parafac4microbiome 1.1.2
- Fixed a URL in README.md to now point towards the correct
website.
parafac4microbiome 1.1.1
corcondia()
is now fully based on the N-way toolbox
implementation.
- Fixed a URL in README.md to now point towards the correct
website.
parafac4microbiome 1.1.0
vanderPloeg2024
now contains all datasets from the
original paper.
- The contents in /data-raw/ are updated to better organize the
studies.
- The Frobenius norm of the tensor is now collapsed into the subject
mode (was the O-norm).
- Fixed an issue where
flipLoadings()
would not flip any
of the modes if there was evidence that all three modes should be
flipped.
- Fixed an issue where
flipLoadings()
would not work when
one model was provided.
- All vignettes are updated to better reflect the updated functions
for this version.
parafac4microbiome 1.0.3
- Minor changes to tests for
parafac_gradient
to make
them more robust towards various platforms checked by CRAN.
parafac4microbiome 1.0.2
- Further rework of
importPhyloseq
,
importTreeSummarizedExperiment
and
importMicrobiotaProcess
to meet CRAN requirements.
parafac4microbiome 1.0.1
- Streamlined examples in
importPhyloseq
,
importTreeSummarizedExperiment
and
importMicrobiotaProcess
.
parafac4microbiome 1.0.0
- Edited DESCRIPTION to meet CRAN requirements.
importPhyloseq
was modified to use rTensor-based cube
folding instead of a for-loop.
importTreeSummarizedExperiment
was modified to use
rTensor-based cube folding instead of a for-loop.
importMicrobiotaProcess
was modified to use
rTensor-based cube folding instead of a for-loop.
parafac4microbiome 0.2.0
- ‘parafac’ is now capable of running an all-at-once optimization
using the methods=“opt” parameter. For now, the default remains
methods=“als” (i.e. the ALS algorithm) because it converges faster to a
similar solution.
importPhyloseq
allows the user to import a phyloseq
object for parafac modelling.
importTreeSummarizedExperiment
allows the user to
import a TreeSummarizedExperiment object for parafac modelling.
importMicrobiotaProcess
allows the user to import a
MicrobiotaProcess object for parafac modelling.
- The text in the vignettes were updated to better reflect the changes
per version 0.1.0.
- The readme and vignettes figures now use sign flipping to make
comparison with the paper easier.
- Some documentation and testing changes anticipating a CRAN
release.
parafac4microbiome 0.1.0
parafac
is now a custom function based on an ALS
algorithm allowing for much more output (see documentation).
initializePARAFAC
initializes the input vectors either
randomly on based on a best-guess SVD model of the unfolded array.
parafac_core_als
contains this ALS algorithm.
parafac_fun
calculates the loss of a parafac model in
anticipation of an all-at-once optimization implementation.
assessNumComponents
and
checkModelStability
have been renamed into
assessModelQuality
and assessModelStability
respectively to clarify their use.
checkModelStability
now works with a minimum and
maximum number of components.
checkModelStability
reports Factor Match Score in a
plot.
calculateFMS
calculates pairwise Factor Match Scores
for a list of model objects.
parafac
, multiwayCenter
,
multiwayScale
and multiwayCLR
are now based on
the new rTensor dependency for tensor unfolding
plotOverallTCCs
has been merged with
plotModelTCCs
.
- Many bugfixes. PARAFAC model solutions should be more stable as a
result.
- Many documentation changes across the board. Overall, the use case
per function should be much clearer.
- Vignettes are updated to reflect and utilize the new changes.
- Removed dependency: paramGUI
parafac4microbiome 0.0.2