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A lot of changes #397

Merged
merged 78 commits into from
Feb 28, 2024
Merged

A lot of changes #397

merged 78 commits into from
Feb 28, 2024

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osorensen
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@osorensen
bookkeeping
f93b77b
@osorensen
removed unnecessary call
f9f55db
@osorensen
marking as const
84a2230
@osorensen
adding more consts
7959b6c
@osorensen
additional safety measures
2a639d6
@osorensen
parallelization working (#355)
7391954 
* parallelization working

* updating tests

* styling

* updating test

* added info about parallelization
@osorensen
correcting an error in docs
a8bdc0d
@osorensen
Merge branch 'develop' of https://github.com/ocbe-uio/BayesMallows in…
2d69ada 
…to develop
@osorensen
update cran-comments
83248f6
@osorensen
updating comments
506d5c4
@osorensen
Merge branch 'master' into develop
a5d84e4
@osorensen
updating news
d25a0f2
@osorensen
deleting submission file
243b8a3
@osorensen
Adding support for sampling from prior (#360)
16a93ba 
* added prior sampling

* updating news

* deleting submission file

* fixing the prior sampling

* styling

* added unit test for SMC starting from prior

* added test for sample_prior

* updating test after merging with TBB

* styling

* updating news
@osorensen
Merge branch 'develop' of https://github.com/ocbe-uio/BayesMallows in…
eddbd22 
…to develop
@osorensen
fixed error in update_mallows.SMCMallows
9b7d4dc
@osorensen
updated failing test and added namespace qualifier
236a21d
@osorensen
added long-running SMC test from prior
144a451
@osorensen
Take care of item names properly (#363)
a62545e 
* fixing item name issue

* updating a unit test

* styling
@osorensen
Can now deal with a single vector of input data (#364)
ec9500c 
* added handling of vector data #361

* styling
@osorensen
updating news
db8a31b
@osorensen
updated set_priors function
78e4f29
@osorensen
closes #370
86723fc
@osorensen
Added a gamma prior (#371)
2a61f42 
* updated set_priors function

* closes #370
@osorensen
Merge branch 'priors-issue-370' of https://github.com/ocbe-uio/BayesM…
45e1eeb 
…allows into develop
@osorensen
Had forgot to implement the change... (#372)
9f4cc7f 
* updated set_priors function

* closes #370

* fixed forgotten implementation
@osorensen
Merge branch 'develop' of https://github.com/ocbe-uio/BayesMallows in…
defa9db 
…to develop
@osorensen
Added lag option (#373)
41cb4ab 
* updated documentation

* adding references section

* more documentation updates

* updated set_priors function

* closes #370

* implemented user-defined lag

* added lag, closes #369

* styling
@osorensen
ready for the change
9fddacd
@osorensen
Merge branch 'develop' of https://github.com/ocbe-uio/BayesMallows in…
ee08f70 
…to develop
@osorensen
removed observation_frequency from cpp return values
212ed23
@osorensen
moved any_missing to setup_rank_data
e4ba5b6
@osorensen
moving augpair to setup_rank_data
d22834a
@osorensen
added test for burnin
8c5b28f
@osorensen
some fixes
39e9a5c
@osorensen
updated news
1b42c5b
@osorensen
rebuilt smc vignette
f79c738
@osorensen
recompiled readme
8e47867
@osorensen
Function for sequential learning (#391)
b244710 
* incremented dev version

* got rid of unused variable

* turned new_data into a list

* main part ready and passing tests

* styling and fixing docs issue

* Updating docs

* small steps

* adding user ids

* added the consistency vector to the particles

* updating examples

* updating more

* updating examples

* passing rcmdchck

* added deprecation notice for old burnin setting

* skipping the deprecation notice

* removed unnecessary brackets

* updated particle handling

* removed unused code

* refactoring complete

* ready for sequential updating

* we have a loop

* small fix

* added learning examples

* added test

* added tests

* styling and updating docs

* updated expected test output

* have to get rid of a test for now due to platform dependence
@osorensen
harmonizing pairwise and partial
60ab54a
@osorensen
Merge branch 'develop' of https://github.com/ocbe-uio/BayesMallows in…
3d7757d 
…to develop
@osorensen
Burnin issue 394 (#396)
a2600d1 
* added burnin

* made iteration number a class member

* simplified alpha update

* got rid of rho_index

* added alpha acceptance rate and test

* preparing for rho_acceptance

* added rho burnin

* added tracking of acceptance

* updating docs and examples

* styling
@osorensen
incremented dev version
35dd003
@osorensen
updated example
190d85d
@osorensen
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The Linter error is a false positive. It reports on the library() statements in this example, but since ggplot2 is listed in Imports I think it is absolutely fine. R CMD check does not report on it either.

BayesMallows/inst/examples/compute_mallows_sequentially_example.R

Lines 1 to 5 in 35dd003

# Observe one ranking at each of 12 timepoints
library(ggplot2)
data <- lapply(seq_len(nrow(potato_visual)), function(i) {
setup_rank_data(potato_visual[i, ])
})

@osorensen
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Should close #394 and #386

@wleoncio
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The Linter error is a false positive. It reports on the library() statements in this example, but since ggplot2 is listed in Imports I think it is absolutely fine. R CMD check does not report on it either.

BayesMallows/inst/examples/compute_mallows_sequentially_example.R

Lines 1 to 5 in 35dd003

# Observe one ranking at each of 12 timepoints
library(ggplot2)
data <- lapply(seq_len(nrow(potato_visual)), function(i) {
setup_rank_data(potato_visual[i, ])
})

Alright, but then perhaps we should add those lines to linter.yml so CI doesn't bothers us about it.

wleoncio
wleoncio approved these changes Feb 28, 2024
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Good job, interesting solution with the burnin() function!

@osorensen
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The Linter error is a false positive. It reports on the library() statements in this example, but since ggplot2 is listed in Imports I think it is absolutely fine. R CMD check does not report on it either.

BayesMallows/inst/examples/compute_mallows_sequentially_example.R

Lines 1 to 5 in 35dd003

# Observe one ranking at each of 12 timepoints
library(ggplot2)
data <- lapply(seq_len(nrow(potato_visual)), function(i) {
setup_rank_data(potato_visual[i, ])
})

Alright, but then perhaps we should add those lines to linter.yml so CI doesn't bothers us about it.

Absolutely. I'll add that now.

@osorensen
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@wleoncio I think I managed to fix the linter issue, but do you know where CodeFactor gets its settings from?

@wleoncio
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@wleoncio I think I managed to fix the linter issue, but do you know where CodeFactor gets its settings from?

Unfortunately, that's still a mystery to me 😅

@osorensen osorensen merged commit 390f601 into master Feb 28, 2024
16 of 17 checks passed
@osorensen osorensen deleted the develop branch February 28, 2024 14:44
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@wleoncio wleoncio wleoncio approved these changes

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@osorensen @wleoncio