statdivlab/radEmu

Issues

• Should I do abundance filtering before running `radEmu`?

  #83 opened 3 months ago by alyssaeaston
  1

• simulate_data has no coverage

  #35 opened 10 months ago by adw96
  3

• Some issues and questions

  #78 opened 4 months ago by tengfei-emory
  5

• include function to estimate power in package

  #15 opened 3 months ago by adw96
  2

• R-CMD-check hitting a problem with the suggests package `phyloseq` not being available

  #64 opened 7 months ago by svteichman
  2

• Surprisingly small p-values when comparing two levels of covariate in the presence of only zeroes

  #65 opened 4 months ago by svteichman
  3

• plotting tools

  #71 opened 4 months ago by adw96
  3

• Analysis 'stalls' - running for 7 hours

  #69 opened 5 months ago by sminot
  7

• question regarding taxon-specific biases

  #76 opened 5 months ago by jorondo1
  2

• add partially verbose option

  #73 opened 5 months ago by svteichman
  0

• Return z-hat's

  #67 opened 6 months ago by adw96
  6

• constrained optimization on score tests

  #59 opened 7 months ago by eidlide
  5

• add tests to confirm that steps within the estimation under the null algorithm get closer to optimum of objective function

  #61 opened 7 months ago by svteichman
  1

• Appropriate use of run_score_tests

  #56 opened 8 months ago by eidlide
  5

• vignette: cluster dependence

  #38 opened 7 months ago by adw96
  1

• Length normalized metagenomic data

  #55 opened 8 months ago by anderson-fsep
  1

• error with `formula = ~ 1`

  #48 opened 8 months ago by adw96
  6

• Explanation of Error Code

  #54 opened 8 months ago by sierrasummer5
  3

• error: index larger than maximal 324

  #52 opened 8 months ago by almita
  5

• github.io site

  #24 opened 8 months ago by adw96
  4

• Too many questions... :)

  #49 opened 8 months ago by tappituffi
  11

• vignette: parallelizing score tests

  #39 opened 8 months ago by adw96
  2

• FDR correction / p-values

  #47 opened 8 months ago by kunstner
  1

• No vignettes found

  #45 opened 8 months ago by Cat-Elin
  5

• would love more descriptive column `covariate`

  #43 opened 8 months ago by adw96
  5

• how to deal with ordered categories

  #31 opened 10 months ago by krmaas
  6

• give B row and colnames

  #27 opened 10 months ago by adw96
  3

• object 'Csparse_transpose' not found

  #36 opened 10 months ago by tengfei-emory
  6

• error rate control in the presence of cluster dependence

  #33 opened 10 months ago by adw96
  1

• test all coefs

  #34 opened 10 months ago by adw96
  0

• Multiple tests failing at methods::as(info,"symmetricMatrix"), at least for me

  #20 opened a year ago by ailurophilia
  2

• make a nice README/homepage

  #28 opened a year ago by adw96
  0

• turn stamps tutorial into vignette

  #14 opened a year ago by adw96
  0

• create "release" to accompany arxiv submission

  #16 opened a year ago by adw96
  0

• github actions to run checks

  #17 opened a year ago by adw96
  0

• Remove Outdated Data Augmentation Functions

  #19 opened a year ago by ailurophilia
  0

• Nicely formatted output for emuFit

  #22 opened a year ago by adw96
  2

• allow X and Y to be dataframes

  #26 opened a year ago by adw96
  0

• phyloseq integration

  #10 opened a year ago by adw96
  2

• streamline tests

  #18 opened a year ago by adw96
  0

• trackB needs fixing in `fit_null`

  #8 opened a year ago by adw96
  1

• Confirm information matrix versus inverse for get_score_stat

  #9 opened a year ago by adw96
  0

• Estimation under null gets stuck?

  #7 opened a year ago by adw96
  6

• X_tilde constructed such that element-wise X_tilde * theta is not equal to X * Beta + z

  #4 opened a year ago by svteichman
  1

• Not finding MLEs

  #2 opened a year ago by adw96
  2

• Update STAMPS 2022 lab for new `emuFit` syntax

  #6 opened a year ago by adw96
  1

• Error in `emuFit(Y, ~covariate, data)`: object 'null_k' not found

  #5 opened a year ago by adw96
  1