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b1eaafb
regenerating doc with roxygen8
jchiquet Jun 5, 2026
33dc9bc
avoid some redudancies in the computations
jchiquet Jun 5, 2026
41a0c77
optimization in zipln + test
jchiquet Jun 8, 2026
09cf498
join optim of M and S in ZIPLN
jchiquet Jun 8, 2026
726bf27
feat: coordonnée Newton diagonal pour PLN et ZIPLN
jchiquet Jun 8, 2026
7e0a15d
pragma lambert
jchiquet Jun 8, 2026
1457fbf
NEWTON for others variants of PLN
jchiquet Jun 8, 2026
2db8193
refactoring newton step
jchiquet Jun 8, 2026
e1c32e6
factorizing newton optimizer for the four basic PLN covariance struct…
jchiquet Jun 8, 2026
6f3ef0b
newton for ve step in PLN variants
jchiquet Jun 8, 2026
bf20ba8
separate nlopt from newton solver for readability
jchiquet Jun 8, 2026
823b013
factorizing Nwton version of VE step in PLN variants
jchiquet Jun 8, 2026
46fe506
use log(S²) paramétristion for nlopt optim
jchiquet Jun 9, 2026
9efb319
logS² dans la version maison Newton de l'optim PLNPCA
jchiquet Jun 9, 2026
977f4bc
added homemade backend
jchiquet Jun 9, 2026
24aa97b
testing homemade newton as default
jchiquet Jun 9, 2026
402e5ca
optimizing Armijo updates
jchiquet Jun 9, 2026
592adcc
testing spectral gradient for PLNPCA
jchiquet Jun 9, 2026
cf51508
hybrid backend for all variants of standard PLN
jchiquet Jun 9, 2026
c6569a7
added optimizer with alternate parametrization for nlopt solver
jchiquet Jun 9, 2026
43a0b1c
make alternative param the default for nlopt and standard PLN variants
jchiquet Jun 9, 2026
b7a7149
use alternative param in all optimizer
jchiquet Jun 10, 2026
0fdfb0d
reparing some tests that failed after factorisation
jchiquet Jun 10, 2026
325bdef
cleaning doc and dead code
jchiquet Jun 10, 2026
28939a0
fix use of PLNLDA_param
jchiquet Jun 10, 2026
56f7bfa
updating devlog
jchiquet Jun 10, 2026
c74f431
updating doc and optim param homogeneisation
jchiquet Jun 10, 2026
cade6b2
more fusion in param optim
jchiquet Jun 10, 2026
897869f
added S3 methods for logLik, AIC, BIC, ICL
jchiquet Jun 10, 2026
d1e7fa9
pkgdown ref
jchiquet Jun 10, 2026
ff8c9c7
improvements and consistency of R code
jchiquet Jun 10, 2026
cf3d960
factorizing roxygen doc
jchiquet Jun 10, 2026
7943242
some fix in doc and dependencies
jchiquet Jun 10, 2026
c0146c0
fixes consecutive to PR changes
jchiquet Jun 10, 2026
85b8c47
fix in tests
jchiquet Jun 10, 2026
f02aa55
fixes C++ + factorisation
jchiquet Jun 10, 2026
16a79a3
avoid redundancies with exp in Newton optim
jchiquet Jun 11, 2026
14a5797
exact block newton for small dataset + removing dead code
jchiquet Jun 11, 2026
6cc41d3
more robust Newton algorithm
jchiquet Jun 11, 2026
4a3336c
script for backend and convergence analysis
jchiquet Jun 11, 2026
bd56a24
res benchmark
jchiquet Jun 12, 2026
cd01635
cleaning code
jchiquet Jun 12, 2026
56900ca
avoid passing S as S² is now the natural parameter in PLN-like algo (…
jchiquet Jun 12, 2026
1de7e65
use S2 instead of S including in doc for PLN, ZIPLN and variantes
jchiquet Jun 12, 2026
62ecfaf
cleaning optim for zipln
jchiquet Jun 12, 2026
d60f9ce
fix test for zipln after first batch of topitmization
jchiquet Jun 12, 2026
156b179
suppressing API for approx_zi which doesn't work in practice.
jchiquet Jun 12, 2026
81b6500
updating DEVLOG
jchiquet Jun 12, 2026
ae976cb
fixing and enhancing torch impl for PLN : bug xies, new param for var…
jchiquet Jun 12, 2026
910c32a
use psi in troch impl of PLNLDA
jchiquet Jun 12, 2026
7042e2b
use log(S²) in PLNPCA for all optimizer (toch, newton, CCSAQ)
jchiquet Jun 12, 2026
6a9d34c
use log(S²) in PLNPCA for all optimizer (toch, newton, CCSAQ)
jchiquet Jun 12, 2026
fa03450
renaming/reorganization
jchiquet Jun 12, 2026
92070c7
suppressing hybrid backend (now useless)
jchiquet Jun 12, 2026
28e2fb7
benchmark plnpca
jchiquet Jun 12, 2026
7094ff7
benchmark directory in inst
jchiquet Jun 12, 2026
93bc20a
fix in init PLNPCA
jchiquet Jun 12, 2026
58f8b19
several init option for PLNPCA, LM + svd by default
jchiquet Jun 13, 2026
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6 changes: 5 additions & 1 deletion .Rbuildignore
Original file line number Diff line number Diff line change
Expand Up @@ -26,12 +26,16 @@
^inst/check$
^inst/torch_for_r$
^inst/case_studies$
^inst/test/
^inst/missing_data$
^inst/simus_PLNnetwork$
^inst/simus_ZIPLN$
^inst/benchmark$
^inst/binom$
^\.github$
^data-raw$
^CRAN-SUBMISSION$
^AUTHORS$
^dev$
^\.claude$
^DEVLOG.*\.md$
snowflake.log
2 changes: 2 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -72,3 +72,5 @@ README.html
pkgdown

tests/testthat/_snaps/

snowflake.log
13 changes: 6 additions & 7 deletions DESCRIPTION
Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ URL: https://pln-team.github.io/PLNmodels/
BugReports: https://github.com/pln-team/PLNmodels/issues
License: GPL (>= 3)
Depends: R (>= 4.1.0)
Imports:
Imports:
cli,
corrplot,
dplyr,
Expand All @@ -48,29 +48,27 @@ Imports:
R6,
Rcpp,
rlang,
scales,
stats,
tidyr,
torch
Suggests:
Suggests:
factoextra,
knitr,
rmarkdown,
spelling,
testthat
LinkingTo:
LinkingTo:
nloptr,
Rcpp,
RcppArmadillo
VignetteBuilder:
VignetteBuilder:
knitr
biocViews:
Encoding: UTF-8
Language: en-US
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Collate:
Collate:
'PLNfit-class.R'
'PLN.R'
'PLNLDA.R'
Expand Down Expand Up @@ -112,3 +110,4 @@ Collate:
'utils-zipln.R'
'utils.R'
'zzz.R'
Config/roxygen2/version: 8.0.0
595 changes: 595 additions & 0 deletions DEVLOG_2026-06-08-09.md

Large diffs are not rendered by default.

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