Update of mobr from 2.0.2 to 3.0.0 #273
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…ing group variable. Note get_mob_stats broken in this snapshot
Analysis still in progress
control for fail when effort = NA and index = 'S_n'
- remove ENS argument from calc_PIE() and instead write a new function calc_SPIE() - both functions get a "replace" argument - throw an error for non-integer values - throw an error when NA's are produced - throw error when ENS argument is supplied -update documentation 48224b3#commitcomment-43913975
…unction calc_PIE and calc_SPIE. Other code style changes and improved documentation.
- both functions get the replace argument - use calc_SPIE when index="S_PIE - documentation #258 (comment)
- adapt warning to this: 242625e - remove repeated word.
…nforce character line limit.
Merge beta_C functions into mobr dev branch
… Other minor documenation changes.
…unction still returns values
This change ports the computation of Heck's formulation of standard devitation for individual based rarefaction found in vegan::rarefy to mobr::rarefaction.
documented here: #269
Spatially-explicit rarefaction
…calc_beta_div which was redundant with calc_comm_div.
…ocumentation of the coverage based methods by citing literature more.
…go on those. Probably need to simplify for time being.
…_div This function plots the result of the function calc_comm_div. Note there are several helper functions. I made it so that these functions do not expect test results (p-values) only plotting of raw diversity values.
…ure to correspond with this change.
dmcglinn
changed the title
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Major update
new features
calc_comm_divnow replacesget_mob_stats. The ancillary plotting functionplot.mob_statsis now replaced withplot_comm_div. We hope to eventuallyadd 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: beta diversity calculations #255.
plot_rarefactionis a bit more versatile with many new argumentsthat provide options for smoothing or averaging rarefaction curves
when making comparisons within or between groups respectively.
beta_Cby Thore Engel has now been absorbed intothe
mobrpackage. Use functioncalc_beta_divorcalc_comm_divwith
betain thescalesargument to compute coverage based betadiversity. Note the index in this case is
S_C(i.e., richness S for agiven level of coverage C)
diversity using
mobrcalledbeta_div_demo