Learn R Programming

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').

Copy Link

Version

Install

install.packages('smatr')

Monthly Downloads

765

Version

3.4-8

License

GPL-2

Maintainer

Last Published

March 18th, 2018

Functions in smatr (3.4-8)

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