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Add NB-GLMM to master branch. #295

Merged
merged 315 commits into from
Nov 9, 2023
Merged

Add NB-GLMM to master branch. #295

merged 315 commits into from
Nov 9, 2023
This pull request is big! We’re only showing the most recent 250 commits.

Commits on Feb 22, 2022

  1. implement fullZ construction from input model forumla

    @MikeDMorgan
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  2. unify RE and FE formula parsing

    @MikeDMorgan
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  3. dont forget the column names

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Commits on Feb 23, 2022

  1. add function import statements

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  2. incorporate basic LMM interface into testNhoods

    @MikeDMorgan
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  3. fix partial deriv indexing error;

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  4. force add RE variable names to sigma update vector

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Commits on Feb 25, 2022

  1. begin migration to Rcpp

    @MikeDMorgan
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  2. Merge branch 'master' into alice_fast

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  3. decomission invertPseudoVar whilst debugging

    @MikeDMorgan
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  4. added inference

    @akluzer
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Commits on Feb 28, 2022

  1. push pseudovariance inversion to cpp

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  2. add package compiled object file

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  3. rewritten to allow slopes

    @akluzer
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Commits on Mar 2, 2022

  1. matrix and glmm computations moved to Rcpp

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  2. add major functions to cpp

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  3. add linked C++ files and fitPLGLMM R wrapper

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Commits on Mar 7, 2022

  1. debugging REML information matrix - not succesful yet

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  2. merge alice branch

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  3. resolve merge conflict with "alice" branch

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  4. transfer SE, df and p value functions to glmm.R

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  5. remove glmm_new.R script

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Commits on Mar 10, 2022

  1. updated intercepts model

    @akluzer
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  2. Delete glmm.R

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  3. Delete glmm_pseudo.R 

    deleting all glmm files
    @akluzer
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  4. Rename glmm_new.R to glmm.R 

    renamed
    @akluzer
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  5. import export added

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  6. Update DESCRIPTION 

    added glmm.R
    @akluzer
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  7. Update DESCRIPTION

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  8. fixed weird typos

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Commits on Mar 14, 2022

  1. glmm.R added to description and namespace

    @akluzer
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  2. added descriptions

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  3. added glm argument because tests were failing

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  4. glmm.R included

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Commits on Mar 15, 2022

  1. implement glmm in Rcpp up to SE steps - further inference currently in R

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Commits on Mar 16, 2022

  1. push vcov into C++ and break up coeff matrix computation

    @MikeDMorgan
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  2. substract Ginv from coefficint matrix LR block in DF calculations

    @MikeDMorgan
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  3. harmonise function names to camel case

    @MikeDMorgan
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  4. remove utils header references

    @MikeDMorgan
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Commits on Mar 17, 2022

  1. added tables

    @akluzer
    akluzer committed Mar 17, 2022
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  2. modified to add glmm

    @akluzer
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  3. added glmm

    @akluzer
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  4. adding glmm

    @akluzer
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  5. neighborhoods sim glmm

    @akluzer
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Commits on Mar 18, 2022

  1. glmm simulation

    @akluzer
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  2. fixed glm argument

    @akluzer
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  3. fixed glm argument

    @akluzer
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  4. integrated glmm

    @akluzer
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  5. updated with new glmm testnhoods

    @akluzer
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Commits on Mar 23, 2022

  1. resolve alice branch merge conflicts

    @MikeDMorgan
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  2. expanded to 2 random effects

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  3. modified

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  4. updated simulations 2 random effects

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  5. updated

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Commits on Mar 24, 2022

  1. tidying up merge conflict resolution

    @MikeDMorgan
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  2. remove default=variable names in functions

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  3. Merge branch 'alice' into alice_fast

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  4. Merge pull request #210 from MarioniLab/alice_fast 

    Refactoring GLMM functions in to Rcpp
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  5. remove condensed initialiseFullZ function for now

    @MikeDMorgan
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  6. Merge pull request #211 from MarioniLab/alice_fast 

    remove condensed initialiseFullZ function for now
    @MikeDMorgan
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  7. remove compiled object files

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  8. introduce compute Va function

