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Ancestral sample#22

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DL42 wants to merge 301 commits into

molpopgen:ancestral_samplefrom

DL42:ancestral_sample

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Commits on Feb 5, 2018

Merge pull request #18 from DL42/ancestral_sample
molpopgen
authored

Commits on Feb 6, 2018

Merge branch 'dev' into ancestral_sample
DL42
committed

Commits on Feb 15, 2018

starting c++ ancestral sampling, adding mutation struct
DL42
committed

Commits on Feb 17, 2018

adding mutations to ancestry_tracker.hpp
David Lawrie
committed

Commits on Feb 21, 2018

adding mutations to wfarg, changing description of EdgesetTable to EdgeTable
David Lawrie
committed
gitignore
DL42
committed

Commits on Feb 23, 2018

changed mutation structure to store node_id and the invariant position of the mutation in fwdpp vector (which in turn has the position and metadata info)
David Lawrie
committed

Commits on Mar 4, 2018

adding new handler for combined recombination/mutation, remove old handler
David Lawrie
committed

Commits on Mar 6, 2018

changing from recmodel to generate_breakpoints
David Lawrie
committed
adding mutations via generate_new_mutations rather than mutate_gamete_recycle
David Lawrie
committed

Commits on Mar 8, 2018

adding mutations to handle_mut_rec

David Lawrie
authored and
DL42
committed
add KTfwd namespace to generate_new_mutations and breakpoints function
DL42
committed
change recombine_gametes to mutate_recombine
DL42
committed

Commits on Mar 13, 2018

removal of update_indexes
DL42
committed

Commits on Mar 15, 2018

Commits on Mar 19, 2018

remove multithreaded versions (for now)
David Lawrie
committed
modified call to accept pop instead of generation
David Lawrie
committed

Commits on Mar 21, 2018

Commits on Mar 22, 2018

amended comment describing pickling of mutations
DL42
committed

Commits on Mar 23, 2018

simulate with initial_tree (for testing purposes)
David Lawrie
committed
subsume ancestry_tracker inside wright-fisher
David Lawrie
committed
return to default of not simulating with initial tree
David Lawrie
committed
fixed bug introduced in commit 309f1096c7aa27677483142687ed402f7b1b17a4
David Lawrie
committed
changed ancestry_tracker to store nodes in reverse time, so need to reverse time or increment it during simplification
David Lawrie
committed
moves garbage collection to the end of the generation
David Lawrie
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comment out exchange_for_async and ancestry_data (last of the async/queue items left)
David Lawrie
committed
removing extra last_gc_time and process variables from argsimplifier and ancestry tracker
David Lawrie
committed
simplified node API and usage
David Lawrie
committed
simplify mutation API
David Lawrie
committed
simplify edge API and fixes no recombination bug
David Lawrie
committed

Commits on Mar 24, 2018

removed lastN from ancestry_tracker
David Lawrie
committed
adding a vector of vector of ints (gen_pop_indexes) to store each generation's next ID
David Lawrie
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replace offspring indexes with pop_gen_indexes
David Lawrie
committed

Commits on Mar 27, 2018

using pair instead of array to store node indexes for a generation
David Lawrie
committed

Commits on Mar 28, 2018

testing ancestral samples (doesn't work)
David Lawrie
committed

Commits on Mar 29, 2018

reorganizing python code around argsimplifier so that simulations are run through the argsimplifier
David Lawrie
committed
renamed argsimplifier argevolver to reflect changes in API organization
David Lawrie
committed

Commits on Apr 1, 2018

adding a python-based gamete sampler to argevolver for taking ancestral samples
David Lawrie
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created sampler that sample X individuals every Y generations (current example is 4 individuals every 125 generations)
David Lawrie
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added separate seed for sampler
David Lawrie
committed

Commits on Apr 2, 2018

Commits on Apr 6, 2018

updating simple prototype with mutations to test msprime & mutations
David Lawrie
committed

Commits on Apr 7, 2018

preprocess mutation vector to remove mutations from the ancestry tracker that have already been removed from the pop mutation vector
David Lawrie
committed

Commits on Apr 8, 2018

allows ancestral samples to be taken of nodes from input trees
David Lawrie
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empty brace initialization for nodes, edges, mutations in ancestry_tracker
David Lawrie
committed
add function to preserve mutation indices of ancient samples created during the simulation
David Lawrie
committed

