[Analogue-commits] r391 - pkg/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Dec 13 05:08:51 CET 2013
Author: gsimpson
Date: 2013-12-13 05:08:51 +0100 (Fri, 13 Dec 2013)
New Revision: 391
Modified:
pkg/man/analogue-package.Rd
Log:
update the package documentation page
Modified: pkg/man/analogue-package.Rd
===================================================================
--- pkg/man/analogue-package.Rd 2013-12-11 14:22:59 UTC (rev 390)
+++ pkg/man/analogue-package.Rd 2013-12-13 04:08:51 UTC (rev 391)
@@ -3,72 +3,149 @@
\alias{analogue}
\docType{package}
\title{
-Analogue methods for palaeoecology
+Analogue and weighted averaging methods for palaeoecology
}
\description{
-Fits Modern Analogue Technique transfer function models
-for prediction of environmental data from species data. Also
-performs analogue matching, a related technique used in palaeo
-ecological restoration.
+Fits Modern Analogue Technique and Weighted Averaging transfer
+ function models for prediction of environmental data from species
+ data, and related methods used in palaeoecology.
}
\details{
\tabular{ll}{
Package: \tab analogue\cr
Type: \tab Package\cr
-Version: \tab 0.4-3\cr
-Date: \tab 2007-09-15\cr
-Depends: \tab R (>= 2.5.0), stats, graphics, vegan\cr
-License: \tab GPL Version 2\cr
-Built: \tab R 2.5.1; ; 2007-08-03 13:44:47; unix\cr
+Version: \tab 0.11-6\cr
+Date: \tab $Date: 2013-10-05 15:11:52 -0600 (Sat, 05 Oct 2013) $\cr
+Depends: \tab R (>= 2.15.0), vegan (>= 1.17-12), lattice, rgl\cr
+Imports: \tab mgcv, MASS, stats, graphics, grid, brglm, princurve\cr
+Suggests: \tab testthat\cr
+Authors at R: \tab c(person(given = c("Gavin", "L."), family = "Simpson",
+ role = c("aut", "cre"),
+ email = "ucfagls at gmail.com"),
+ person(given = "Jari", family = "Oksanen",
+ role = "aut"))\cr
+BugReports: \tab
+http://r-forge.r-project.org/tracker/?func=browse&group_id=69&atid=338\cr
+NeedsCompilation: \tab yes\cr
+License: \tab GPL-2\cr
+ByteCompile: \tab true\cr
+URL: \tab http://analogue.r-forge.r-project.org\cr
+Packaged: \tab 2013-10-14 20:41:41 UTC; gavin\cr
+Built: \tab R 3.0.2; x86_64-unknown-linux-gnu; 2013-10-14 20:41:48 UTC; unix\cr
}
Index:
\preformatted{
+ImbrieKipp Imbrie and Kipp foraminifera training set
+Pollen North American Modern Pollen Database
RMSEP Root mean square error of prediction
+Stratiplot Palaeoecological stratigraphic diagrams
+abernethy Abernethy Forest Pollen Sequence
analog Analogue matching
analogue-package Analogue methods for palaeoecology
bayesF Bayes factors
bootstrap Bootstrap estimation and errors
+bootstrap.wa Bootstrap estimation and errors for WA models
bootstrapObject Bootstrap object description
+caterpillarPlot Caterpillar plot of species' WA optima and
+ tolerance range.
+chooseTaxa Select taxa (variables) on basis of maximum
+ abundance attained and number of occurrences.
cma Close modern analogues
+crossval Cross-validation of palaeoecological transfer
+ function models
+densityplot.residLen Lattice density plot for residual lengths
+deshrink Deshrinking techniques for WA transfer
+ functions
dissimilarities Extract dissimilarity coefficients from models
distance Flexibly calculate dissimilarity or distance
measures
+fitted.logitreg Fitted values for the training set from
+ logistic regression models
+fuse Fused dissimilarities
getK Extract and set the number of analogues
+gradientDist Positions of samples along a unit-length
+ ordination gradient.
+hist.residLen Histogram plot for residual lengths
+histogram.residLen Lattice histogram plot for residual lengths
join Merge species data sets on common columns
(species)
+logitreg Logistic regression models for assessing
+ analogues/non-analogues
mat Modern Analogue Technique transfer function
models
mcarlo Monte Carlo simulation of dissimilarities
minDC Extract minimum dissimilarities
-plot.bayesF Bayes factor plots
+optima Weighted averaging optima and tolerance ranges
+panel.Loess Loess smooths to stratigraphic diagrams
+panel.Stratiplot Panel function for stratigraphic diagrams
+pcr Prinicpal component regression transfer
+ function models
+performance Transfer function model performance statistics
plot.dissimilarities Plots the distribution of extracted
dissimilarities
+plot.logitreg Produces plots of analogue logistic regression
+ models
plot.mat Plot diagnostics for a mat object
-plot.mcarlo Plott Monte Carlo simulated dissimilarity
+plot.mcarlo Plot Monte Carlo simulated dissimilarity
distributions
plot.minDC Plot of minimum dissimilarity per sample
+plot.prcurve Plot a fitted principal curve in PCA space
+plot.residLen Plot method for residual lengths
plot.roc Plot ROC curves and associated diagnostics
+plot.wa Plot diagnostics for a weighted averaging model
+plot3d.prcurve Interactive 3D plof of a principal curve in
+ principal coordinate space
+prcurve Fits a principal curve to m-dimensional data
+predict.logitreg Posterior probability of analogue-ness for
+ fossil samples
predict.mat Predict method for Modern Analogue Technique
models
+predict.pcr Predicted values from a principal components
+ regression
+predict.wa Predict from a weighted average model
+rankDC Rank correlation between environmental and
+ species dissimilarities.
reconPlot Stratigraphic plots of palaeoenvironmental
reconstructions
+residLen Squared residual length diagnostics
+residuals.prcurve Residuals of a principal curve fit.
rlgh Round Loch of Glenhead Diatoms
roc ROC curve analysis
+scores.prcurve 'scores' method for principal curve objects of
+ class '"prcurve"'.
screeplot.mat Screeplots of model results
+smoothSpline Smoother plugin function for use in fitting a
+ principal curve
+splitSample Select samples from along an environmental
+ gradient
+sppResponse Species responses along gradients.
+stdError Standard error of MAT fitted and predicted
+ values
summary.analog Summarise analogue matching results
summary.bootstrap.mat Summarise bootstrap resampling for MAT models
summary.cma Summarise the extraction of close modern
analogues
summary.mat Summarise Modern Analogue Technique models
summary.predict.mat Summarise MAT model predictions
-swapdiat SWAP sub-fossil diatom training set
-swappH SWAP pH training set
+swapdiat SWAP sub-fossil diatom and pH training set
+swappH SWAP sub-fossil diatom and pH training set
+timetrack Timetracks of change in species composition
+tran Common data transformations and
+ standardizations
+varExpl Variance explained by ordination axes
+wa Weighted averaging transfer functions
+weightedCor Weighted correlation test of WA reconstruction
}
+
+Further information is available in the following vignettes:
+\tabular{ll}{
+\code{analogue_methods} \tab Analogue Methods in Palaeoecology (source, pdf)\cr
}
+}
\author{
-Gavin L. Simpson.
+Gavin L. Simpson, Jari Oksanen
-Maintainer: Gavin L. Simpson <gavin.simpson at ucl.ac.uk>
+Maintainer: Gavin L. Simpson <ucfagls at gmail.com>
}
\keyword{ package }
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