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Commits on Mar 25, 2022

  1. resolve refactoring merge conflicts

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Commits on Apr 1, 2022

  1. added glm tests

    @akluzer
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  2. latest updates

    @akluzer
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  3. rebased glmm

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  4. resolved conflicts after rebase

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  5. readded satterthwaite

    @akluzer
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  6. resolving unstaged change

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Commits on Apr 6, 2022

  1. push miloR shared object

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Commits on Apr 8, 2022

  1. introduce genetic GLMM framework

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  2. make current GLMM tests run with C++ fitGLMM - still need to make tes… 

    …ts run consistently, currently relies on a set seed which does not 100% create the faithful conditions
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  3. comment print statements in testNhoods

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Commits on Apr 20, 2022

  1. fitGLMM now works with a) any number of random effects, b) arbitrary … 

    …covariance matrix, c) random effects + arbitrary covariance matrix
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  2. tweak indexing in pseudovars for a minor speed gain

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Commits on Apr 22, 2022

  1. remove runGLMM functions and add first set of test_glmm unit tests

    @MikeDMorgan
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  2. add simulated family data

    @MikeDMorgan
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  3. add basic singular hessian error checking

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  4. add updated so

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  5. latest update

    @akluzer
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  6. latest changes

    @akluzer
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  7. add family simulated data docs

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Commits on Apr 26, 2022

  1. add C++ utility functions

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  2. hopefully resolved Z column naming issues

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Commits on Apr 27, 2022

  1. add checks for zero eigenvalues in D - indicator of poorly conditione… 

    …d model?
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  2. update testNhood tests with new warnings

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Commits on Apr 29, 2022

  1. resolve RNG issue with irreproducible tests

    @MikeDMorgan
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  2. compiled package object

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  3. add PKG Makevars

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  4. update docs for CHECK

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  5. add compiled docs

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Commits on May 9, 2022

  1. update DESCRIPTION

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  2. resolve merge conflicts with alice branch

    @MikeDMorgan
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  3. add missing std call

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  4. add the other missing std:: calls

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  5. remove untracked vignettes from repo

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Commits on May 10, 2022

  1. add MouseThymusAgeing specific install to workflow

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  2. Update RCMD_check.yml 

    Fix YAML
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  3. Merge branch 'master' into genetic_case

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  4. remove local miloR.so object

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Commits on May 11, 2022

  1. Export inference functions to R env

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Commits on May 12, 2022

  1. Merge pull request #217 from MarioniLab/genetic_case 

    Merging in most up to date version of C++ versions
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  2. add LIBS to Makevars

    Michael Morgan committed May 12, 2022
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  3. resolve merge

    @akluzer
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  4. fixing merge

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  5. fixing merge

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  6. add Makevars.win

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  7. added R_glmm.R

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  8. added R_glmm.R

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  9. added R_glmm.R

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  10. add BLAS libs ref to Makevars

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  11. small changes -- all working now

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Commits on May 13, 2022

  1. fixed SE in fitGLMM

    @akluzer
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  2. added tagwise dispersion

    @akluzer
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  3. ensure compiled objects are not added to repo by adding to .gitignore

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Commits on May 16, 2022

  1. remove R_glmm.R and dont link BLAS/LAPACK libs in Makevars

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  2. trying to debug confounded speed slow-down and broken coeff_mat

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  3. add all the file Mike you plonker

    @MikeDMorgan
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  4. dont add any compiled objects

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Commits on May 17, 2022

  1. resolve outstanding coeff index and random variable naming issues for… 

    … fitGeneticPLGlmm
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  2. doc rebuild

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Commits on May 25, 2022

  1. resolving conflicts

    @akluzer
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  2. more user-friendly warnings and errors

    @akluzer
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Commits on May 27, 2022

  1. resolving Z colname issue

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Commits on May 31, 2022

  1. resolving conflicts

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  2. more user-friendly warnings and errors

    @akluzer @MikeDMorgan
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  3. Merge branch 'alice' into genetic_case

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Commits on Jun 9, 2022

  1. add K to genetic partial derivatives and include K in the constructio… 

    …n of G
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  2. continued debugging of singular Hessian

