Code

Systematics Normalization Project#291

Code

Closed

abbywlsn wants to merge 135 commits intodevosoft:masterdevosoft/Empirical:masterfrom abbywlsn:systematics-normalizationabbywlsn/Empirical:systematics-normalizationCopy head branch name to clipboard

+13,601-249

Commits

Commits on May 10, 2018

• Beginning of new OEE tracker

  emilydolson

  committed
  308ccba

  Copy full SHA for 308ccba

• Actually track stats; not compiling yet

  emilydolson

  committed
  904516d

  Copy full SHA for 904516d

Commits on May 11, 2018

• OEE stats work

  emilydolson

  committed
  8ff0fa4

  Copy full SHA for 8ff0fa4

• OEE output file works

  emilydolson

  committed
  ea10926

  Copy full SHA for ea10926

Commits on May 12, 2018

• Fixed pointer problem

  emilydolson

  committed
  778ba78

  Copy full SHA for 778ba78

• Add skeletonize helper

  emilydolson

  committed
  2cd6791

  Copy full SHA for 2cd6791

Commits on May 14, 2018

• Compiles with Avida

  emilydolson

  committed
  817d845

  Copy full SHA for 817d845

Commits on May 24, 2018

• Merge branch 'master' of github.com:devosoft/Empirical into OEE

  emilydolson

  committed
  06bafe8

  Copy full SHA for 06bafe8

Commits on Aug 30, 2018

• Added a few math tools + updates to work with latest version of emscripten

  emilydolson

  committed
  b452d29

  Copy full SHA for b452d29

• Pull in latest changes from master

  emilydolson

  committed
  b4b1559

  Copy full SHA for b4b1559

Commits on Sep 2, 2018

• Preliminary fix for synchronous generations (there were problems when offspring replace parents)

  emilydolson

  committed
  3cda74e

  Copy full SHA for 3cda74e

Commits on Sep 3, 2018

• Improving OEE tests

  emilydolson

  committed
  d027295

  Copy full SHA for d027295

• finished OEE metric tests

  emilydolson

  committed
  466ddec

  Copy full SHA for 466ddec

Commits on Sep 4, 2018

• Fixed diversity

  emilydolson

  committed
  2d215f7

  Copy full SHA for 2d215f7

• Time and memory improvements to OEE

  emilydolson

  committed
  3c3351c

  Copy full SHA for 3c3351c

Commits on Sep 5, 2018

• Make sure to lump identical skeletons together

  emilydolson

  committed
  8357dd8

  Copy full SHA for 8357dd8

Commits on Sep 8, 2018

• Added destruction time/canopy filter

  emilydolson

  committed
  1dd6b02

  Copy full SHA for 1dd6b02

• Fix diversity

  emilydolson

  committed
  e287dae

  Copy full SHA for e287dae

Commits on Sep 25, 2018

• Use bloom filter for novelty to keep RAM under control

  emilydolson

  committed
  8f251d9

  Copy full SHA for 8f251d9

Commits on Sep 26, 2018

• Prune top of phylogeny

  emilydolson

  committed
  5171c87

  Copy full SHA for 5171c87

Commits on Oct 8, 2018

• Added snapshoting to Systematics class.

  amlalejini

  committed
  e1999c5

  Copy full SHA for e1999c5

• Fixed Systematics snapshot field descriptions.

  amlalejini

  committed
  7ed2026

  Copy full SHA for 7ed2026

• Merge pull request devosoft#2 from amlalejini/sys-snapshot

  Show description for 8eb4f70
  emilydolson

  authored
  8eb4f70

  Copy full SHA for 8eb4f70

• Skeletonize during taxon's lifetime to make sure we use the right fitness function

