smatr v3.4-8

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(Standardised) Major Axis Estimation and Testing Routines

Methods for fitting bivariate lines in allometry using the major axis (MA) or standardised major axis (SMA), and for making inferences about such lines. The available methods of inference include confidence intervals and one-sample tests for slope and elevation, testing for a common slope or elevation amongst several allometric lines, constructing a confidence interval for a common slope or elevation, and testing for no shift along a common axis, amongst several samples. See Warton et al. 2012 <doi:10.1111/j.2041-210X.2011.00153.x> for methods description.

Readme

smatr: (Standardised) Major Axis Estimation and Testing Routines

smatr is an R package for fitting (Standardised) Major Axis Lines to bivariate data. The package is described in the following publication:

Warton, David I., Duursma, Remko A., Falster, Daniel S. and Taskinen, Sara (2012) smatr 3 - an R package for estimation and inference about allometric lines. Methods in Ecology and Evolution, 3(2), 257-259. doi:10.1111/j.2041-210X.2011.00153.x.

Abstract:

1. The Standardised Major Axis Tests and Routines (SMATR) software provides tools for estimation and inference about allometric lines, currently widely used in ecology and evolution. 2. This paper describes some significant improvements to the functionality of the package, now available on R in smatr version 3. 3. New inclusions in the package include sma and ma functions that accept formula input and perform the key inference tasks; multiple comparisons; graphical methods for visualising data and checking (S)MA assumptions; robust (S)MA estimation and inference tools.

The package was programmed by David Warton, Remko Duursma and Daniel Falster and is maintained by Remko Duursma here.

Installation

You can simply install this package from CRAN,

install.packages("smatr")

Or install the development version from bitbucket,

devtools::install_bitbucket ("smatr", "remkoduursma")

Meta

Please report any issues or bugs.

To cite package smatr in publications use:

   Warton, David I., Duursma, Remko A., Falster, Daniel S. and Taskinen,
  Sara (2012) smatr 3 - an R package for estimation and inference about
  allometric lines Methods in Ecology and Evolution, 3(2), 257-259.  doi:10.1111/j.2041-210X.2011.00153.x.

Get citation information for smatr in R with citation(package = 'smatr').

Functions in smatr

Name Description
b.com.est Common slope estimation
elev.com Test for equal elevation among several lines fitted with (standardised) major axes of common slope.
elev.test One-sample test of a (standardised) major axis elevation
coef.sma Extract coefficients from a 'sma' or 'ma' fit
leafmeas Leaf mass per area and photosynthetic rate for plant species from different sites
leaflife Leaf longevity and leaf mass per area for plant species from different sites
fitted.sma Returns fitted values
lr.b.com Likelihood ratio statistic, assuming a common slope (called by slope.com)
line.cis Slope and elevation of a (standardised) major axis, with confidence intervals
com.ci Calculates a confidence inteval for a common slope (called by slope.com)
makeLogMinor Generate spacing for minor tick marks on a plot with log-scaled axes
alpha.fun Utility functions for robust fitting
residuals.sma Extract model residuals
print.sma Print an object of class 'sma'.
meas.est Measurement error variance estimation from repeated measures
plotutils Utility plotting functions
slope.com Common slope test amongst several allometric lines
seqLog Sequence Generation
plot.sma Draw an X-Y plot
slope.test One-sample test of a (standardised) major axis slope
sma (Standardized) major axis estimation and testing for one or several samples
shift.com Test for no mean shift along a common (standardised) major axis
multcompmatrix Multiple comparisons graphical matrix
smatr-package (Standardised) Major Axis Estimation and Testing Routines
summary.sma Print a summary
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License GPL-2
URL http://web.maths.unsw.edu.au/~dwarton, http://www.bitbucket.org/remkoduursma/smatr
Collate 'alpha.fun.R' 'b.com.est.R' 'coef.sma.R' 'com.ci.R' 'defineAxis.R' 'elev.com.R' 'elev.test.R' 'fitted.sma.R' 'huber.M.R' 'line.cis.R' 'logLik_sma.R' 'lr.b.com.R' 'ma.R' 'makeLogMinor.R' 'meas.est.R' 'multcompmatrix.R' 'nicePlot.R' 'plot.sma.R' 'predict.sma.R' 'print.sma.R' 'residuals.sma.R' 'robust.factor.R' 'seqLog.R' 'shift.com.R' 'slope.com.R' 'slope.test.R' 'sma.R' 'summary.sma.R'
NeedsCompilation no
Packaged 2018-03-18 20:51:38 UTC; remko
Repository CRAN
Date/Publication 2018-03-18 21:15:22 UTC

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