Code

Add mr.mash-rss#4

Code

Merged

pcarbo merged 107 commits intostephenslab:masterstephenslab/mr.mash.alpha:masterfrom morgantelab:mastermorgantelab/mr.mash.alpha:masterCopy head branch name to clipboardMay 6, 2024

+3,137-354

Commits

Commits on Mar 1, 2023

• Copy files for rss version

  fmorgante

  committed
  7236efc

  Copy full SHA for 7236efc

Commits on Mar 3, 2023

• Rename file

  fmorgante

  committed
  dc371e5

  Copy full SHA for dc371e5

Commits on Mar 4, 2023

• Start modifying functions to use xtx and xtY

  fmorgante

  committed
  36b4b38

  Copy full SHA for 36b4b38

Commits on Mar 6, 2023

• Keep modifying rss functions

  fmorgante

  committed
  7eb2d3d

  Copy full SHA for 7eb2d3d

• Small change

  fmorgante

  committed
  c2269ce

  Copy full SHA for c2269ce

• More changes to rss functions

  fmorgante

  committed
  054e380

  Copy full SHA for 054e380

• Bump up version

  fmorgante

  committed
  6b30309

  Copy full SHA for 6b30309

• Fix inputs bug

  fmorgante

  committed
  0aeac28

  Copy full SHA for 0aeac28

• Run devtools::document()

  fmorgante

  committed
  1c4134f

  Copy full SHA for 1c4134f

• Bump up version and add author

  fmorgante

  committed
  affbea6

  Copy full SHA for affbea6

• Fix bug

  fmorgante

  committed
  859ae7e

  Copy full SHA for 859ae7e

• Fiz issue with order of arguments

  fmorgante

  committed
  cef442b

  Copy full SHA for cef442b

• Remove junk code

  fmorgante

  committed
  9611a25

  Copy full SHA for 9611a25

• Remove junk code 2

  fmorgante

  committed
  de3ce24

  Copy full SHA for de3ce24

• Fix naming issue

  fmorgante

  committed
  5028f1e

  Copy full SHA for 5028f1e

• Fix bug

  fmorgante

  committed
  773ba28

  Copy full SHA for 773ba28

Commits on Mar 7, 2023

• Fix bug

  fmorgante

  committed
  8a0f740

  Copy full SHA for 8a0f740

• Fix another bug

  fmorgante

  committed
  737e9bf

  Copy full SHA for 737e9bf

• Fix yet another bug

  fmorgante

  committed
  518be0d

  Copy full SHA for 518be0d

• Try fixing a bug

  fmorgante

  committed
  d1bb9a5

  Copy full SHA for d1bb9a5

• Fix bug

  fmorgante

  committed
  37cba8e

  Copy full SHA for 37cba8e

• Fix bug

  fmorgante

  committed
  e0d4548

  Copy full SHA for e0d4548

• Add YtY

  fmorgante

  committed
  c8a2ebe

  Copy full SHA for c8a2ebe

• Add YtY

  fmorgante

  committed
  024fedb

  Copy full SHA for 024fedb

• Fix missing part

  fmorgante

  committed
  47ea0f1

  Copy full SHA for 47ea0f1

• Bump up version

  fmorgante

  committed
  53a92da

  Copy full SHA for 53a92da

Commits on Mar 8, 2023

• Add case of standardized X

  fmorgante

  committed
  c18728f

  Copy full SHA for c18728f

Commits on Mar 9, 2023

• Fix bug

  fmorgante

  committed
  709c6a3

  Copy full SHA for 709c6a3

• Bump up version

  fmorgante

  committed
  d3c7d96

  Copy full SHA for d3c7d96

Commits on Mar 14, 2023

• Add code to perform the inner loop in Rcpp

  fmorgante

  committed
  061cd45

  Copy full SHA for 061cd45

• Fix bugs -- ELBO still wrong

  fmorgante

  committed
  258e9b3

  Copy full SHA for 258e9b3

• Run devtools::document()

