adw96/DivNet

Issues

• Correlations of estimates in bipartite dataset

  #144 opened 6 months ago by AlexaBennett
  0

• DivNet on Transcripts per Million (TPM) values derived from metagenomic data

  #141 opened a year ago by lingyi-owl
  4

• Is there a minimum number of samples required for testBetaDiversity?

  #142 opened a year ago by emi-panzetta
  0

• X covariate table and the intercept

  #140 opened a year ago by AngusBall
  2

• DivNet on rRNA gene counts derived from metagenomes?

  #128 opened 2 years ago by mgabriell1
  7

• Diversity estimates not plausible

  #126 opened 2 years ago by ARetter90
  16

• R "killed" or cores not returning data

  #136 opened 2 years ago by AlexaBennett
  4

• code coverage audit

  #123 opened 2 years ago by adw96
  2

• Estimating Shannon Evenness with uncertainty and other parameters associated with diversity values

  #114 opened 3 years ago by cramjaco
  1

• Error in default_network(sigma)

  #117 opened 2 years ago by ivanllampy
  5

• Choice of base ASV and influence on reproducibility

  #119 opened 3 years ago by erikrikarddaniel
  7

• rename master to main

  #122 opened 3 years ago by adw96
  1

• vignette detailing general guidance for using covariates...

  #106 opened 3 years ago by adw96
  3

• Can phylodivnet be added to betaDiversity vignette?

  #107 opened 3 years ago by msmcfarlin
  5

• Cannot allocate vector of size with suspiciously large phyloseq object

  #115 opened 3 years ago by cramjaco
  6

• simplifyBeta() missing functionality for aitchison distance

  #116 opened 3 years ago by msmcfarlin
  3

• testBetaDiversity pseudo F-statistic calculation

  #118 opened 3 years ago by pooranis
  2

• Problem with simplifyBeta()

  #111 opened 3 years ago by msmcfarlin
  6

• use speedyseq instead of phyloseq

  #100 opened 3 years ago by adw96
  1

• unit tests

  #87 opened 3 years ago by adw96
  2

• problems with beta_diversity.Rmd

  #88 opened 3 years ago by adw96
  12

• Include DIVNET-rs alternate implementation on DIVNET homepage

  #71 opened 3 years ago by benyoung93
  1

• CRAN check is now failing

  #86 opened 3 years ago by adw96
  0

• testDiversity does not work for beta diversity measures

  #67 opened 3 years ago by mmp3
  3

• simplifyBeta does not work with special characters in sample names

  #73 opened 3 years ago by aimirza
  3

• Paired samples using betta_random/testDiversity

  #55 opened 3 years ago by kunstner
  5

• Tracking accept values in the EM loop

  #46 opened 3 years ago by mooreryan
  4

• Understanding the use of "X" in divnet() function

  #53 opened 3 years ago by gregpoore
  4

• "X" vs formula confusion

  #63 opened 3 years ago by AdrianS85
  2

• Diversity for subsets of the total profile

  #74 opened 4 years ago by aimirza
  3

• INPUT of divnet()

  #66 opened 4 years ago by ari9609
  1

• Beta diversity test for binomial covariate

  #75 opened 4 years ago by aimirza
  3

• how can I make the estimation speed up and escape the limit error?

  #64 opened 4 years ago by Ivy-ops
  3

• divnet fails silently if one of the parallelization packages is not installed.

  #68 opened 4 years ago by mmp3
  2

• default X is specified differently for phyloseq W and matrix W

  #61 opened 4 years ago by pooranis
  1

• Install error

  #65 opened 4 years ago by EmilyHoedt
  4

• DivNet error bars

  #59 opened 4 years ago by mooreryan
  1

• R warning

  #58 opened 4 years ago by adityabandla
  8

• Release of the package

  #60 opened 4 years ago by llrs
  1

• get rid of appveyor testing remnants

  #57 opened 5 years ago by adw96
  1

• set seed for vignette for reproducibility

  #51 opened 5 years ago by adw96
  0

• Verifying DivNet getting started vignette

  #50 opened 5 years ago by laracp
  5

• Understanding the use of "X" in divnet() function

  #52 opened 5 years ago by gregpoore
  0

• Bray-curtis statistical test

  #49 opened 5 years ago by adriaaula
  5

• fix link to tutorial

  #41 opened 5 years ago by adw96
  0

• full phyloseq object and otu_table give different results

  #44 opened 5 years ago by adw96
  0

• Problems with lams parameters

  #48 opened 5 years ago by adw96
  1

• feature request: Plot Diversity Estimates per Factor

  #42 opened 5 years ago by kunstner
  2

• Converting to Exponential Shannon

  #43 opened 5 years ago by ianartmor
  3

• DivNet::shannon_true with zeroes, duh

  #40 opened 5 years ago by adw96
  1