Commits on Apr 9, 2018

custom make_mut_queue: add mutations to the mutation queue if they have 0 count *AND* if they are not in the preservation lookup
David Lawrie
committed
custom update_mutations: remove mutation positions from lookup if have 0 count *AND* if not in preservation lookup
David Lawrie
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Revert "allows ancestral samples to be taken of nodes from input trees"
David Lawrie
committed
make total_generations an attribute of argevolver, use as one point of reference for total_generations in rest of simulation
David Lawrie
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rearranges _anc_sampler to be a member of argevolver's __init and __call__ functions
David Lawrie
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return pop from ArgEvolver
David Lawrie
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only encode mutation_id into metadata for MutationTable
David Lawrie
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Commits on Apr 12, 2018

prototype merge_sites function
David Lawrie
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Commits on Apr 14, 2018

preserve fixations
David Lawrie
committed
replaces pickle with struct, packs the pos.mutation index into an int formatted byte string
David Lawrie
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remove copy of pop.mutation.array as it is no longer needed during simplification
David Lawrie
committed

Commits on Apr 19, 2018

take in reference to pybind11 array in preserve_mutations_sample
David Lawrie
committed

Commits on May 4, 2018

faster metadata creation using numpy.view (still uses struct.unpack for getting back the mutation_id)
David Lawrie
committed

Commits on May 25, 2018

update to fwdpy11 1.5: compiles, no idea if it runs
David Lawrie
committed
removed deleted files from setup.py
David Lawrie
committed
simulation runs
David Lawrie
committed

Commits on Jun 1, 2018

Commits on Jun 5, 2018

preserve all fixations and test lookup table
David Lawrie
committed

Commits on Jun 6, 2018

Commits on Jun 8, 2018

initial injection of juvenile migration code with two demes, seems to work
David Lawrie
committed

Commits on Jul 3, 2018

small two-population simulation with human out-of-africa demography, segmentation fault 11
David Lawrie
committed

Commits on Jul 4, 2018

default simulation runs
David Lawrie
committed

Commits on Jul 9, 2018

expand final population size
David Lawrie
committed
set migration boundaries to prevent too large/small migration
David Lawrie
committed

Commits on Jul 31, 2018

small changes
David Lawrie
committed

Commits on Aug 8, 2018

alterations to reflect underlying changes in fwdpy11 population and parameter classes
David Lawrie
committed
update reflects changes in fwdpy11 diploid class (separating metadata from gametes)
David Lawrie
committed
fwdpy11 changed parental data tuple to parent array
David Lawrie
committed
error in previous commit
David Lawrie
committed
np.random.choice gave error on linux dev machine when final_pop2_size was 0
David Lawrie
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added extra print statement to printout number of rows, fixed evolver.pop.mut_lookup (is just a dictionary, not function?)
David Lawrie
committed

Commits on Aug 13, 2018

requirements file
David Lawrie
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more flexible initial starting points
David Lawrie
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fixing string to int bugs
David Lawrie
committed
added neutral theta as parameter
David Lawrie
committed

Commits on Aug 15, 2018

bug fix
David Lawrie
committed
bug fix2
David Lawrie
committed
fixed input bug for pop1 and when making a single population simulation
David Lawrie
committed

Commits on Aug 23, 2018

Commits on Sep 11, 2018

test evolver in interactive window
David Lawrie
committed
made sure anc_sampling was of type int
David Lawrie
committed
fixing tabs
David Lawrie
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fixing parsed args to args
David Lawrie
committed
moved anc_sam conversion to int to evolve_arg and fixed indexing in sample_index
David Lawrie
committed

Commits on Sep 12, 2018

fix sample taking
David Lawrie
committed
fix sample dtype
David Lawrie
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create sample list from node list
David Lawrie
committed
change results to evolver
David Lawrie
committed

Commits on Sep 13, 2018

first commit for multi-sample fst analysis
DL42
committed

Commits on Sep 14, 2018

syntax and bug fixes
David Lawrie
committed
(test_evolve and evolve_arg) moved args.anc_sam1/2 manipulation back to test_evolve, add burn_in generations to the args.anc_sam1/2
David Lawrie
committed
eliminated last reference to burn-in scale and fixed indentation
David Lawrie
committed
just return fst_list and comment out print statements
David Lawrie
committed
temp
David Lawrie
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Merge branch 'as_dev' into ancestral_sample
David Lawrie
committed

Commits on Sep 19, 2018

added concurrent futures
David Lawrie
committed
fixes
David Lawrie
committed
define fst_list
David Lawrie
committed
Merge branch 'as_dev' into ancestral_sample
David Lawrie
committed

Commits on Sep 30, 2018

print mean, median, and std fst results out to file
David Lawrie
committed

Commits on Oct 1, 2018

allow setting of initial migration rate (good for when I wan the sister populations to have the same size)
David Lawrie
committed
better migration checking when pop 2 doesn't exist
David Lawrie
committed

Commits on Oct 2, 2018

output linearized fst results and expected linearized fst results for each sample according to their population and sample generation
David Lawrie
committed

