mobr shiny todo

[dmcglinn]

• 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    • Change primary author of mobr from Xiao to Dan as the page is no longer maintained by Xiao.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)

[caroliver]

Good evening @dmcglinn,

Looking into getting some of the plots for the MoB Metrics tab, I am getting some of the following errors when using the get_mob_stats function:

f_0 gives me the error:
object ‘op’ not found

S_asymp & PIE gives me the error:
need finite y_lim values

S_n gives the error:

"Number of individuals for rarefaction: 1"
Warning: Error in &: operations are possible only for numeric, logical or complex types
 [No stack trace available]
Warning in get_mob_stats(mob_in(), group_param_mob(), index = c("N", "S",  :
 The number of individuals for rarefaction analysis is too low and is set to the minimum of 1 individuals.

I am currently looking into these myself but wanted to go ahead and send them your way in case you had any suggestions on how to best go about handling them! This is all in my attempt to get all possible indexes to be calculated for the MoB Metrics tab plots... currently there were only three available in the app: N, S, S_PIE. Please let me know if you do in fact want all indices to be available or if there is a select few that would be better for the app.

All indices I'm working on: N, S, S_n, S_asymp, f_0, pct_rare, PIE, S_PIE
(Currently the bolded ones I have working as of right now)

Thank you!

[caroliver]

NOTE: Latest application code is now up on my forked mobr_app repo under the branch updated_application. Please run the following code before trying to run the application to make sure that the dev branch of mobr is installed and being used by the library(mobr) function call: install_github('MoBiodiv/mobr', ref = 'dev')

Please let me know if there are any issues viewing the application!

[dmcglinn]

are you still having trouble with those univariate metrics that were giving you errors?

[dmcglinn]

Is the mob_stats metric S_n still causing errors?