NEWS.md

In douglasgscofield/dispersalDiversity: Analyse individual and genetic diversity of dispersal processes in biological populations

0.9.9001 (development version)

• createAlleleTables will create a class allele_divtables object from genotype data in a class genalex object, and will attempt to convert other objects to class genalex using as.genalex from the readGenalex package prior to creating the allele tables
• Diversity tests no longer compare log-likelihood values against an analytic Χ2 distribution, which was almost always incorrect
• The calculation of distances for diversity tests is much more efficient in time and space, so tests may be performed on data with very high counts, such as diversity of OTUs quantified via read counts
• Diversity tests return class diversity_test, which has print and plot methods
• Gamma accumulation functions return class gamma_accum, which has a plot method
• diversity, alleleDiversityTest, alleleContrastTest, and alleleContrastTest3 have methods for divtable and allele_divtables
• Lists of allele diversity tables have class allele_divtables
• Diversity site-by-source tables have class divtable, with methods to convert from table, xtabs, matrix, and data.frame
• diversity returns separate lists for diversity values calculated using the standard diversity calculations (q), classical corrections (r), and Nielsen et al. (2003 Molecular Ecology) corrections (q.nielsen).
• nielsenTransform is an exported function
• membershipPlot with fill.method = "colour" will use the RColorBrewer package if it is available; the default palette is "Dark2" and this can be changed with fill.palette. Also, "colour" is a fill.method synonym for "color".
• membershipPlot will on option write the plot to a PDF file; the option to write to an EPS file is removed
• membershipPlot drops the method argument along with the plotting of pie charts
• The datasets granaries_2002_Qlob and granaries_2004_Qlob are provided, which include assignments of Quercus lobata acorns harvested from acorn woodpecker granaries in 2002 and 2004 to seed source trees.
• Numerous functions have been renamed (e.g., pmiDiversity to diversity) and data structures reconfigured (e.g., the return value from diversity)

0.1

• Initial version available via Github. This is tagged with 0.1 and a tarball is available as a release.

douglasgscofield/dispersalDiversity documentation built on March 30, 2021, 9:50 a.m.