute parallelized distance.
*
* compute distance and call function thread_dist
* that call one of function R_euclidean or R_...
*
* \param x input matrix
* \param nr,nc number of row and columns
* nr individuals with nc values.
* \param d distance half matrix.
* \param diag if we compute diagonal of dist matrix (usualy: no).
* \param method 1, 2,... method used (correspond to the enum)
* \param nbprocess: number of threads to create
* \param ierr error return; 1 good; 0 missing values
*/
static void distance(double *x, int *nr, int *nc, T *d, int *diag,
int *method,int *nbprocess, int * ierr);
......@@ -65,7 +79,7 @@ template<class T> class distance_T
* \param nr1,nr2,nc number of row (nr1:x, nr2:y) and columns
* nr individuals with nc values.
* \param i1, i2: indice of individuals (individual i1, centroid i2)
* \param method 1, 2,... method used
* \param method 1, 2,... method used (correspond to the enum)
* \param ierr for NA 0 if no value can be comuted due to NA
* \param opt optional parameter required for spearman
*/
......
src/hclust.cpp
View file @ 3e46b8d9
......@@ -3,7 +3,7 @@
* \brief Hierarchical Clustering.
*
* \date Created : 14/11/02
* \date Last Modified : Time-stamp: <2005-10-09 14:43:14 antoine>
* \date Last Modified : Time-stamp: <2007-10-03 20:33:11 antoine>
*
* \author F. Murtagh, ESA/ESO/STECF, Garching, February 1986.
......@@ -122,20 +122,6 @@ void hcluster(double *x, int *nr, int *nc, int *diag, int *method, int *iopt ,in
/** Return indice
* \brief The upper half diagonal distance matrix is stored as a vector...
* so distance between individual i and j is stored at postion ioffst(i,j)
* \param n number of individuals (distance matrix is nxn)
* \param i,j: indices in matrix
*/
int ioffst(int n,int i,int j)
/* Map row I and column J of upper half diagonal symmetric matrix
* onto vector. i < j
*/
{
return j+i*n-(i+1)*(i+2)/2 ;
}
/*+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/
/* */
......@@ -162,18 +148,7 @@ int ioffst(int n,int i,int j)
/* */
/*-------------------------------------------------------------*/
/** Hierachical clustering subroutine
* \brief compute hierachical clustering from a distance matrix
* This routine is called by hclust
* \param n number of individuals
* \param ia, ib result (merge)
* \param iia, iib result (merge)
* \param iorder result (order)
*
* \note this is an adaptation of the fortran function designed from the
* R core team.
*/
void hcass2( int *n, int *ia, int *ib,int *iorder, int *iia, int *iib)
void hierclust::hcass2( int *n, int *ia, int *ib,int *iorder, int *iia, int *iib)
{
int i,j,k,k1,k2,loc;
......
src/hclust.h
View file @ 3e46b8d9
......@@ -6,8 +6,20 @@ extern "C"
void hcluster(double *x, int *nr, int *nc, int *diag, int *method, int *iopt ,int *ia , int *ib,int *iorder,double *crit,double *membr,int *nbprocess,int * precision, int * result);
int ioffst(int n,int i,int j);
};
namespace hierclust
{
/** Hierachical clustering subroutine
* \brief compute hierachical clustering from a distance matrix
* This routine is called by hclust
* \param n number of individuals
* \param ia, ib result (merge)
* \param iia, iib result (merge)
* \param iorder result (order)
*
* \note this is an adaptation of the fortran function designed from the
* R core team.
*/
void hcass2( int *n, int *ia, int *ib,int *iorder, int *iia, int *iib);
}
};
src/hclust_T.cpp
View file @ 3e46b8d9
......@@ -296,7 +296,7 @@ namespace hclust_T
hcass2(n,ia,ib,iorder,iia,iib);
hierclust::hcass2(n,ia,ib,iorder,iia,iib);
/*
......
src/hclust_T.h
View file @ 3e46b8d9
......@@ -17,6 +17,19 @@ namespace hclust_T
double *membr,T *diss,int *result);
/** \brief Return indice
*
* The upper half diagonal distance matrix is stored as a vector...
* so distance between individual i and j is stored at postion ioffst(i,j)
*
* \param n number of individuals (distance matrix is nxn)
* \param i,j: indices in matrix
*/
inline int ioffst(int n,int i,int j)
{
return j+i*n-(i+1)*(i+2)/2 ;
}
}
#endif
......
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