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Remove pytorch warning message #828
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153584d
add cbmr.py file
yifan0330 59a3742
create a design matrix function for cbmr
yifan0330 3371a98
add test file for cbmr
yifan0330 8d2a151
modify pre-process and training function in cbmr
yifan0330 d014234
modify the dataset.anotations in cbmr
yifan0330 f741eeb
add documentation in utils functions
yifan0330 e326758
update model structure
yifan0330 85a6d11
update optimizer function
yifan0330 fe80124
[skip ci][wip] update loss function
yifan0330 3edaa74
update _fit function in CBMR
yifan0330 cadffa6
[wip][skip ci] allow other data types as pre-process inputs
yifan0330 c632d29
use a sparse array instead of numpy
yifan0330 a22048d
[skip ci][wip] allow for multiple-group cbmr
yifan0330 ab450fa
[skip ci][wip] fix conflict to merge
yifan0330 0f2a93a
solve conflicts
yifan0330 b3ee6f1
[skip CI][wip] modify settings in pre_process
yifan0330 0262c66
[skip ci][wip] implemented group-wise CBMR and fix problems
yifan0330 7fd47bc
[skip ci][wip] add results as inputs to MetaResults
yifan0330 b2b84a4
Merge branch 'main' of https://github.com/neurostuff/NiMARE into enha…
yifan0330 48d4b57
[skip ci][wip] modify standardization of group moderators
yifan0330 5e6107f
[skip ci][wip] implement NB regression
yifan0330 c686558
[skip ci][wip]remove vox2idx function and simplify the code
yifan0330 171d5a6
[skip ci][wip]develp CNB model
yifan0330 b786a3d
adjustment to Firth penalty
f7cc042
Merge branch 'main' of https://github.com/neurostuff/NiMARE into enha…
1a822d6
Merge branch 'main' of https://github.com/neurostuff/NiMARE into enha…
e051015
[skip CI][wip] implement index2voxel function
c38aa31
[skip CI][wip] add implementation for SE of regression coefficient
27a8c8e
[skip CI][WIP] implementing CBMRInference
c0da20d
[skip CI][wip] implement spatial homogeneity test
8be35d8
[skip ci][wip] implement CBMRInference group-wise comparison
8e73380
formalize GLH contrast variable
e6c1b92
[skip ci][wip] implemented Cov in GLH for all three models
988c5b4
[skip CI][wip] add a demonstration for CBMREstimator & CBMRInference
a746b9a
Merge branch 'main' of https://github.com/neurostuff/NiMARE into enha…
f4cd61e
[skip CI][wip] modify example files for demonstrating CBMR
024797d
add documentation to functions.
7c1b8ad
solve some issues suggested by flake8
9882c51
[skip CI][WIP] fix a bug in log-likelihood function of CNB model
b0a5e2d
Merge branch 'enhance_cbmr' of github.com:yifan0330/NiMARE into yifan…
jdkent 5824abb
Merge pull request #3 from jdkent/yifan/enhance_cbmr
yifan0330 f70e6ac
[skip CI][WIP] Update code according to comments
d103ceb
[skip CI][WIP] solve conflicts in code
7de6b78
restructure code
jdkent 1253adb
[skip CI][WIP] replace variable name and remove study_level_moderators
e00a621
[skip CI][WIP] changed variables names to be more intuitive.
bd88e32
reorganize model classes to be partially initialized
jdkent f64ad48
[skip CI][WIP] set some params as attribute of CBMREstimator Class.
c5dfec6
restruct inference code to models
7a65550
add some code for overdispersion model class.
6b51276
change model to use optimizer
jdkent 320a712
change model names
jdkent ea0ad27
refactor the optimizer functions into the model class
b55433d
create a fit method for models
jdkent b525887
resolve conflicts
jdkent a62f26c
add summary to model fit
2ec109f
function name suggestions
jdkent 2f9ad20
make square_root an attribute
jdkent 6e3f425
allow categorical variables in CBMR
dac6287
fix a bug
e1c801f
new changes on inference class
404ff61
solve conflict
e580951
restruct code in CBMRInference
5b19e4d
add documentation foor create_contrast function
ea73c72
add new steps: remove duplicate rows in contrast matrix
9c2e7aa
modify documentation and comments
02bc3fa
change function name to snake case
050d470
restruct code and remove repetition
a761b07
reconstruct code, remove repeated code
06629b8
correct testing cases of z_to_p function
17bd65e
add regular expression code to CBMRInference
3eb6432
[skip CI][WIP] update example file based on reconstructed code
e842394
[skip CI][WIP] Tried standardized categorical covariates
a07d359
Raise deprecation warnings with Python 3.6 and 3.7 (#754)
JulioAPeraza c87b134
[MAINT] Fix various errors due to major version changes in dependenci…
jdkent 12ff95b
Remove "dataset" `return_type` option from kernel transformers (#752)
JulioAPeraza 252ab43
[skip ci] Update CHANGELOG
jdkent cb3b1ac
Support nibabel 5.0.0 (#762)
JulioAPeraza d8918f6
Do not zero out one-tailed z-statistics for p-values > 0.5 (#693)
JulioAPeraza 7a70ed3
Link to NeuroStars software support category instead of neuro questio…
tsalo 6a986b2
Revert "Do not zero out one-tailed z-statistics for p-values > 0.5" (…
JulioAPeraza ea43cec
create a design matrix function for cbmr
yifan0330 dac143f
[skip CI][WIP] solve conflicts
2f14d55
update model structure
yifan0330 9d02762
use a sparse array instead of numpy
yifan0330 514166f
[skip CI][WIP] solve conflict
8e237a1
solve conflicts.
