mobr_app functions and their currently implemented parameters

All parameters that are BOLD are currently implemented while those in ITALICS are not. Please let me know if you would like any of the parameters not currently implemented to be added.

make_mob_in

• community matrix data
• plot attribute data
• coord_names (0, 1, or 2 can be specified - data entered using text field if necessary)

plot_rarefaction

• mob_in
• env_var
• method (individual, sample, and spatial)
• dens_ratio
• pooled
• col
• lwd
• log
• leg_loc

plot_abu

• mob_in
• env_var
• type (can select between rank or species) 
• pooled
• col
• lwd
• log
• leg_loc

get_mob_stats

• mob_in
• group_var
• index (Currently works for: N, S, f_0, pct_rare, S_PIE)
• effort_samples
• effort_min
• extrapolate
• return_NA
• rare_thres
• n_perm
• boot_groups
• conf_level
• cl

get_delta_stats

• mob_in
• group_var
• ref_group
• tests
• type
• stats (set as a text entry field - user must format correctly or error)
• inds (set as a text entry field - user must format correctly or error) 
• log_scale
• min_plots
• density_stat
• n_perm
• overall_p

Need to check which branch is the most relevant for updates. A quick look at the commit history of both branches suggests this isn't necessary straightforward.

Add description of sample code used when 'Sample Code' is selected in the Data Tab. Sample code being used are the inv_comm and inv_plot_attr data files.

• Add user entry for coord_names for new make_mob_in function

• Look into updating the sample data & how it is stored/entered
  - see if more sample data sets can be used
  - update current references to master branch of the mobr_app repo

• update app to work with mobr dev branch (which will be merged soon into master as mobr v2.0 is rolled out)
  • some of the arguments to make_mob_in and get_delta_stats have changed
  • the graphical output has changed for the delta analysis
• Add submit issues link for shiny app too (currently only implemented for R package)
• Issues with data
  • is it necessary for the app to have a data file when the mobr package ships with data?
    • at data input panel give user option of either specifying path to file or choosing one of the default datasets the mobr ships with these can be loaded as data(inv_comm); data(inv_plot_attr) there are several other datasets to load as well see: https://github.com/MoBiodiv/mobr/tree/master/data
• minor text changes (where "->" indicates change LHS to RHS)
  • Home (in general let's use sentence case throughout the home page unless it is the title of a tab in that case treat it as a proper noun)
    • Data Tab -> Data Input
    • DataTab -> Data Input
    • you -> your
    • Community Matrix -> community matrix
    • Plot Data -> plot data
    • CSV -> csv
    • Plot Rarefaction -> Exploratory Analysis
    • Add clear Caroline Oliver author of mobr shiny app somewhere on the home page
    • Change primary author of mobr from Xiao to Dan as the page is no longer maintained by Xiao. She should be retained as second author however.
    • throughout change MoB-R to mobr when referring to the R package, when simply referring to the method just use the acronym MoB
    • change title of app to "Measurement of Biodiversity Shiny App"
    • on link tabs box fix typo: fromthe -> from the
  • On data input change options from "Use Personal Data" -> "User Supplied Data" and "Use Sample Data" -> "Example Data"
  • Exploratory analysis tab
    • fix typo "Exploritory" -> "Exploratory"
    • SR = Spacial Rarefaction -> sSBR = spatial sample-based rarefaction
    • IR = Indiviudal Rarefaction -> IBR = individual-based rarefaction
    • Abu = Abundance -> SAD = species abundance distribution
  • Individual MoB Metrics panel
    • add an acronym definitions like you did for the Exploratory analysis tab
      • S = species richness, N = total community abundance, S_n = rarefied richness to n individuals, S_PIE = effective number of species for the probability of interspecific encounter (PIE)

I have noticed inconsistency in how the data is downloaded and saved as either a csv file or as a pdf. Many cdv's are now reading as null and some plot pdf downloads have multiple copies of the graphs within a single pdf. I will be looking into this and working on fixing it so that the output data is correctly represented when downloaded by the user.

• coord_names in make_mob_in need to be a parameter the user can specify (but note here #7 @caroliver notes that this implemented)
• change the argument to get_delta_stats from ref_group to ref_level
• update the plotting of the get_delta_stats output

migrated from MoBiodiv/mobr#190:

When trying to print out the various statistics for the get_delta_stats function, the 'stats' tab in the app reads 'NULL' for all variables.