    @MikeDMorgan
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  3. adapt partial derivs to take an arbitrary cXc matrix and correspondin… 

    …g Z - doesnt have to be identity
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Commits on Jun 27, 2022

  1. capture iteration information from both LMM functions

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  2. playing around with definitions of Z and I

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Commits on Jul 1, 2022

  1. allow user-defined initial values for thetas and sigmas - useful for … 

    …debugging
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  2. add conjugate gradient method for solving MMEs and use Cholesky of G … 

    …trick to make MMEs more diagonal
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Commits on Oct 11, 2022

  1. add working HE and HE-NNLS solvers. Still need to resolve HE-NNLS inf… 

    …inite loop with small variances
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  2. fix renaming of res variable bug

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Commits on Nov 16, 2022

  1. resolve infinite loop bug - need different constaint values for genet… 

    …ic and non-genetic model
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  2. Added function to visualize the number of neighboring cells per neigh… 

    …borhood and condition
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  3. fixed sparse matrix to dataframe conversion

    @nickhir @MikeDMorgan
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  4. Refactored plotNhoodCounts.

    @nickhir @MikeDMorgan
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  5. Refactored plotNhodds and optimized subsetting.

    @nickhir @MikeDMorgan
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  6. Implemented basic unit tests for plotNhoodCounts

    @nickhir @MikeDMorgan
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  7. plotNhoodCounts now accepts logical vectors.

    @nickhir @MikeDMorgan
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  8. refactored nhoods to subset.nhoods in plotNhoodCounts

    @nickhir @MikeDMorgan
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  9. Force logical subset.nhoods vector to be same length as the number of… 

    … rows of nhooCounts(x)
    @nickhir @MikeDMorgan
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  10. removed redundant paste0

    @nickhir @MikeDMorgan
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  11. Update issue templates

    @emdann @MikeDMorgan
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  12. Added contrast tutorial to readme

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  13. Update README.md 

    Add more info for reporting issues under __Support__
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  14. adding error message for wrong input

    @emdann @MikeDMorgan
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  15. adding constructor from Matrix

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  16. Update NEWS.md 

    Update news file with on-going additions - plotNhoodCounts
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  17. fixed type error and missing spatial FDR column

    @MikeDMorgan
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Commits on Nov 21, 2022

  1. resolve glmm and testNhood failing tests

    @MikeDMorgan
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  2. resolve glmm and testNhood failing tests

    @MikeDMorgan
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  3. resolve inconsistent pass/fail in singular hessian test

    @MikeDMorgan
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Commits on Nov 22, 2022

  1. fixing R CMD check warnings on documentation and compilation

    @MikeDMorgan
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  2. fix for compilation warnings in R CMD check

    @MikeDMorgan
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Commits on Nov 23, 2022

  1. add missing function imports

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  2. add documentation to R-facing C++ functions and begin dealing with Bi… 

    …ocCheck warnings/errors
    @MikeDMorgan
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  3. add docs to Rcpp functions

    @MikeDMorgan
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  4. resolve BiocCheck documentation warnings and errors

    @MikeDMorgan
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  5. resolve mismatched double quote in docs

    @MikeDMorgan
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  6. resolve error in initialiseG example

    @MikeDMorgan
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  7. fix for initialiseG example error

    @MikeDMorgan
    MikeDMorgan committed Nov 23, 2022
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  8. fix stupid typos in examples

    @MikeDMorgan
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  9. fix stupid typos in examples

    @MikeDMorgan
    MikeDMorgan committed Nov 23, 2022
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  10. update sim_family data

    @MikeDMorgan
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  11. re-add family simulation data

    @MikeDMorgan
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Commits on Dec 9, 2022

  1. add check and tests to catch random variable formula errors

    @MikeDMorgan
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  2. update use of aes_string to aes

    @MikeDMorgan
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Commits on Jan 30, 2023

  1. resolve devel merge conflicty

    Morgan committed Jan 30, 2023
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  2. Merge branch 'master' into genetic_case

    Morgan committed Jan 30, 2023
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  3. expand variance form to include Poisson variance

    @MikeDMorgan
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  4. unit tests for variance forms

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Commits on Feb 9, 2023

  1. debugging Poisson variance in singular Hessian issue

    @MikeDMorgan
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  2. switch to user input kinship matrix

    @MikeDMorgan
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Commits on Feb 13, 2023

  1. debugging GLMM with kinship and multiple observations per individual

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  2. debugged GRM with multiple observations per individual - beware confo… 

    …unding between GRM columns and fixed effects!!
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Commits on Feb 14, 2023

  1. introduce line search for dispersion parameter estimation

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  2. remove Poisson variance from current implementation - needs a huge am… 

    …ount more debugging to work
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  3. woops - I deleted the dispersion estimation step from edgeR - stooopid!

