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kalis v2 #4

Merged
merged 43 commits into from
Nov 13, 2024
Merged

kalis v2 #4

merged 43 commits into from
Nov 13, 2024

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louisaslett
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This PR adds new functionality required for the LOCATOR methodology in forthcoming paper.

The most important additions include:

  • Checkpointing for faster scanning of genomes for sequential inference at consecutive variants;
  • An order n clustering algorithm for real numbers where clusters are defined by a fixed separating distance;
  • Functions for constructing and testing clade matrices (expected genetic relatedness matrices) and discrete sprig calls.

Together with a variety of smaller enhancements.

ryanchrist and others added 27 commits September 23, 2024 11:43
@ryanchrist
Introducing O(n) clustering algorithm (blobby) and C-core for clade c…
55c3672 
…alling and clade matrix construction
@ryanchrist
Introducing R interface for Clade/Sprig calling and Clade Matrix (gen…
e0df97f 
…eralized eGRM) construction
@ryanchrist
Introducing optimal checkpointing routines and iterator interface for…
2805f31 
… using checkpointing to have kalis sequentially visit (infer ancestries at) consecutive target variants
@ryanchrist
Introducing efficient algorithm for parallelized implicit matrix trac…
ca8fc82 
…e and Hilbert-Schmidt norm calculation
@ryanchrist
Introducing tests for CladeMat
add21d5
@ryanchrist
Adding vignette for iterating over target loci sequentially
9a6a9e6
@ryanchrist
Registrations required for previous C commits
a23711f
@ryanchrist
Reducing memory footprint of loading haplotypes
bd5eb3c
@ryanchrist
Changing rhdf5 h5write call to h5writeDataset based on some prior fai…
073ec63 
…led runs -- might need to revisit this if in the new context we need to revert back to h5write .
@ryanchrist
Minor bug fixes to Probs
d7e3e6f
@ryanchrist
roxygenize all updates
7f9252b
@ryanchrist
reintroducing inputting haplotypes to kalis vignette
9749c4b
@ryanchrist
iterating ready to go!
2fbd289
@louisaslett
Fixes for CHECK error:
1338a48 
W  checking dependencies in R code (488ms)
   '::' or ':::' import not declared from: ‘data.table’
   Namespaces in Imports field not imported from:
     ‘methods’ ‘prettyunits’
     All declared Imports should be used.
   There are ::: calls to the package's namespace in its code. A package
     almost never needs to use ::: for its own objects:
     ‘ResetTable’ ‘pkgVars’
@louisaslett
Fixes for CHECK errors:
31c64cc 
W  checking S3 generic/method consistency ...
   targets:
     function(x)
   targets.kalisIterator:
     function(iter)

   print:
     function(x, ...)
   print.kalisIterator:
     function(iter)

   plot:
     function(x, ...)
   plot.kalisIterator:
     function(iter)
   See section ‘Generic functions and methods’ in the ‘Writing R
   Extensions’ manual.
@louisaslett
Partial fix for CHECK errors:
718f617 
N  checking R code for possible problems (3.8s)
   DistMat.GM: no visible binding for global variable ‘sd’
   MakeSolveSchedule : <anonymous>: no visible binding for global variable
     ‘sequential’
   MakeSolveSchedule : <anonymous>: no visible binding for '<<-'
     assignment to ‘first.index’
   MakeSolveSchedule : <anonymous>: no visible binding for global variable
     ‘first.index’
   MakeSolveSchedule : <anonymous>: no visible binding for '<<-'
     assignment to ‘last.index’
   MakeSolveSchedule : <anonymous>: no visible binding for global variable
     ‘last.index’
   MakeSolveSchedule : <anonymous>: no visible global function definition
     for ‘SolveSchedule’
   MakeSolveSchedule : <anonymous>: no visible global function definition
     for ‘optimize’
   MakeSolveSchedule : <anonymous>: no visible global function definition
     for ‘tail’
   MakeUpdateCache : <anonymous>: no visible binding for global variable
     ‘d’
   UpdateMatrixInPlace: no visible global function definition for
     ‘getFromNamespace’
   obj_func_for_SolveSchedule: no visible binding for '<<-' assignment to
     ‘sch.k’
   obj_func_for_SolveSchedule: no visible binding for global variable
     ‘sch.k’
   obj_func_for_SolveSchedule: no visible binding for global variable
     ‘nrow.sch’
   obj_func_for_SolveSchedule: no visible binding for '<<-' assignment to
     ‘sch.i’
   obj_func_for_SolveSchedule: no visible binding for global variable
     ‘sch.i’
   obj_func_for_SolveSchedule: no visible global function definition for
     ‘SolveSchedule’
   plot.kalisIterator: no visible global function definition for ‘axis’
   Undefined global functions or variables:
     SolveSchedule axis d first.index getFromNamespace last.index nrow.sch
     optimize sch.i sch.k sd sequential tail
   Consider adding
     importFrom("graphics", "axis")
     importFrom("stats", "optimize", "sd")
     importFrom("utils", "getFromNamespace", "tail")
   to your NAMESPACE file.
@louisaslett
Fix N checking Rd line widths ...
2b0341b 
   Rd file 'WriteHaplotypes.Rd':
     \examples lines wider than 100 characters:
        # ... write them to a file, giving alphabetic letters "A" through "T" as the #' # haplotype names ...

