#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 2.1.2
# Update package to have an explicit dependency on markdown per request from CRAN
# Add .travis.yml to allow checking on Linux using Travis
# Fix minor issues to eliminate WARNINGS and NOTES related to qpdf and .Rbuildignore omissions.
# NOTE: a few custom modifications were made for individual users and these updates have NOT been incorporated in the CRAN version at this time. These will need to be addressed in a future update.

#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.

