Calculate Multivariate Richness via UTC and sUTC

Functions to calculate Unique Trait Combinations (UTC) and scaled Unique Trait Combinations (sUTC) as measures of multivariate richness. The package can also calculate beta-diversity for trait richness and can partition this into nestedness-related and turnover components. The code will also calculate several measures of overlap.


News

Known Bugs or issues:

# The code does not adequately check that the incoming data is in the correct format.
# Code does not switch from data frame to matrix, but instead is expected to crash with an otherwise suitable data frame (categorization step)
# Some R functions may produce lists that look like matrices.  These will crash this script.
# Categorization is acheived via rounding.  This is not an inherent property of MVR, but was a quick and easy convenience used by me.
# Currently all traits must be rounded to the same decimal place.  Again, not an inherent property of MVR, but a programming short-cut for convenience.
# Script is not yet set up to work with abundance data, consequently, the unequal.abund option does not appear anywhere else in the script.
# st.range option is non-functional, currently all standardization needs to be performed outside of the script.
# log.trans option may not work.  I found it easier to log-transform the data in Excel, and then load it into R, so I have not rigorously tested these options.
# No option to calculate traitspace from non-overlapping categories (e.g., as in species richness example). These trait spaces need to be calculated outside of the package and entered as inputs
# No option to turn off raw mvo, and this output is bulky and may clutter up the output
# Under some inputs, the calc.mvo function returns an error.  See additional details

CHANGES IN VERSION 2.1.1

Fixed minor issues to make package CRAN-compatible

CHANGES IN VERSION 2.1.0

Added code for conducting a sensitivity analysis

CHANGES IN VERSION 2.0.3

Made integer an accepted format, as apparently a matrix can be in integer format, and it is a bit tricky to get it out of integer format but to retain the specific matrix formatting.

CHANGES IN VERSION 2.0.2

Added examples back into code

Fixed a bug in part.mvr.beta caused by R converting a 1 row matrix to vector format

CHANGES IN VERSION 2.0.1

Converted documentation to use roxygen2

Code formatted & revised to be submitted to CRAN

CHANGES IN VERSION 2.0.0

Fixed/removed keywords from man pages (I misunderstood how they worked)

Changed umvr and smvr to utc and sutc

CHANGES IN VERSION 1.0.1

Fixed an error in part.mvr.beta to handle the situation when there is no overlap among species

Improved package documentation and expanded examples.

Additional details on known bugs:

#Under some inputs, the calculation of overlap does not work properly
    # ON 16 Mar 2014 Received the following error:
      # Error in matrix(b.mat, nrow = length(br.nams2), dimnames = list(br.nams2,  : data is too long
        # traceback()
          #7: matrix(b.mat, nrow = length(br.nams2), dimnames = list(br.nams2, bc.nams)) at MVR.r#489
          #6: calc.mvo(com.mat, dups) at MVR.r#271
          #5: calc.mvd(cat.mat, in.com, traitspace, calc.ovr) at MVR.r#113
          #4: mvfd(rt.mat, com.mat, resolution = resolution) at #6
          #3: calc.fd(sub.mat, com.mat, index.type) at #64
          #2: do.scnII(this.index, b.mat, i, this.combo, sp.rich.vec, num.rand) at #17
          #1: scnII(IndexType, combo.vec, b.mat, sp.rich.vec, lcv, lit, num.rand) at #18
      # Appears to be a bug in calc.ovr (although it is possible it is external to calc.mvo).
      # The temporary fix was to set calc.ovr = 0 and re-run the code.

Reference manual

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install.packages("multirich")

2.1.1 by Alexander Keyel, 3 years ago


Browse source code at https://github.com/cran/multirich


Authors: Alexander Keyel


Documentation:   PDF Manual  


GPL (>= 2) license


Suggests knitr


See at CRAN