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Commits on Feb 15, 2023

  1. remove Poisson GLMM tests

    @MikeDMorgan
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  2. udpate NEWS with recent fixed

    @MikeDMorgan
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  3. fix p-value computation bug

    @MikeDMorgan
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  4. p-value bug fixed

    @MikeDMorgan
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Commits on Feb 17, 2023

  1. bug checking GRM inputs

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Commits on Mar 2, 2023

  1. switch phi estimation from bisect to golden section search

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  2. we want to __maximise__ the liklihood you fecking dingbag

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Commits on Mar 3, 2023

  1. move dispersion estimation to outside main parameter estimation loop

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  2. std::sqrtf is apparently NOT standard - switch to std::sqrt

    @MikeDMorgan
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Commits on Mar 6, 2023

  1. switch phi estimation to 1 initial and 1 internal optimisation - this… 

    … relies _heavily_ on getting a good phi at the beginning
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  2. add BiocParallel for parallelisation

    @MikeDMorgan
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Commits on Mar 7, 2023

  1. switch to MME for phi estimation

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  2. add BiocParallel function imports to NAMESPACE

    @MikeDMorgan
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  3. remove incorrect Matrix import statements

    @MikeDMorgan
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  4. turn off offsets in GLMM for now

    @MikeDMorgan
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Commits on Mar 8, 2023

  1. remove tests on offsets for GLMM for now

    @MikeDMorgan
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  2. add missing MatrixGenerics import statement

    @MikeDMorgan
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  3. fix bug in DF calculation that was double squaring the SE matrix

    @MikeDMorgan
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  4. reinstate offsets tests now this is working properly

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Commits on Mar 13, 2023

  1. fix bug in formula parsing to allow multiple fixed effect variables

    @MikeDMorgan
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  2. allow nhood subsetting in annotateNhoods

    @MikeDMorgan
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  3. fix bugs in plotNhoods to allow nhood subsetting

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Commits on Mar 14, 2023

  1. add the checkSeparation function for checking potential of model sepa… 

    …ration with input variables
    @MikeDMorgan
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  2. fix extraneous comment line in checkSeparation example

    @MikeDMorgan
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  3. add unit tests for checkSeparation

    @MikeDMorgan
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  4. fix annotateNhood unit test fault

    @MikeDMorgan
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  5. fix bug in plotNhoods

    @MikeDMorgan
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Commits on Mar 15, 2023

  1. add simple GLMM vignette

    @MikeDMorgan
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  2. update CI actions

    @MikeDMorgan
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  3. switch all C++ errors to Rcpp

    @MikeDMorgan
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  4. resolve how to use BiocParallel error catching

    @MikeDMorgan
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  5. more BiocParallel error catching

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Commits on Mar 16, 2023

  1. fudge prettier error message until we can get the full traceback from… 

    … BiocParallel
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  2. add missing BiocParallel function imports

    @MikeDMorgan
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  3. add missing BiocParallel function imports to NAMESPACE

    @MikeDMorgan
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  4. add even MORE BiocParallel function imports

    @MikeDMorgan
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  5. resolve bug in error reporting for partial failures

    @MikeDMorgan
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Commits on Mar 20, 2023

  1. revised error reporting with deeper callstack from BiocParallel update

    @MikeDMorgan
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  2. update R dependencies for Github Actions

    @MikeDMorgan
    MikeDMorgan committed Mar 20, 2023
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  3. major version bump

    @MikeDMorgan
    MikeDMorgan committed Mar 20, 2023
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  4. update Actions workflow versinos

