From: Benjamin Auder Date: Mon, 2 Feb 2015 15:42:38 +0000 (+0100) Subject: add documentation (remove .gitignore under man/) X-Git-Url: https://git.auder.net/variants/Chakart/img/doc/css/app_dev.php?a=commitdiff_plain;h=f310ba7f9b7654597890ecec1edd68aa2fe39509;p=synclust.git add documentation (remove .gitignore under man/) --- diff --git a/man/.gitignore b/man/.gitignore deleted file mode 100644 index d6b7ef3..0000000 --- a/man/.gitignore +++ /dev/null @@ -1,2 +0,0 @@ -* -!.gitignore diff --git a/man/drawMapWithSites.Rd b/man/drawMapWithSites.Rd new file mode 100644 index 0000000..e71bc95 --- /dev/null +++ b/man/drawMapWithSites.Rd @@ -0,0 +1,16 @@ +% Generated by roxygen2 (4.0.2): do not edit by hand +\name{drawMapWithSites} +\alias{drawMapWithSites} +\title{Draw (France or...) map with all sites of colors 'cols'} +\usage{ +drawMapWithSites(M, cols = rep(1, nrow(M))) +} +\arguments{ +\item{M}{Coordinates matrix (in columns)} + +\item{cols}{Vector of colors for each row of M [default: all black]} +} +\description{ +Draw (France or...) map with all sites of colors 'cols' +} + diff --git a/man/drawNeighborhoodGraph.Rd b/man/drawNeighborhoodGraph.Rd new file mode 100644 index 0000000..6ad5b46 --- /dev/null +++ b/man/drawNeighborhoodGraph.Rd @@ -0,0 +1,16 @@ +% Generated by roxygen2 (4.0.2): do not edit by hand +\name{drawNeighborhoodGraph} +\alias{drawNeighborhoodGraph} +\title{Draw neighborhoods graph on top of a country map (or any other map)} +\usage{ +drawNeighborhoodGraph(M, NI) +} +\arguments{ +\item{M}{Coordinates matrix (in columns)} + +\item{NI}{Neighborhoods of M rows (list of integer vectors)} +} +\description{ +Draw neighborhoods graph on top of a country map (or any other map) +} + diff --git a/man/findSyncVarRegions.Rd b/man/findSyncVarRegions.Rd new file mode 100644 index 0000000..2008da6 --- /dev/null +++ b/man/findSyncVarRegions.Rd @@ -0,0 +1,63 @@ +% Generated by roxygen2 (4.0.2): do not edit by hand +\name{findSyncVarRegions} +\alias{findSyncVarRegions} +\title{Direct clustering from a neighborhoods graph, or get regions from (Poisson) +distribution parameters optimization, using convex relaxation.} +\usage{ +findSyncVarRegions(method, M, k, alpha, gmode, K, dtype, cmeth, pcoef = 1, + h = 0.001, eps = 0.001, maxit = 1000, showLL = TRUE, disp = TRUE) +} +\arguments{ +\item{method}{Global method: "direct" or "convex"} + +\item{M}{Matrix of observations in rows, the two last columns +corresponding to geographic coordinates; +set to NULL to use our initial dataset (625 rows / 9 years)} + +\item{k}{Number of neighbors} + +\item{alpha}{Weight parameter for intra-neighborhoods distance computations; +0 = take only geographic coordinates into account; +1 = take only observations over the years into account; +in-between : several levels of compromise; +-1 or any negative value : use a heuristic to choose alpha.} + +\item{gmode}{Neighborhood type. 0 = reduced [mutual] kNN; 1 = augmented kNN (symmetric); +2 = normal kNN; 3 = one NN in each quadrant; (NON-symmetric). +NOTE: gmode==3 automatically sets k==4 (at most!)} + +\item{K}{Number of clusters} + +\item{dtype}{Distance type, in {"simple","spath","ectd"}. +NOTE: better avoid "simple" if gmode>=2} + +\item{cmeth}{Clustering method, in {"KM","HC","spec"} for k-means (distances based) +or hierarchical clustering, or spectral clustering (only if gmode>=2)} + +\item{pcoef}{Penalty value for convex optimization [default: 1.0]} + +\item{h}{Step in the min LL algorithm [default: 1e-3]} + +\item{eps}{Threshold to stop min.LL iterations [default: 1e-3]} + +\item{maxit}{Maximum number of iterations in the min LL algo [default: 1e3]} + +\item{showLL}{Print trace of log-likelihood evolution [default: true]} + +\item{disp}{True [default] for interactive display (otherwise nothing gets plotted)} +} +\value{ +list with the following entries. M: data matrix in input; NI: computed neighborhoods; + dists: computed distances matrix; clusts: partition into K clusters, as an integer vector; + cxpar: parameters obtained after convex optimization (if applicable) +} +\description{ +Direct clustering from a neighborhoods graph, or get regions from (Poisson) +distribution parameters optimization, using convex relaxation. +} +\examples{ +cvr = findSyncVarRegions("convex",M=NULL,k=10,alpha=0.1,gmode=1,K=5,dtype="spath",cmeth="HC") +drawMapWithSitez(cvr$M, cvr$clusters) +drawNeighboroodGraph(cvr$M, cvr$NI) +} + diff --git a/man/plotCurves.Rd b/man/plotCurves.Rd new file mode 100644 index 0000000..e83c5c9 --- /dev/null +++ b/man/plotCurves.Rd @@ -0,0 +1,16 @@ +% Generated by roxygen2 (4.0.2): do not edit by hand +\name{plotCurves} +\alias{plotCurves} +\title{Plot a matrix of curves (in rows)} +\usage{ +plotCurves(M, cols = rep(1, nrow(M))) +} +\arguments{ +\item{M}{Coordinates matrix (in columns)} + +\item{cols}{Vector of colors for each row of M [default: all black]} +} +\description{ +Plot a matrix of curves (in rows) +} +