statdivlab radEmu issues

statdivlab / radEmu

Other

49 stars 8 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

what exactly does the estimate value represent?

#84 almita opened 5 days ago
1
Should I do abundance filtering before running `radEmu`?

#83 alyssaeaston closed 2 weeks ago
1
Allow users to input data with a TreeSummarizedExperiment object

#82 gthopkins closed 2 weeks ago
4
Add plotting function for radEmu output

#81 gthopkins closed 1 month ago
2
Write plot.radEmu in NAMESPACE

#80 gthopkins closed 1 month ago
0
Address points 2 and 3 in issue #78

#79 svteichman closed 1 month ago
1
Some issues and questions

#78 tengfei-emory opened 1 month ago
5
Add plotting function for radEmu

#77 gthopkins closed 1 month ago
4
question regarding taxon-specific biases

#76 jorondo1 closed 2 months ago
2
Minor fix, to use `emuFit()` with `penalize` and `B`, make it easier to use with `fitted_model`, test these updates

#75 svteichman closed 2 months ago
0
Address issue #65 by checking for zero-comparison parameters and adding a flag

#74 svteichman closed 2 months ago
3
add partially verbose option

#73 svteichman opened 2 months ago
0
update "emuFit.Rd" based on fix to documentation to note that `verbose = FALSE` not `TRUE` by default

#72 svteichman closed 2 months ago
0
plotting tools

#71 adw96 closed 1 month ago
3
add option to set `constraint_fn` to a numeric, automatically choosing a single category constraint

#70 svteichman closed 2 months ago
1
Analysis 'stalls' - running for 7 hours

#69 sminot closed 2 months ago
7
Add z_hat nuisance parameters to output

#68 gthopkins closed 3 months ago
2
Return z-hat's

#67 adw96 closed 3 months ago
6
add check to `emuFit()` to throw an error for a category with only zero counts across samples

#66 svteichman closed 3 months ago
2
Surprisingly small p-values when comparing two levels of covariate in the presence of only zeroes

#65 svteichman closed 1 month ago
3
R-CMD-check hitting a problem with the suggests package `phyloseq` not being available

#64 svteichman opened 3 months ago
4
update `simulate_data()` function so that it will work with `B` with arbitrary number of rows `p`

#63 svteichman closed 3 months ago
0
add update to re-order covariate data if it has different rownames than response data

#62 svteichman closed 4 months ago
0
add tests to confirm that steps within the estimation under the null algorithm get closer to optimum of objective function

#61 svteichman closed 4 months ago
1
Return information about optimization under the null (for running score tests).

#60 svteichman closed 4 months ago
1
constrained optimization on score tests

#59 eidlide closed 4 months ago
5
First draft of cluster vignette

#58 svteichman closed 4 months ago
3
remove cluster vignette

#57 svteichman closed 5 months ago
0
Appropriate use of run_score_tests

#56 eidlide closed 5 months ago
5
Length normalized metagenomic data

#55 anderson-fsep closed 5 months ago
1
Explanation of Error Code

#54 sierrasummer5 closed 5 months ago
3
Fix phyloseq implementation

#53 svteichman closed 5 months ago
1
error: index larger than maximal 324

#52 almita closed 5 months ago
5
Addressing issue from data from Amy's email

#51 svteichman closed 5 months ago
0
Address issue #48, intercept-only model

#50 svteichman closed 5 months ago
1
Too many questions... :)

#49 tappituffi closed 5 months ago
11
error with `formula = ~ 1`

#48 adw96 closed 5 months ago
6
FDR correction / p-values

#47 kunstner closed 5 months ago
1
Update readme to link to github.io website containing html versions of our function documentation and vigette

#46 svteichman closed 5 months ago
0
No vignettes found

#45 Cat-Elin closed 5 months ago
5
Update `emuFit()` so it won't run into error with `penalize = FALSE`

#44 svteichman closed 5 months ago
0
would love more descriptive column `covariate`

#43 adw96 closed 5 months ago
5
Parallel vignette

#42 svteichman closed 5 months ago
0
Address issue #38, a vignette for using radEmu with clustered data (take two)

#41 svteichman closed 5 months ago
1
Address issue #38, a vignette for using radEmu with clustered data

#40 svteichman closed 6 months ago
1
vignette: parallelizing score tests

#39 adw96 closed 5 months ago
2
vignette: cluster dependence

#38 adw96 closed 4 months ago
1
Create github.io webpage using pkgdown

#37 MariaAVC closed 7 months ago
1
object 'Csparse_transpose' not found

#36 tengfei-emory closed 7 months ago
6
simulate_data has no coverage

#35 adw96 opened 7 months ago
3