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Silently convert vector to matrix with one row in setup_rank_data #361

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osorensen opened this issue Jan 26, 2024 · 0 comments
Closed

Silently convert vector to matrix with one row in setup_rank_data #361

osorensen opened this issue Jan 26, 2024 · 0 comments
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enhancement New feature or request

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@osorensen
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Being able to specify one row at a time is useful in SMC, and currently this requires providing rankings = mat[i, , drop = FALSE], which is a bit annoying.

library(BayesMallows)
setup_rank_data(1:10)
#> Error in rep(1, nrow(rankings)): invalid 'times' argument

Created on 2024-01-26 with reprex v2.1.0
@osorensen osorensen added the enhancement New feature or request label Jan 26, 2024
osorensen added a commit that referenced this issue Jan 26, 2024
@osorensen
added handling of vector data #361
32c2194
osorensen added a commit that referenced this issue Jan 26, 2024
@osorensen
solving #361
d7525b7
osorensen added a commit that referenced this issue Jan 26, 2024
@osorensen
Can now deal with a single vector of input data (#364)
ec9500c 
* added handling of vector data #361

* styling
osorensen added a commit that referenced this issue Feb 16, 2024
@osorensen
Update based on some recent developments (#379)
8850531 
* bookkeeping

* removed unnecessary call

* marking as const

* adding more consts

* additional safety measures

* parallelization working (#355)

* parallelization working

* updating tests

* styling

* updating test

* added info about parallelization

* correcting an error in docs

* update cran-comments

* updating comments

* updating news

* deleting submission file

* Adding support for sampling from prior (#360)

* 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

* fixed error in update_mallows.SMCMallows

* updated failing test and added namespace qualifier

* added long-running SMC test from prior

* Take care of item names properly (#363)

* fixing item name issue

* updating a unit test

* styling

* Can now deal with a single vector of input data (#364)

* added handling of vector data #361

* styling

* updating news

* updated set_priors function

* closes #370

* Added a gamma prior (#371)

* updated set_priors function

* closes #370

* Had forgot to implement the change... (#372)

* updated set_priors function

* closes #370

* fixed forgotten implementation

* Added lag option (#373)

* updated documentation

* adding references section

* more documentation updates

* updated set_priors function

* closes #370

* implemented user-defined lag

* added lag, closes #369

* styling

* ready for the change

* Resampling issue 365 (#376)

* updated set_priors function

* closes #370

* ready for the change

* implemented the resampler in cpp

* added various resampling options. tests are missing

* fixed numerical overflow problem and forgotten mcmc loop

* added a simple test for the resampler

* styling

* added missing memory header

* removed two tests where my M1 mac gives different results

* removed git conflict marker

* added a line shift

* removing const-ref from built-in types

* refactoring limits functions for pairwise augmentation

* increasing test strictness

* added some more work

* moving distance code into implementation file

* moved partition function code into cpp files

* added code for reproducing Liu et al 2019 review

* changed updating frequency for pkgdown. closes #380

* adding ignore to codecov

* fixing #381 (#382)

* Heatplot issue 381 (#383)

* fixing #381

* added unit test for #381

* updated news
osorensen added a commit that referenced this issue Feb 28, 2024
@osorensen
A lot of changes (#397)
390f601 
* bookkeeping

* removed unnecessary call

* marking as const

* adding more consts

* additional safety measures

* parallelization working (#355)

* parallelization working

* updating tests

* styling

* updating test

* added info about parallelization

* correcting an error in docs

* update cran-comments

* updating comments

* updating news

* deleting submission file

* Adding support for sampling from prior (#360)

* 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

* fixed error in update_mallows.SMCMallows

* updated failing test and added namespace qualifier

* added long-running SMC test from prior

* Take care of item names properly (#363)

* fixing item name issue

* updating a unit test

* styling

* Can now deal with a single vector of input data (#364)

* added handling of vector data #361

* styling

* updating news

* updated set_priors function

* closes #370

* Added a gamma prior (#371)

* updated set_priors function

* closes #370

* Had forgot to implement the change... (#372)

* updated set_priors function

* closes #370

* fixed forgotten implementation

* Added lag option (#373)

* updated documentation

* adding references section

* more documentation updates

* updated set_priors function

* closes #370

* implemented user-defined lag

* added lag, closes #369

* styling

* ready for the change

* Resampling issue 365 (#376)

* updated set_priors function

* closes #370

* ready for the change

* implemented the resampler in cpp

* added various resampling options. tests are missing

* fixed numerical overflow problem and forgotten mcmc loop

* added a simple test for the resampler

* styling

* added missing memory header

* removed two tests where my M1 mac gives different results

* removed git conflict marker

* added a line shift

* removing const-ref from built-in types

* refactoring limits functions for pairwise augmentation

* increasing test strictness

* added some more work

* moving distance code into implementation file

* moved partition function code into cpp files

* added code for reproducing Liu et al 2019 review

* changed updating frequency for pkgdown. closes #380

* adding ignore to codecov

* fixing #381 (#382)

* Heatplot issue 381 (#383)

* fixing #381

* added unit test for #381

* updated news

* updated tests

* Swap issue 368 (#384)

* first refactoring of leap-and-shift

* renamed back

* made proposal class

* made rank proposal class

* updated tests

* fixed bug in call to leapandshift

* removing work docs

* some more back and forth

* added the LeapAndShift class to SMC

* inherited the constructor for ProposalDistribution

* figured out there is a swap function

* made distfun a class member

* swap proposal implemented for rho

* updated news and tests

* refactored propose_swap

* making class for swap proposal

* added the active set strategy or whatever it's called to augmented rankings

* removed unnecessary update_leap_and_shift_indices functions

* could remove distfun from ProposalDistribution

* refactoring

* styling

* incremented dev version

* corrected typo in docs

* refactor

* removed unused argument

* changed argument order

* moved metric into the parameters class

* fixed a bug

* simplifying the tidy function

* simplified n_assessors argument

* removed observation_frequency from cpp return values

* moved any_missing to setup_rank_data

* moving augpair to setup_rank_data

* added test for burnin

* some fixes

* updated news

* rebuilt smc vignette

* recompiled readme

* Function for sequential learning (#391)

* 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

* harmonizing pairwise and partial

* Burnin issue 394 (#396)

* 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

* incremented dev version

* updated example

* styling

* styling

* pleasing CodeFactor

* fixed bug in acceptance rate for compute_mallows_sequentially

* not linting examples

* small improvement of docs to plot_elbow
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@osorensen