  emilydolson

  committed
  09a45e5

  Copy full SHA for 09a45e5

• Merge branch 'OEE' of github.com:emilydolson/Empirical into OEE

  emilydolson

  committed
  343080f

  Copy full SHA for 343080f

Commits on Oct 12, 2018

• Improve interface for MODES

  emilydolson

  committed
  338a892

  Copy full SHA for 338a892

Commits on Oct 18, 2018

• Add methods to weighted graph

  emilydolson

  committed
  644d333

  Copy full SHA for 644d333

• Began library of distance metrics

  emilydolson

  committed
  c3758d4

  Copy full SHA for c3758d4

• Temporary work-around

  emilydolson

  committed
  8b53070

  Copy full SHA for 8b53070

Commits on Oct 19, 2018

• Added fixes to graph and OEE

  emilydolson

  committed
  d36befd

  Copy full SHA for d36befd

Commits on Oct 30, 2018

• Add ability to display current value of range inputs

  emilydolson

  committed
  fe6c43b

  Copy full SHA for fe6c43b

Commits on Nov 12, 2018

• Improvemetns to sytematics

  emilydolson

  committed
  3257a04

  Copy full SHA for 3257a04

Commits on Nov 19, 2018

• Fix bug when orgs die of natural causes

  emilydolson

  committed
  69e8cb9

  Copy full SHA for 69e8cb9

Commits on Jan 17, 2019

• Little clean-ups

  emilydolson

  committed
  2a9e18b

  Copy full SHA for 2a9e18b

Commits on Jan 25, 2019

• Add not equals operator

  emilydolson

  committed
  40a62a1

  Copy full SHA for 40a62a1

• Added bounds-checking on histograms

  emilydolson

  committed
  59379bd

  Copy full SHA for 59379bd

Commits on Jan 26, 2019

• Made niche width explicit

  emilydolson

  committed
  6270797

  Copy full SHA for 6270797

• Being allowing the use of WorldPosition with systematics

  emilydolson

  committed
  ae2aa0d

  Copy full SHA for ae2aa0d

• Merge in master

  emilydolson

  committed
  642acd5

  Copy full SHA for 642acd5

Commits on Jan 27, 2019

• Fix discrepancy in data node name

  emilydolson

  committed
  aa99dcb

  Copy full SHA for aa99dcb

• Fixed circular dependency

  emilydolson

  committed
  8ec1ced

  Copy full SHA for 8ec1ced

• Fix const fitness function issue

  emilydolson

  committed
  f96e934

  Copy full SHA for f96e934

Commits on Jan 28, 2019

• Little fixes to make everything work efficiently

  emilydolson

  committed
  1e59808

  Copy full SHA for 1e59808

Commits on Jan 29, 2019

• Data tracking improvements

  emilydolson

  committed
  9b96455

  Copy full SHA for 9b96455

Commits on Apr 10, 2019

• Start actually using WorldPosition in systematics

  emilydolson

  committed
  14fd55b

  Copy full SHA for 14fd55b

• Merge

  emilydolson

  committed
  3bc36e8

  Copy full SHA for 3bc36e8

• Actually save merge fix

  emilydolson

  committed
  fbdb99e

  Copy full SHA for fbdb99e

Commits on Apr 23, 2019

• Fix syntax errors ; add max depth

  emilydolson

  committed
  5ae6826

  Copy full SHA for 5ae6826

• Fix missing braces

  emilydolson

  committed
  e861c75

  Copy full SHA for e861c75

• Merge

  emilydolson

  committed
  1e3782d

  Copy full SHA for 1e3782d

• It would help if I actually saved the file

  emilydolson

  committed
  b986cfb

  Copy full SHA for b986cfb

• Need to be explicit about position tracking

  emilydolson

  committed
  f16e8fa

  Copy full SHA for f16e8fa

• Styles can also control CSS classes

  emilydolson

  committed
  38a6dc1

  Copy full SHA for 38a6dc1

Commits on Apr 24, 2019

• Merge in new argmanager

  emilydolson

  committed
  9627273

  Copy full SHA for 9627273

• Add preliminary automatic config web interface

  emilydolson

  committed
  d17e407

  Copy full SHA for d17e407

• Remove uneccesary prin statements

  emilydolson

  committed
  79fe0c2

  Copy full SHA for 79fe0c2

Commits on Apr 25, 2019

• Make it possible to exclude settings

  emilydolson

  committed
  5fc16fb

  Copy full SHA for 5fc16fb

• Print group labels

  emilydolson

  committed
  3df1199

  Copy full SHA for 3df1199

Commits on May 10, 2019

• Improve guess at good parameter ranges

  emilydolson

  committed
  1fa815c

  Copy full SHA for 1fa815c

• Add preliminary spatial stats

  emilydolson

  committed
  d814bf7

  Copy full SHA for d814bf7

• Add Sackin index

  emilydolson

  committed
  c42deb6

  Copy full SHA for c42deb6

Commits on May 13, 2019

• Made systematics manager doubly-linked, added CollessLike metric

  emilydolson

  committed
  98ad638

  Copy full SHA for 98ad638

Commits on May 14, 2019

• Not storing ancestors no longer breaks everything

  emilydolson

