vignette and documentation todo

MoBiodiv / mobr

Tools for analyzing changes in diversity across scales

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vignette and documentation todo #261

Open dmcglinn opened 3 years ago

dmcglinn commented 3 years ago

Consider more than one vignette: 1) one for reading data in and getting structured 2) mobr basics 3) Gradient analysis study: ants on elevations 4) Unbalanced study example: marine protected area study

Documentation of functions:

Needs to have warnings and notes about assumptions of extent and balance

roelvanklink commented 2 years ago

I just ran through the vignette (https://rdrr.io/github/MoBiodiv/mobr/f/vignettes/mobr_intro.Rmd), and a few things could do with simple improvements:

when plotting the individual based rarefaction curve, the x-axis label reads 'number of samples'. I think this should be 'number of individuals' example: plot_rarefaction(fire_mob_in, 'group', ref_level = 'unburned', 'IBR')

roelvanklink commented 2 years ago

When loading the data from Chase (2010), it throws an error message: "Warning message: In make_mob_in(tank_comm, tank_plot_attr, coord_names = c("x", "y")) : Row names of community and plot attributes tables do not match which may indicate different identities or orderings of samples"

It's great that this message exists, but you might not want it thrown in an example dataset. Are the dataframes matching?

roelvanklink commented 2 years ago

I like the vignette for loading the data and playing around with it. I think it would be helpful if the reader would understand the acronyms for the options for calculating and plotting ('IBR', 'SBR' 'nsSBR', 'rad', 'sad', etc), like you did for the metrics. We also don't know what 'plot f_0' means

roelvanklink commented 2 years ago

script load('../vignettes/fire_stats.Rdata') doesn't seem to work is the package was already installed previously (i.e. not installed from github for this session). Not sure if this is important.

dmcglinn commented 2 months ago

these are great suggestions @roelvanklink sorry it has taken us so long to get to these suggestions but hopefully they can be implemented in the next couple of releases.