    @MikeDMorgan
    MikeDMorgan committed Mar 20, 2023
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Commits on Mar 22, 2023

  1. allow users to override colour_by option to plotNhoodGroups

    @MikeDMorgan
    MikeDMorgan committed Mar 22, 2023
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Commits on Apr 26, 2023

  1. add RCurl dependency to Windows CI

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    MikeDMorgan committed Apr 26, 2023
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Commits on Apr 27, 2023

  1. sparsify heavy matrix multiplication functions for big speed-ups

    @MikeDMorgan
    MikeDMorgan committed Apr 27, 2023
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Commits on May 16, 2023

  1. expand on use of contrasts in vignette and clarify docs in testNhoods

    @MikeDMorgan
    MikeDMorgan committed May 16, 2023
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  2. add user-specified cell numbers for subset analyses

    @MikeDMorgan
    MikeDMorgan committed May 16, 2023
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  3. add unit test for cell.sizes in testNhoods

    @MikeDMorgan
    MikeDMorgan committed May 16, 2023
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Commits on May 22, 2023

  1. plotNhoodGraph was returning NULL when passing colour_by

    @MikeDMorgan
    MikeDMorgan committed May 22, 2023
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  2. Merge branch 'devel' into genetic_case

    @MikeDMorgan
    MikeDMorgan committed May 22, 2023
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  3. Merge branch 'devel' into genetic_case

    @MikeDMorgan
    MikeDMorgan committed May 22, 2023
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  4. fix bug

    @MikeDMorgan
    MikeDMorgan committed May 22, 2023
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  5. Merge branch 'master' into devel

    @MikeDMorgan
    MikeDMorgan committed May 22, 2023
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  6. Merge branch 'devel' into genetic_case

    @MikeDMorgan
    MikeDMorgan committed May 22, 2023
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Commits on Jul 17, 2023

  1. Merge pull request #221 from MarioniLab/genetic_case 

    Merge all Milo-GLMM code into `alice` branch prior to devel.
    @MikeDMorgan
    MikeDMorgan authored Jul 17, 2023
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  2. tweak plotNhoods docs

    @MikeDMorgan
    MikeDMorgan committed Jul 17, 2023
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  3. Merge branch 'genetic_case' into alice

    @MikeDMorgan
    MikeDMorgan committed Jul 17, 2023
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  4. Merge branch 'master' into alice

    @MikeDMorgan
    MikeDMorgan committed Jul 17, 2023
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Commits on Sep 19, 2023

  1. properly implement ML estimation, fix solver option bug and resolve p… 

    …artial derivative list/matrix issue
    @MikeDMorgan
    MikeDMorgan committed Sep 19, 2023
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Commits on Oct 3, 2023

  1. remove print statements from debugging

    @MikeDMorgan
    MikeDMorgan committed Oct 3, 2023
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Commits on Oct 12, 2023

  1. Merge pull request #289 from MarioniLab/alice 

    Introduce Milo NB-GLMM to devel in preparation for manuscript submission.
    @MikeDMorgan
    MikeDMorgan authored Oct 12, 2023
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  2. Merge branch 'master' into devel

    @MikeDMorgan
    MikeDMorgan committed Oct 12, 2023
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  3. Merge branch 'master' into devel

    @MikeDMorgan
    MikeDMorgan committed Oct 12, 2023
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  4. Add GLMM vignette to landing page tutorials.

    @MikeDMorgan
    MikeDMorgan authored Oct 12, 2023
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  5. add GLMM vignette html for README link

    @MikeDMorgan
    MikeDMorgan committed Oct 12, 2023
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  6. git push1;95;0cMerge branch 'devel' of github.com:MarioniLab/miloR in… 

    …to devel
    @MikeDMorgan
    MikeDMorgan committed Oct 12, 2023
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  7. Update RMD to html for GLMM vignette

    @MikeDMorgan
    MikeDMorgan authored Oct 12, 2023
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Commits on Nov 9, 2023

  1. update docs to fix BiocCheck warnings

    @MikeDMorgan
    MikeDMorgan committed Nov 9, 2023
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  2. Merge branch 'master' into devel

    @MikeDMorgan
    MikeDMorgan authored Nov 9, 2023
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