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Create inits from fit and draws objects #937

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merged 34 commits into from
May 4, 2024
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ae46447
adds feature to make inits from fit and draws objects
SteveBronder Mar 21, 2024
a89f31f
update to import stats::aggregate
SteveBronder Mar 21, 2024
0ebe16d
remove use of \() anonymous function
SteveBronder Mar 21, 2024
099a352
fix pareto_smooth call with explicit argument
avehtari Mar 28, 2024
e4ec68e
Merge branch 'master' into feature/fit-inits
jgabry Mar 28, 2024
6c1092b
update stevebronder from ctb to auth
SteveBronder Apr 3, 2024
7da1f17
remove extra files
SteveBronder Apr 3, 2024
872405f
remove extra file
SteveBronder Apr 3, 2024
d85f3b5
add tests for partial variable matching and allow draws objs with les…
SteveBronder Apr 4, 2024
6cd3a63
update r-setup action version
SteveBronder Apr 4, 2024
a7c3400
update rtools version for github actions
SteveBronder Apr 4, 2024
feee313
update rtools for github workflow
SteveBronder Apr 4, 2024
1197ad4
fix init test
SteveBronder Apr 4, 2024
a8297d3
register s3 methods
jgabry Apr 15, 2024
c9a74c1
Merge branch 'master' into feature/fit-inits
jgabry Apr 15, 2024
67f029a
try to fix r cmd check warning about s3 methods
jgabry Apr 15, 2024
e2d3c41
update docs for init object
SteveBronder Apr 17, 2024
238e9bb
Merge remote-tracking branch 'origin' into feature/fit-inits
SteveBronder Apr 17, 2024
9821640
update docs and failing test
SteveBronder Apr 18, 2024
1b2ab35
kickoff again
SteveBronder Apr 18, 2024
20dfe3d
add context to test inits
SteveBronder Apr 18, 2024
2bbfbbf
update docs for inits
SteveBronder Apr 18, 2024
e867c24
add Sys.sleep(1) to test_inits and remove capture.output
SteveBronder Apr 18, 2024
12974f7
Merge branch 'master' into feature/fit-inits
andrjohns Apr 19, 2024
392941e
testing
SteveBronder Apr 19, 2024
e03a643
Merge remote-tracking branch 'origin/feature/fit-inits' into feature/…
SteveBronder Apr 19, 2024
df7617d
fix merge conflicts
jgabry Apr 22, 2024
f14641e
Merge branch 'master' into feature/fit-inits
jgabry Apr 22, 2024
e711265
remove set.seed() in each init test
SteveBronder May 3, 2024
213cfe7
update
SteveBronder May 3, 2024
25d0a74
update for stringi temporary fix
SteveBronder May 3, 2024
cd4eedd
trying workaround for stringi
SteveBronder May 3, 2024
d984931
...
SteveBronder May 3, 2024
ef9e718
remove things to try to fix stringi cli error
SteveBronder May 3, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/Test-coverage.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -63,6 +63,6 @@ jobs:
- name: Test coverage (Windows)
if: runner.os == 'Windows'
run: |
options(covr.gcov = 'C:/rtools40/mingw64/bin/gcov.exe');
options(covr.gcov = 'C:/rtools44/mingw64/bin/gcov.exe');
covr::codecov(type = "tests", function_exclusions = "sample_mpi")
shell: Rscript {0}
2 changes: 1 addition & 1 deletion .github/workflows/cmdstan-tarball-check.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@ jobs:
matrix:
config:
- {os: macOS-latest, r: 'release', rtools: ''}
- {os: windows-latest, r: 'release', rtools: '42'}
- {os: windows-latest, r: 'release', rtools: '44'}
- {os: ubuntu-20.04, r: 'release', rtools: ''}
env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
Expand Down
4 changes: 3 additions & 1 deletion DESCRIPTION
Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@ Authors@R:
person(given = "Andrew", family = "Johnson", role = c("aut", "cre"),
email = "[email protected]",
comment = c(ORCID = "0000-0001-7000-8065")),
person(given = "Steve", family = "Bronder", role = "aut"),
person(given = "Ben", family = "Bales", role = "ctb"),
person(given = "Mitzi", family = "Morris", role = "ctb"),
person(given = "Mikhail", family = "Popov", role = "ctb"),
Expand All @@ -18,7 +19,8 @@ Authors@R:
email = "[email protected]", comment = c(ORCID = "0000-0003-1878-3253")),
person(given = "Jacob", family = "Socolar", role = "ctb"),
person(given = "Martin", family = "Modrák", role = "ctb"),
person(given = "Steve", family = "Bronder", role = "ctb"))
person(given = "Ven", family = "Popov", role = "ctb")
)
Description: A lightweight interface to 'Stan' <https://mc-stan.org>.
The 'CmdStanR' interface is an alternative to 'RStan' that calls the command
line interface for compilation and running algorithms instead of interfacing
Expand Down
10 changes: 10 additions & 0 deletions NAMESPACE
Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,15 @@ S3method(as_draws,CmdStanMCMC)
S3method(as_draws,CmdStanMLE)
S3method(as_draws,CmdStanPathfinder)
S3method(as_draws,CmdStanVB)
S3method(process_init,"function")
S3method(process_init,CmdStanLaplace)
S3method(process_init,CmdStanMCMC)
S3method(process_init,CmdStanMLE)
S3method(process_init,CmdStanPathfinder)
S3method(process_init,CmdStanVB)
S3method(process_init,default)
S3method(process_init,draws)
S3method(process_init,list)
export(as.CmdStanDiagnose)
export(as.CmdStanGQ)
export(as.CmdStanLaplace)
Expand Down Expand Up @@ -40,3 +49,4 @@ export(write_stan_json)
export(write_stan_tempfile)
import(R6)
importFrom(posterior,as_draws)
importFrom(stats,aggregate)
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