Commits on Oct 4, 2018

single population simulation
David Lawrie
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changes to test comparison with coalescent theory for sister populations:
David Lawrie
committed

Commits on Dec 11, 2018

adding simulation command lines
David Lawrie
committed

Commits on Jan 6, 2019

created new split/recover and split migration models so that ancestral population can permanently lose individuals after split or recover the population size afterwards
David Lawrie
committed

Commits on Jan 7, 2019

allow selection coefficient to be set by user and make use of fwdpy11 regions
David Lawrie
committed

Commits on Jan 21, 2019

got separate msprime simulation working (same interface for simplicity)
David Lawrie
committed

Commits on Jan 23, 2019

fixes
David Lawrie
committed

Commits on Jan 31, 2019

allow number of generations in flat demography to be set by user
David Lawrie
committed
add option to create custom filename for outfile
David Lawrie
committed
indentation fix
David Lawrie
committed

Commits on Feb 1, 2019

add user defined boolean where split rate is an exact rather than random variable
David Lawrie
committed

Commits on Feb 2, 2019

upgraded msprime simulation to model split_loss and split_recovery models
David Lawrie
committed

Commits on Feb 19, 2019

Commits on Mar 29, 2019

adding option for two-locus simulation
David Lawrie
committed

Commits on Apr 1, 2019

flanking, recombining deleterious regions w/ central, non-recombining neutral region
David Lawrie
committed

Commits on Apr 4, 2019

Commits on Apr 11, 2019

add cores option, fixes compilation on new fwdpy11 versions
David Lawrie
committed
BGS command lines
DL42
committed

Commits on Apr 12, 2019

first simulation script
DL42
committed
fixing BGC->BGS, fixing shell commands
DL42
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conversion to msprime 0.6.1
David Lawrie
committed
new shell scripts
David Lawrie
committed

Commits on Apr 13, 2019

check error
David Lawrie
committed
fixes and mutation printing
David Lawrie
committed
tried to use table collection API, but no dice
David Lawrie
committed
deduplicate sites, non-discarding of populations during simplification
David Lawrie
committed
removed population_table function, unnecessary, handled in ArgEvolver now
David Lawrie
committed

Commits on Apr 14, 2019

updated seed values for shellcmd files and added R values to test
David Lawrie
committed
results

DL42
authored and
David Stuart Lawrie
committed
removed the call to make a python interactive after running bash script (forms an error file on cluster)
David Lawrie
committed
updated shell commands for interleaved model
David Lawrie
committed
updated shell commands for HK95 model
David Lawrie
committed
moved small replicate results to store them for later if needed
David Lawrie
committed

Commits on Apr 15, 2019

decreased number of cores, sometimes 128 ran out of memory
David Lawrie
committed
large replicate results, missing HKBGS_R2 because I set R to 11000

DL42
authored and
David Stuart Lawrie
committed
fixes R parameter for HKBGS_R2
David Lawrie
committed

Commits on Apr 16, 2019

Results for HKBGS_R2
David Stuart Lawrie
committed

Commits on Apr 17, 2019

r plot scripts and tables
David Lawrie
committed
small fix to R script
David Lawrie
committed
final improvement to R script
David Lawrie
committed

Commits on Apr 21, 2019

no pop size change demography model with background selection
David Lawrie
committed
fixes to command line and shell commands (recombination rate and misc)
David Lawrie
committed
simulation results no popsize changes
David Stuart Lawrie
committed

Commits on Apr 22, 2019

print sample pi for every sample
David Lawrie
committed
fix
David Lawrie
committed
results and fixes
David Stuart Lawrie
committed

Commits on Apr 23, 2019

long burn-in HK results
David Stuart Lawrie
committed
delete file
David Stuart Lawrie
committed

Commits on Apr 25, 2019

upgraded test_msprime to msprime v0.6.1 and pi_array, removed unneeded code from test_evolve.py, created command to run msprime with no recombination
David Lawrie
committed
fix in test_msprime, changed split rate to 1 (duplication)
David Lawrie
committed
code to output tree sequences to files
David Lawrie
committed

Commits on Apr 26, 2019

tree sequences are not pickle-able, output ts file in run_sim
David Lawrie
committed
test_msprime fixes and results
David Stuart Lawrie
committed
further fixes to test_msprime and removal of extra zeros from results
David Lawrie
committed
fixes to ts_output and shell commands
David Lawrie
committed
got tree sequence output for HK and IBGS R1, rsynced to Irvine/BGS_results\n\nstatistic results equivalent to previous sim runs, not committed
David Stuart Lawrie
committed

