From 94b35816ba76a7885db61489fcf1c8258164dc4d Mon Sep 17 00:00:00 2001
From: dicook <visnut@gmail.com>
Date: Wed, 26 Jun 2024 00:23:45 +1000
Subject: [PATCH] only change to norm_bin docus

---
 man/anomaly_index.Rd       | 12 +++++++
 man/guided_anomaly_tour.Rd | 67 ++++++++++++++++++++++++++++++++++++++
 man/mahal_dist.Rd          | 18 ++++++++++
 man/norm_bin.Rd            |  4 +--
 4 files changed, 99 insertions(+), 2 deletions(-)
 create mode 100644 man/anomaly_index.Rd
 create mode 100644 man/guided_anomaly_tour.Rd
 create mode 100644 man/mahal_dist.Rd

diff --git a/man/anomaly_index.Rd b/man/anomaly_index.Rd
new file mode 100644
index 00000000..299c5b01
--- /dev/null
+++ b/man/anomaly_index.Rd
@@ -0,0 +1,12 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/anomaly-pursuit.r
+\name{anomaly_index}
+\alias{anomaly_index}
+\title{Anomaly index.}
+\usage{
+anomaly_index()
+}
+\description{
+Calculates an index that looks for the best projection of
+observations that are outside a pre-determined p-D ellipse.
+}
diff --git a/man/guided_anomaly_tour.Rd b/man/guided_anomaly_tour.Rd
new file mode 100644
index 00000000..a9e81f27
--- /dev/null
+++ b/man/guided_anomaly_tour.Rd
@@ -0,0 +1,67 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/tour-guided-anomaly.r
+\name{guided_anomaly_tour}
+\alias{guided_anomaly_tour}
+\title{A guided anomaly tour path.}
+\usage{
+guided_anomaly_tour(
+  index_f,
+  d = 2,
+  alpha = 0.5,
+  cooling = 0.99,
+  max.tries = 25,
+  max.i = Inf,
+  ellipse,
+  ellc = NULL,
+  ellmu = NULL,
+  search_f = search_geodesic,
+  ...
+)
+}
+\arguments{
+\item{index_f}{the section pursuit index function to optimise. The function
+needs to take two arguments, the projected data, indexes of anomalies.}
+
+\item{d}{target dimensionality}
+
+\item{alpha}{the initial size of the search window, in radians}
+
+\item{cooling}{the amount the size of the search window should be adjusted
+by after each step}
+
+\item{max.tries}{the maximum number of unsuccessful attempts to find
+a better projection before giving up}
+
+\item{max.i}{the maximum index value, stop search if a larger value is found}
+
+\item{ellipse}{pxp variance-covariance matrix defining ellipse, default NULL.
+Useful for comparing data with some hypothesized null.}
+
+\item{ellc}{This can be considered the equivalent of a critical value, used to
+scale the ellipse larger or smaller to capture more or fewer anomalies. Default 3.}
+
+\item{ellmu}{This is the centre of the ellipse corresponding to the mean of the
+normal population. Default vector of 0's}
+
+\item{search_f}{the search strategy to use}
+
+\item{...}{arguments sent to the search_f}
+}
+\description{
+The guided anomaly tour is a variation of the guided tour that is
+using an ellipse to determine anomalies on which to select target planes.
+}
+\details{
+Usually, you will not call this function directly, but will pass it to
+a method that works with tour paths like \code{\link{animate_slice}},
+\code{\link{save_history}} or \code{\link{render}}.
+}
+\examples{
+animate_xy(flea[, 1:6], guided_anomaly_tour(anomaly_index(),
+  ellipse=cov(flea[,1:6])), ellipse=cov(flea[,1:6]), axes="off")
+}
+\seealso{
+\code{\link{slice_index}} for an example of an index functions.
+\code{\link{search_geodesic}}, \code{\link{search_better}},
+  \code{\link{search_better_random}} for different search strategies
+}
diff --git a/man/mahal_dist.Rd b/man/mahal_dist.Rd
new file mode 100644
index 00000000..7a67a42b
--- /dev/null
+++ b/man/mahal_dist.Rd
@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/linear-algebra.r
+\name{mahal_dist}
+\alias{mahal_dist}
+\title{Calculate the Mahalanobis distance between points and center.}
+\usage{
+mahal_dist(x, vc)
+}
+\arguments{
+\item{x}{matrix of data}
+
+\item{vc}{pre-determined variance-covariance matrix}
+}
+\description{
+Computes the Mahalanobis distance using a provided variance-covariance
+matrix of observations from 0.
+}
+\keyword{algebra}
diff --git a/man/norm_bin.Rd b/man/norm_bin.Rd
index 390c2045..1a7376f9 100644
--- a/man/norm_bin.Rd
+++ b/man/norm_bin.Rd
@@ -14,11 +14,11 @@ norm_kol(nr)
 }
 \description{
 Compares the similarity between the projected distribution and a normal distribution.
-\itemize{
+}
+\details{
 \item norm_bin: compares the count in 100 histogram bins
 \item norm_kol: compares the cdf based on the Kolmogorov–Smirnov test (KS test)
 }
-}
 \examples{
 # manually compute the norm_kol index
 # create the index function