  fmorgante

  committed
  fdb6c86

  Copy full SHA for fdb6c86

Commits on Mar 15, 2023

• Fix issue with ELBO rss computation

  fmorgante

  committed
  d8e7088

  Copy full SHA for d8e7088

• Simplify computation

  fmorgante

  committed
  2998424

  Copy full SHA for 2998424

• Bump up version

  fmorgante

  committed
  3969ca2

  Copy full SHA for 3969ca2

Commits on Mar 16, 2023

• Add utility function

  fmorgante

  committed
  dc313be

  Copy full SHA for dc313be

• Add input checks and deal with intercept

  fmorgante

  committed
  1e731b0

  Copy full SHA for 1e731b0

• Add coeff and predict functions for the mr.mash.rss class

  fmorgante

  committed
  eb85cf4

  Copy full SHA for eb85cf4

• Add clarification

  fmorgante

  committed
  f5ff3f2

  Copy full SHA for f5ff3f2

• Add dependency and bump up version

  fmorgante

  committed
  b0c9f9b

  Copy full SHA for b0c9f9b

• Fix example

  fmorgante

  committed
  2981c39

  Copy full SHA for 2981c39

• Fix names

  fmorgante

  committed
  d647671

  Copy full SHA for d647671

• Run devtools::document()

  fmorgante

  committed
  54c8206

  Copy full SHA for 54c8206

• Bump up version

  fmorgante

  committed
  ce29106

  Copy full SHA for ce29106

• Fix issue

  fmorgante

  committed
  65a7206

  Copy full SHA for 65a7206

Commits on Mar 17, 2023

• Fix bug

  fmorgante

  committed
  36cc185

  Copy full SHA for 36cc185

Commits on Mar 21, 2023

• Add Deborah to license

  fmorgante

  committed
  774aba4

  Copy full SHA for 774aba4

Commits on Mar 22, 2023

• Improve simulation function

  fmorgante

  committed
  9332146

  Copy full SHA for 9332146

• Bump up version

  fmorgante

  committed
  3e24d3b

  Copy full SHA for 3e24d3b

• Fix some conflicts

  Show description for 1005f72
  fmorgante

  committed
  1005f72

  Copy full SHA for 1005f72

• Add seed argument

  fmorgante

  committed
  1b6fac6

  Copy full SHA for 1b6fac6

• Run devtools::document()

  fmorgante

  committed
  d265d1b

  Copy full SHA for d265d1b

• Additional improvements

  fmorgante

  committed
  62d0602

  Copy full SHA for 62d0602

• Run devtools::document()

  fmorgante

  committed
  7cdcec3

  Copy full SHA for 7cdcec3

• Fix bugs

  fmorgante

  committed
  03b6b0c

  Copy full SHA for 03b6b0c

• Handle covariance matrices that are not PD

  fmorgante

  committed
  8d921f7

  Copy full SHA for 8d921f7

• Run devtools::document()

  fmorgante

  committed
  5cb2ecd

  Copy full SHA for 5cb2ecd

• Bump up version

  fmorgante

  committed
  8caa78e

  Copy full SHA for 8caa78e

• Fix issues with rng

  fmorgante

  committed
  c4455ee

  Copy full SHA for c4455ee

• Add flag to deal with large matrices

  fmorgante

  committed
  4e512d4

  Copy full SHA for 4e512d4

• Bump up version

  fmorgante

  committed
  f828389

  Copy full SHA for f828389

• Improve efficiency

  fmorgante

  committed
  d8fcccf

  Copy full SHA for d8fcccf

• Run devtools::document()

  fmorgante

  committed
  4998392

  Copy full SHA for 4998392

• Bump up version

  fmorgante

  committed
  dcab9d5

  Copy full SHA for dcab9d5

Commits on Mar 25, 2023

• Add arma compilation flags

  fmorgante

  committed
  39e7caf

  Copy full SHA for 39e7caf

• Bump up version

  fmorgante

  committed
  0bd9d02

  Copy full SHA for 0bd9d02

• Add additional flags

  fmorgante

  committed
  63b7ba2

  Copy full SHA for 63b7ba2

Commits on Mar 30, 2023

• Fix computations

  fmorgante

  committed
  86bba4b

  Copy full SHA for 86bba4b

• Run devtools::document()

  fmorgante

  committed
  df5f41c

  Copy full SHA for df5f41c

• Bump up version

  fmorgante

  committed
  93a5ba3

  Copy full SHA for 93a5ba3

• Add option for update order

  fmorgante

  committed
  5b42823

  Copy full SHA for 5b42823

• Run devtools::document()

