idiv2: to do list

[rueuntal]

• [ ] smooth out sSBR by averaging it over at a minimum 20 runs. Currently the sSBR looks very jagged which largely reflects the particulars of the random walk that it took in sampling. By doing this several times a smoother and a less biased estimate of the expected S can be obtained although it will be slower.
• [x] improve documentation for function rarefaction so it is clear what the different methods accomplish
• [x] add subset.mob_in function that aids in pulling out a reduced number of rows of the mob_in object - this can be really useful when wanting to only work with certain treatment combinations
• [x] acknowledge Marc Taylor for plotStacked function (https://github.com/marchtaylor/sinkr/blob/master/R/plotStacked.R) also thank Anne Chao and collegues for various functions --> this also requires us to copy and paste there functions for our purposes rather than maintain the dependancies on their package.
• [x] stacked bar chart with pie charts
• [x] implement spatial anaylsis when geographic coordinates are not available this changes interpretation from implicit and explicit spatial aggregation to just focusing on implicit spatial aggregation
• [x] get rid of plot_rarefy and move that code into plot.mob_out which currently calls that function.
• [x] implement the same log argument in plot.mob_out as in mob_out
• [x] remove the function that does the 3d plot (and breaks when the code is executed on a server)
• [x] change ScaleBy to ref_group
• [x] Anova type output based on a ref group
• [x] Agree on how to scale between # individuals and # plots
• [x] Regression type
  • [x] Regression analysis
  • [x] null tests for regression?
    • [x] test 1 - complete individual randomization
    • [x] test 2 -
    • [x] test 3
    • [ ] sensitivity analysis
• [x] function at the beginning to check that rows (plots) between two data frames match
• [x] define object class mob_out (print, plot) and mob_in (print, t-test, summary -> t-test table)
  • [x] summary.mob_in should provide p-values rather than quantiles
• [x] other functions
  • [x] print
  • [x] plot
    • [x] rarefaction plots these will pair with the delta S plots
      • [x] rarefaction plot legend sometimes mislabels the curves (high priority)
  • [x] modify plot.mob_out to either plot delta curves or raw curves or both
    • [x] It appears that plot.mob_out sometimes log transforms the x axis depending on mob_out$log_scale and sometimes does not. This needs to be made consistent across the figures. (high priority)
    • [x] improve code in plot.mob_out
    • [x] add number of samples to axis see old axis labels
    • [x] nick requests that for the individual based rarefaction we show the entire curve across all samples and not just for the smallest number of individuals common across the groups.
  • [x] trim delta plots to ignore n < 5 individuals due to the artifact that it must interested at 0.
  • [x] box plots of univariate analyses
    • [x] N vs trt
    • [x] S rarefied vs trt
    • [x] PIE rarefied vs trt
    • [x] Beta PIE rarefied vs trt
    • [x] S vs trt
  • [ ] summary
• [x] cleanup and combine categorical case (anova) with continuous case (regression)
  • [x] break out null algos back into separate functions #30
• [ ] test for composition? (*maybe later)
• [ ] complex exp design with more than one factor? (*maybe later)
• [x] package up
• [x] figure out what's going on with null test for N
• [x] modify function rarefaction so it will accept a vector for sample based rarefaction
• [x] add extrapolated S to the boxplot
• [x] fix null test for aggregation
• [ ] add output of number of permutations to mobr object output from get_delta_stats
• [ ] occupancy data (low priority can only be applied to spatial rarefaction)
• [x] track down warning message from rarefaction for coffee and cattle datasets: "1: In rarefaction(comm, "indiv", inds) :" Also the ant 2014 dataset is producing the following error: "In deltaS_N(comm_perm[plot_levels == x, ], plot_dens_level, ... : Extrapolating the rarefaction curve because the number of rescaled individuals is smaller than the inds argument "effort" larger than total number of samples
• [x] document package
  • [x] mobr.package documentation
• [ ] note in the documentation of the function rarefaction that sample-based rarefaction is not actually used anywhere in the mob methods.
• [x] provide 3d plot option for headless machine (low priority) currently implemented with rgl
• [x] repeat sensitivity analysis for the discrete case after fixing the warnings & also implement with larger number of iterations

[dmcglinn]

Folks keep adding things to the list of ToDo as you encounter them in the code

[dmcglinn]

@rueuntal and @FelixMay where are we on this list of to do's from last meeting?

[FelixMay]

@dmcglinn I feel responsible for the boxplots and for a vignette for mobr. However, with the latter I would like to wait until the normal function documentation is there. So let me know when you documented the functions. I will only be able to devote time, after November 9, which means after our iDiv conference

[rueuntal]

Hey @dmcglinn - sorry about the delay! My family are in town, so I'm a bit lagging behind. If I remember correctly, there are a few things that we have agreed not to include, at least not in this first release:

• analysis for composition

• complex experiment designs with multiple factors

• (continuous case - did we agree to postpone this as well?)

  The remaining big things on my mind at the moment are:

• make sure that the supporting functions (e.g., plot, summary, etc.) work and the outputs match what we have in mind;

• help documents for each function;

• bump up the number of iterations for the sensitivity analysis, to be done on iDiv's server.

Anything else?

[FelixMay]

Hey @dmcglinn, I will take care of the documentation for the mob_stats and the boxplots function. However, so far I only worked on the master branch. Should I add the new stuff to the 4cur branch? Does that mean I also have to fork this branch or can I chose when I push and pull to which branch this happens? Thanks!

[dmcglinn]

Hey Felix

I'm going to merge 4cur with master today after Xiao has a chance to approve my PR. So you'll be able to just work with master shorty.

Dan

On Nov 29, 2016, at 3:51 AM, Felix May [email protected] wrote:

Hey @dmcglinn, I will take care of the documentation for the mob_stats and the boxplots function. However, so far I only worked on the master branch. Should I add the new stuff to the 4cur branch? Does that mean I also have to fork this branch or can I chose when I push and pull to which branch this happens? Thanks!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

[FelixMay]

Hi Dan, Yeah cool. Then I am in again – and I have no more excuses of not contributing ;o)

Felix

Von: Dan McGlinn [mailto:[email protected]] Gesendet: Dienstag, 29. November 2016 12:20 An: MoBiodiv/mobr [email protected] Cc: May, Felix [email protected]; Mention [email protected] Betreff: Re: [MoBiodiv/mobr] idiv2: to do list (#21)

Hey Felix

I'm going to merge 4cur with master today after Xiao has a chance to approve my PR. So you'll be able to just work with master shorty.

Dan

On Nov 29, 2016, at 3:51 AM, Felix May <[email protected]mailto:[email protected]> wrote:

Hey @dmcglinn, I will take care of the documentation for the mob_stats and the boxplots function. However, so far I only worked on the master branch. Should I add the new stuff to the 4cur branch? Does that mean I also have to fork this branch or can I chose when I push and pull to which branch this happens? Thanks!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/MoBiodiv/mobr/issues/21#issuecomment-263544707, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AO8i0XO4ErVX85_7Uifr1EZQ2CHmVrDmks5rDApHgaJpZM4JFAVD.

[dmcglinn]

I just added additional items from the Felix to do list to a more general todo list for @rueuntal and myself