Commits on May 29, 2019

fixes population table when initializing from neutral tree sequence
David Lawrie
committed
adding josh schraiber's continuity to project
David Lawrie
committed
initial stab at full integration of continuity with project, probably needs a lot of cleanup and corrections
David Lawrie
committed
small fixes and testing lines (reads not being sliced right)
David Lawrie
committed
further attempts to get Josh's continuity program working ... still doesn't
David Lawrie
committed
continuity analyses successfully run in python 3 for both my simulation and continuity simulation
David Lawrie
committed
fixes continuity analyses so I can take multiple ancient samples and compare them (one at a time) to the first (modern) sample
David Lawrie
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output continuity results
David Lawrie
committed

Commits on Jun 28, 2019

make simulation like mine
David Lawrie
committed

Commits on Jun 30, 2019

continuity simulation working!
David Lawrie
committed
fixing random number seeds in test_evolve so continuity within test_evolve has the right distribution of random numbers (previously was generating too similar random numbers across simulations for …
David Lawrie
committed
fixed msprime's current population sampling to be the same as fwdpy11's (haploid) ... doesn't seem to change Fst results at all
David Lawrie
committed
outputting branch length estimations for split times in addition to likelihoods
David Lawrie
committed
preparing for cluster (no joblib/matplotlib), cluster commands
David Lawrie
committed
fixing cluster commands for fwdpy11 and num_process/replicated for continuity
David Lawrie
committed
stop openBlas from spamming threads in numpy calculations
David Lawrie
committed
continuity results for continuity and fwdpy11 with different rates of recombination
David Stuart Lawrie
committed

Commits on Jul 3, 2019

increase replicates to 10,0000
David Lawrie
committed

Commits on Jul 4, 2019

Commits on Jul 5, 2019

large replicate sim results, fix to continuity shell commands
David Stuart Lawrie
committed
deleted excess simulation functions, added test for bug in msprime when file is run by python as main
David Lawrie
committed
large replicate sim results for continuity
David Stuart Lawrie
committed
Merge branch 'ancestral_sample' of https://github.com/DL42/fwdpy11_arg_example into ancestral_sample
David Stuart Lawrie
committed

Commits on Jul 7, 2019

combined continuity msprime sim results files
David Lawrie
committed
BGS continuity tests for demographic model 2C with recombination rate 11000
David Lawrie
committed

Commits on Jul 8, 2019

msprime doesn't like seeds of 0
David Lawrie
committed
BGS continuity results
David Stuart Lawrie
committed

Commits on Jul 12, 2019

reorganize files, new R figure code, fix mistake in test_msprime, fix 2E
David Lawrie
committed
reorganize HKBGS results for BGS results
David Lawrie
committed
rename of folder
David Lawrie
committed
continuity BGS with duplication demography 1
David Lawrie
committed
new msprime results
David Stuart Lawrie
committed
continuity BGS results for demography scenario 1 + nohup_msprime_2B
David Stuart Lawrie
committed
corrected sim2C to sim1
David Lawrie
committed
forgot to add to previous commit
David Lawrie
committed
2C > 2B
David Lawrie
committed
continuity BGS with duplication demography 1 and recombination rate 11000
David Lawrie
committed
eliminated extra file
David Lawrie
committed
continuity BGS2 rec111 results + fwdpy11 neutral 2E
David Stuart Lawrie
committed

Commits on Nov 1, 2019

reorganize HK results and add csv results and modify gitignore
David Lawrie
committed
add and modify rplots
David Lawrie
committed
rename 2C to 2B
David Lawrie
committed

Commits on Nov 4, 2019

made separate axes for graphs
David Lawrie
committed

Commits on Nov 5, 2019

multipanel plot 2
David Lawrie
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plot 1 tiff
David Lawrie
committed

Commits on Nov 6, 2019

plot 2 reformatted
David Lawrie
committed
convert to jpg for google docs, regularize sizes, make plot titles "A", "B" bold in neutral_2 plot
David Lawrie
committed

Commits on Nov 19, 2019

ignore pptx and tex files, have LaTex output figures using tikzLatex package, use eta for Fst, add symbols for BGS plots, remove msprime results from plot2.pdf, put non-duplication msprime vs fwdpy…
David Lawrie
committed

Commits on Dec 3, 2019

new combined plot 1
David Lawrie
committed
increase replicates BGS_1_rec_3 by 16x for 1/4 se
David Lawrie
committed
new results
David Stuart Lawrie
committed

Commits on Dec 5, 2019

rename sim2C to sim2B files
David Lawrie
committed
new continuity BGS plots
David Lawrie
committed

Commits on Dec 6, 2019

changing legend keyheight for linetype legend (spacing out neutral and theoretical expectation) and increasing pdf size for some of the plots
David Lawrie
committed
regularizing BGS plots and legends
David Lawrie
committed
r_plot for pi
David Lawrie
committed