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Sync cran branch with current master #112

Merged
merged 52 commits into from Nov 17, 2020
Merged

Sync cran branch with current master #112

merged 52 commits into from Nov 17, 2020

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gaow
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@gaow gaow commented Nov 17, 2020

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pcarbo and others added 30 commits July 14, 2020 21:22
@pcarbo
Minor fixes to code in susie().
75d7206
@pcarbo
Small fixes to the susie roxygen2 docs.
6c9e418
@pcarbo
Working on streamlining roxygen2 docs for susie and related functions.
a935f47
@pcarbo
More streamlining of susie roxygen2 docs.
c00d2e5
@pcarbo
Creating susie_get_methods roxygen2 docs.
0ee4c3b
@pcarbo
Filled out rest of roxygen2 docs, susie_get_methods.
f7d0569
@pcarbo
Some minor fixes to susie_plot_iteration.
3a4aa3f
@pcarbo
Combined roxygen2 docs for susie_plot and susie_plot_iteration.
16df1b2
@pcarbo
Fixed a couple documentation issues.
ed2a050
@pcarbo
susie_plot no longer produces a side effect due to calling options().
45b6556
@pcarbo
Working on susie roxygen2 docs; added CITATION file.
881923b
@pcarbo
Updated TODO.txt.
73c6836
@pcarbo
More merging of susie roxygen2 docs.
7e9f906
@pcarbo
Minor edits to susie_suff_stat roxygen2 docs and elsewhere.
9f6d467
@pcarbo
Removed var_y = 1 default in susie_suff_stat.
d3e4ee4
@pcarbo
Merge branch 'master' into cran.
5ca2ed4
@pcarbo
Made a few minor improvements to the roxygen2 docs and example for th…
d17822b 
…e susie function.
@pcarbo
Working on improvements to susie_suff_stat roxygen2 docs.
c8cf7fb
@pcarbo
Revised roxygen2 docs for susie_rss, and fixed a few bugs / Bad Pract…
4b4100b 
…ices in the error handling.
@pcarbo
Revised roxygen2 docs for susie_rss; added susie_rss example.
bd2bf38
@pcarbo
Fixed up susie_get_methods help page.
d0dca8c
@pcarbo
Made a few minor fixes to susie_plot.
0744009
@pcarbo
Made several minor revisions to roxygen2 docs for susie_trendfilter.
3993e14
@pcarbo
Some small edits to the roxygen2 docs for the plotting functions.
2e6a911
@pcarbo
Revised single_effect_regression and susie help pages.
04cc48c
@pcarbo
Added scaffolding for data set help pages.
d475994
@gaow
Add SNP level lbf #109
a420f31
@gaow
Rename variable lbf to lbf_variable #109
d25aa44
@gaow
Add documentation to data #111
8527b26
@gaow
Add documentation to univariate regrssion
1f77b97
gaow and others added 22 commits October 4, 2020 11:13
@gaow
Add various utils funciton documentation #111
da43d76
@gaow
Add more examples #111
c38b1aa
@zouyuxin
Update helper_testthat.R
ae45b82
@pcarbo
Various fixes to roxygen2 docs, including @examples.
dcad280
@pcarbo
Revised roxygen2 docs for some functions, including examples.
4354699
@pcarbo
Fixed drawing of legend in susie_plot.
4416736
@gaow
Merge branch 'master' into cran
4da1825
@zouyuxin
move sampling function to susie_utils
0d821f4
@zouyuxin
exclude single effect with 0 prior variance
89b2a3c
@zouyuxin
add unit test for sampling function
2f7e24c
@zouyuxin
update document
a4f0b9e
@gaow
Add column names to output if available #93
b8af2c6
@gaow
Add effects pruning to s_init
784e94d
@gaow
Add a check on s_init #92
ec226ac
@gaow
Add a note to remove covariate effects #82
3128e6e
@gaow
Include both claimed coverage and requested coverage in CS result #69
156616e
@gaow
Add print summary #52
38cdc4b
@gaow
Allow for init object having smaller effects than specified L
29bb268
@gaow
Update vignettes
dbbf7f5
@pcarbo
Re-saved N3finemapping.RData using version = 2.
b1662e3
@pcarbo
Compressed N3finemapping.RData using resaveRdaFiles.
2952cb9
@gaow
Fix a bug with check projection
7ff497c
@gaow gaow merged commit 67927e2 into master Nov 17, 2020
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3 participants
@gaow @pcarbo @zouyuxin