Major update ### new features - calc_comm_div now
replaces get_mob_stats. The ancillary plotting function
plot.mob_stats is now replaced with
plot_comm_div. We hope to eventually add back in
bootstrapping confidence intervals for the statistics but that is not
currently supported. If you would like to know more about this design
decision see the discussion here:
https://github.com/MoBiodiv/mobr/issues/255. -
plot_rarefaction is a bit more versatile with many new
arguments that provide options for smoothing or averaging rarefaction
curves when making comparisons within or between groups respectively. -
The R package beta_C by Thore Engel has now been absorbed
into the mobr package. Use function
calc_beta_div or calc_comm_div with
beta in the scales argument to compute
coverage based beta diversity. Note the index in this case is
S_C (i.e., richness S for a given level of coverage C) - a
vignette was added to demonstrate how to make computations of beta
diversity using mobr called beta_div_demo
data.frame from the function
plot_abu which does not change how this function behaves
but adheres to CRAN standards.ref_level can be specified in
get_mob_stats, plot_rarefaction and
plot_sad which allows for the reference (i.e., control)
group to be specified which all others are compared to. This is similar
to the implementation in the function get_delta_statsget_delta_stats as described in McGlinn et al. (2020get_delta_stats -> plot.mob_outsphere_dist did not appear to be calculating
great circle distances from latitude and longitude coordinates correctly
using the Haversine formula. This was corrected with a new function this
is correct according to comparisons with
fields::rdist.earth and
geosphere::distHaversine.overlap_effects which provided an
overlapped image of the three components SAD, N, and agg across scale.
This may be added back in the futureget_delta_stats
function which computes the differences in richness across all possible
scales.