   These lines will be truncated in the PDF manual.
@louisaslett
Change to markdown \code and \link's and also fix W checking Rd cross…
5d325b5 
…-references ...

   Missing link or links in Rd file 'CladeMat_old.Rd':
     ‘kalisClades’ ‘kalisSprigs’

   Missing link or links in Rd file 'Neighbors.Rd':
     ‘kalisClades’

   Missing link or links in Rd file 'Sprigs_old.Rd':
     ‘kalisNeighbors’ ‘kalisClades’

   See section 'Cross-references' in the 'Writing R Extensions' manual.
@louisaslett
Update all doc \code and \link to markdown versions, including spotti…
2ea7fdd 
…ng a few instances in v1 codebase.
@louisaslett
Correct indentation of YAML and markdown blocks
6550df1
@louisaslett
Turn off tests on package check for speed (kalis tests take ~30 minutes)
8fa8200
@louisaslett
Eliminate compiler warnings about printing size_t's when int expected…
d8f78a0 
… (no concern here, these do not affect the algorithm so cast freely to ints)
@louisaslett
Avoid compiler warnings about using undefined pointers
43d2d4c
@louisaslett
Eliminate apparently redundant variable causing compiler warnings
7beab0a
@louisaslett
Update configure script to have strict POSIX shell support
667c798
@louisaslett
Eliminate dangling a.out.dSYM after configure run on Macs
e641ceb
@louisaslett
Add cleanup script to remove temporary files created during configure…
ff8ee3e 
… run
louisaslett and others added 15 commits October 1, 2024 17:40
@louisaslett
Remove general checkpointing solution into separate dev branch and el…
e7df962 
…iminiate from release code base
@louisaslett
Remove incorrectly tracked vignette files from version control
f595d72
@louisaslett
Eliminate some dev testing code from MakeUpdateCache (still tracked i…
6faf7a7 
…n general_checkpoint_solver branch)
@louisaslett
Include vignette building in installation instructions
20794ef
@louisaslett
First batch of documentation fixes, some TODO items remain in these.
1c9543a
@louisaslett
Update to description file with ORCIDs, first kalis paper, and bug re…
4d751e3 
…ports URL.
@louisaslett
Second batch of documentation fixes, many TODOs remain.
e4243e2
@louisaslett
Remove exit() call from CladeMat() C function.
a6015ba
@louisaslett
Allocation checks not required for R_alloc (see Writing R Extensions)
047287b
@ryanchrist
documenting new kalis v2 functions
cc97b94
@louisaslett
Tweaks to added documentation
4cde13f
@louisaslett
Fix pkgdown maths
1ad8095
@louisaslett
Add kalis paper to all v1 functions and tidy other references in v1 f…
a9ed50a 
…unction docs
@louisaslett
Documentation and exported function review by Ryan (pushed by me)
13dbdc4
@louisaslett
Final documentation sweep for correct references, and other minor tweaks
1b02952
@louisaslett
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Sending v2 to deployment! 🚀

@louisaslett louisaslett merged commit c350a1a into master Nov 13, 2024
1 check passed
@louisaslett louisaslett deleted the v2 branch November 13, 2024 18:20
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@louisaslett @ryanchrist