  fmorgante

  committed
  fe5cf36

  Copy full SHA for fe5cf36

• Bump up version

  fmorgante

  committed
  f850a79

  Copy full SHA for f850a79

• Add option for a random order of updates

  fmorgante

  committed
  b987f1f

  Copy full SHA for b987f1f

• Run devtools::document

  fmorgante

  committed
  32de28a

  Copy full SHA for 32de28a

• Bump up version

  fmorgante

  committed
  bcf658a

  Copy full SHA for bcf658a

Commits on Mar 31, 2023

• Add some rss version unit tests

  fmorgante

  committed
  6b153b0

  Copy full SHA for 6b153b0

• Bump up version

  fmorgante

  committed
  e2dc8ac

  Copy full SHA for e2dc8ac

• Update README and run pkgdown::build_site()

  fmorgante

  committed
  230d4bd

  Copy full SHA for 230d4bd

Commits on Apr 17, 2023

• Fix bug

  fmorgante

  committed
  b012f8f

  Copy full SHA for b012f8f

• Bump up version

  fmorgante

  committed
  363c428

  Copy full SHA for 363c428

Commits on Apr 27, 2023

• Fix example

  fmorgante

  committed
  e667df9

  Copy full SHA for e667df9

• Merge branch 'rss_dev' of github.com:morgantelab/mr.mash.alpha into rss_dev

  fmorgante

  committed
  92e0681

  Copy full SHA for 92e0681

• Run devtools::document()

  fmorgante

  committed
  ab6660b

  Copy full SHA for ab6660b

• Bump up version

  fmorgante

  committed
  614497d

  Copy full SHA for 614497d

Commits on Oct 27, 2023

• Use updated flashier interface

  fmorgante

  committed
  9c0445b

  Copy full SHA for 9c0445b

• Bump up version

  fmorgante

  committed
  e89af04

  Copy full SHA for e89af04

Commits on Nov 15, 2023

• Fix bug

  fmorgante

  committed
  77b5ac5

  Copy full SHA for 77b5ac5

• Minor improvement

  fmorgante

  committed
  78b3970

  Copy full SHA for 78b3970

Commits on Jan 11, 2024

• Add tests for diagonal update of V

  fmorgante

  committed
  f59ca6c

  Copy full SHA for f59ca6c

Commits on Apr 24, 2024

• Merge branch 'rss_dev'

  fmorgante

  committed
  4b528d9

  Copy full SHA for 4b528d9

• Fix merge conflicts

  fmorgante

  committed
  0cd4d61

  Copy full SHA for 0cd4d61

• Fix bug

  fmorgante

  committed
  596b8e1

  Copy full SHA for 596b8e1

Commits on Apr 26, 2024

• Revert to not using Rfast for the simulations

  fmorgante

  committed
  b527c65

  Copy full SHA for b527c65

• Bump up version

  fmorgante

  committed
  c615adb

  Copy full SHA for c615adb

• Remove remotes

  fmorgante

  committed
  e723a2c

  Copy full SHA for e723a2c

• Merge branch 'rss_dev'

  fmorgante

  committed
  565d08a

  Copy full SHA for 565d08a

• Remove unused argument

  fmorgante

  committed
  f8b0516

  Copy full SHA for f8b0516

• Run devtools::document() and pkgdown::build_site()

  fmorgante

  committed
  7d0755d

  Copy full SHA for 7d0755d

• Bump up version

  fmorgante

  committed
  8cac9b4

  Copy full SHA for 8cac9b4

• Fix license and re-run pkgdown::build_site()

  fmorgante

  committed
  9c4d9ef

  Copy full SHA for 9c4d9ef

Commits on Apr 28, 2024

• Minor changes/clean up

  fmorgante

  committed
  67df4b0

  Copy full SHA for 67df4b0

• Add some input checks

  fmorgante

  committed
  bf60a7d

  Copy full SHA for bf60a7d

• Bump up version

  fmorgante

  committed
  330af92

  Copy full SHA for 330af92

• Run devtools::document() and pkgdown::build_site()

  fmorgante

  committed
  7971652

  Copy full SHA for 7971652

Commits on Apr 30, 2024

• Use TBB explicitly

  fmorgante

  committed
  9406b34

  Copy full SHA for 9406b34

• Bump up version

  fmorgante

  committed
  771925b

  Copy full SHA for 771925b