5b4df2c
[skip ci][wip] modify standardization of group moderators
yifan0330 a4f67c0
[skip CI][wip] implement index2voxel function
b6d912b
[skip CI][wip] add implementation for SE of regression coefficient
01aab8b
[skip CI][wip] add a demonstration for CBMREstimator & CBMRInference
5f732ab
[skip CI][WIP] fix a bug in log-likelihood function of CNB model
f745b63
[skip CI][WIP] Update code according to comments
2f10a96
refactor the optimizer functions into the model class
59432d9
create a fit method for models
jdkent 02c9c69
allow categorical variables in CBMR
116c8c2
restruct code in CBMRInference
1913f60
[skip CI][WIP] update example file based on reconstructed code
18bafd3
solve conflict
aa773d5
[skip CI][WIP] solve conflicts
8000f1c
solve conflicts
6390ce0
[skip CI][WIP] work on example file
b20dd74
[skip CI][WIP] complete example file for cbmr.
d82d485
[skip CI][WIP] implement an option to specify the reference subtype f…
c73bdbb
[skip CI][WIP] rewrite cbmr example in py file.
c0049e0
[skip CI][WIP] modify corrector class to be consistent with cbmr outputs
650cda4
[skip CI][WIP] add FDR/FWE correction methods to test
9904123
add testing cases with more coverage for CBMREstimator
f517b9f
[skip CI] [WIP] added new changes
e9f2cae
run black and isort
jdkent 8efc82a
wip: working through refactor
jdkent 15df47c
more refactor
jdkent 2f68a02
merge with main
jdkent 45004c7
remove debug info
jdkent 88ecc31
fix errors
jdkent d90b73e
test firth penalty
jdkent 5fd2402
black formating
jdkent addd0ba
more formatting
jdkent 618a2ee
remove peaks2maps
jdkent d3d813f
remove redundant def
jdkent 7d477d2
change documentation line
jdkent 1fc008d
move patsy into function
jdkent 448f376
add necessary installs
jdkent 13b90f9
update example notebook with api
jdkent 5ac3b0c
increase spacing and tolerance
jdkent 2aa0906
fix estimator name
jdkent 1645c40
sync utils with main
jdkent 0b453f6
update to main on z_to_p test
jdkent f605cd1
remove conperm workflow
jdkent 5446f44
remove whitespace
jdkent 45f2ee6
fix some errors
jdkent 30e34e2
make explicit where to document
jdkent f26282e
make StandardizeField a transformer
jdkent ba12a80
add functorch for python 3.6
jdkent 38fb4e5
try to use older version of functorch
jdkent 2307161
loosen restriction
jdkent d386573
fix bugs in cbmr example file
52f830b
[skip CI][WIP] fix bugs in testing function for cbmr_update
2b56139
add documentation for models.py
69f1b87
add documentation for cbmr.py
18ae03f
add documentation for utils.py
02db35c
add description for CBMREstimator
42e12cd
change lr to a smaller value
2643ecb
edit description function and add reference.
109897f
check if result.__description is a string.
1dd2299
resolve merge conflict
0f46781
set random seed
f4d4b49
simplify the log-likelihood function of NB model
383dc22
simplify the log-likelihood function of NB model
1171c30
implement wald test for CBMRInference
7529a6f
edit testing function for cbmr
0696e05
edit testing function for correctors
1f47e5f
fix linting error
5651c07
fix linting error
7be1632
fix linting error
395dae2
fixed linting error
c938ec3
fix linting error
931d2c1
fix linting error
73fe525
fix linting error
3745624
fix linting error
da7577b
fix linting error
6e79adc
fix linting error
2b8827a
remove unused test datasets
da2fbe2
fix linter error
c288695
add cbmr to docs/api.rst
cabdfce
edit example file for cbmr
e7bc4c1
remove the standardize_field function as it's replicated in the Stand…
ab751a5
use pass instead of return in the abstract methods
a95e116
added a test for StandardizeField class.
4705c47
edit example file of cbmr methods.
d48cd41
fix linter error.
677e6a5
fix a linter error.
d3487f5
fix a linter error
6a7b4c9
fix merge
jdkent 93cff60
fix names of notebooks
jdkent 4bbe51e
remove functorch (it was absorbed into torch)
jdkent 8e34a5c
[skip ci] merge
jdkent b36ef7d
fix math mode and links in cbmr example.
5ab8a2b
fix math mode
c442bda
add a test with none moderator variable for CBMRInference
yifan0330 20e8908
add a separate test for moderators=None
yifan0330 e026add
merge from upstream, solve conflict
yifan0330 3730e4b
Replace functorch.hessian by torch.func.hessian to remove pytorch war…
yifan0330 0dbe8e9
Merge branch 'fix_cbmr' of https://github.com/yifan0330/NiMARE into f…
yifan0330 668311e
solve lint error
yifan0330 9e34484
fix a bug with L-BFGS algorithm and speed up the execution time
yifan0330 b3fb1e2
Merge branch 'main' of https://github.com/neurostuff/NiMARE into fix_…
yifan0330 c68866e
fix lint code error
yifan0330 2531c19
fix a lint error
yifan0330 710c50a
improve cbmr efficiency by using groupby.
yifan0330 f9a9d8d
fix a bug
yifan0330 a471cb4
fix a bug
yifan0330 e90921e
improve the efficiency of line 455 transform function in diagnostics.py
yifan0330 e96cd76
solve lint code error
yifan0330 8347750
fix lint code error
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nice! this is several orders of magnitude faster! 🚀