  committed
  5a0d2fd

  Copy full SHA for 5a0d2fd

Commits on May 15, 2019

• Make phylogeny tests more sstringent

  emilydolson

  committed
  0d23ad4

  Copy full SHA for 0d23ad4

• CollessLike index currently doesn't agree with value reported in paper

  emilydolson

  committed
  b1673db

  Copy full SHA for b1673db

Commits on May 20, 2019

• More precise e

  emilydolson

  committed
  94e26a1

  Copy full SHA for 94e26a1

Commits on May 21, 2019

• Fixed CollessLike metric

  emilydolson

  committed
  2e3e824

  Copy full SHA for 2e3e824

• Remove print statements

  emilydolson

  committed
  dbdd023

  Copy full SHA for dbdd023

Commits on May 23, 2019

• mrca can get pruned if tree is being cleared

  emilydolson

  committed
  454d092

  Copy full SHA for 454d092

Commits on Jun 13, 2019

• Add method to get all lines from a file

  emilydolson

  committed
  12ec2d4

  Copy full SHA for 12ec2d4

Commits on Jan 29, 2020

• Register new systematics metrics

  emilydolson

  committed
  00fbd16

  Copy full SHA for 00fbd16

Commits on Jan 30, 2020

• Minor bug fixes

  emilydolson

  committed
  273eb7a

  Copy full SHA for 273eb7a

Commits on Feb 11, 2020

• Can't remove parent until repro done

  emilydolson

  committed
  df82c1b

  Copy full SHA for df82c1b

• Merge branch 'memic_model' of github.com:emilydolson/Empirical into memic_model

  emilydolson

  committed
  9684946

  Copy full SHA for 9684946

Commits on Feb 13, 2020

• Fix seg-fault on exctinction in synchronous world

  emilydolson

  committed
  402bb05

  Copy full SHA for 402bb05

Commits on May 26, 2020

• Merge in updates from my postdoc year

  emilydolson

  committed
  514fa39

  Copy full SHA for 514fa39

• Fix vector being passed by reference

  emilydolson

  authored
  8f30304

  Copy full SHA for 8f30304

• Revert World_structure.h

  emilydolson

  authored
  a398dfd

  Copy full SHA for a398dfd

• Revert World_select.h

  emilydolson

  authored
  a195f40

  Copy full SHA for a195f40

• Add comment back in

  emilydolson

  authored
  47e6bef

  Copy full SHA for 47e6bef

• Revert .gitignore

  emilydolson

  authored
  9300561

  Copy full SHA for 9300561

• change name of count to avoid conflict with Lexer

  emilydolson

  authored
  ca6e845

  Copy full SHA for ca6e845

• Revert Ptr.h

  emilydolson

  authored
  72e96cb

  Copy full SHA for 72e96cb

• Revert assert.h

  emilydolson

  authored
  83245fa

  Copy full SHA for 83245fa

• Revert init.h

  emilydolson

  authored
  c2cb58f

  Copy full SHA for c2cb58f

• Put systematics tests in the right place

  emilydolson

  committed
  0da2d16

  Copy full SHA for 0da2d16

• Merge the two test_systematics.cc files

  emilydolson

  committed
  8cb86d8

  Copy full SHA for 8cb86d8

Commits on May 27, 2020

• Switch has back to pass-by-reference

  emilydolson

  authored
  e445f36

  Copy full SHA for e445f36

• Fix image example to work in light Slider.h not existing anymore

  emilydolson

  committed
  c34c09f

  Copy full SHA for c34c09f

• Fix web tests to work with latest version of all dependencies

  emilydolson

  committed
  a19359d

  Copy full SHA for a19359d

• Merge branch 'memic_merge' of github.com:emilydolson/Empirical into memic_merge

  emilydolson

  committed
  35f7ecf

  Copy full SHA for 35f7ecf

• Source emscripten in travis so it can actually be used

  emilydolson

  committed
  a3b7049

  Copy full SHA for a3b7049

• whether this is 5 or 5px seems to vary by browser

  emilydolson

  committed
  390645a

  Copy full SHA for 390645a

• Does emcc not compile to native anymore?

  emilydolson

  committed
  0b12e3e

  Copy full SHA for 0b12e3e

• Fix typo

  emilydolson

  committed
  4a66b34

  Copy full SHA for 4a66b34

Commits on May 28, 2020

• Split Travis config into multiple parallel builds

  emilydolson

  committed
  fc1d8ae

  Copy full SHA for fc1d8ae

• Compile web examples with web tests and native with native

  emilydolson

  committed
  7172d0c

  Copy full SHA for 7172d0c

• if WASM=0 we can't use g4 flag

  emilydolson

  committed
  ee67fd7

  Copy full SHA for ee67fd7

Commits on May 29, 2020

• Merge branch 'master' into memic_merge

  emilydolson

  authored
  02db9e6

  Copy full SHA for 02db9e6

Commits on May 30, 2020

• Make show value default to false

  emilydolson

  committed
  9c15c57

  Copy full SHA for 9c15c57

• Merge branch 'memic_merge' of github.com:emilydolson/Empirical into memic_merge

  emilydolson

  committed
  c53aae8

  Copy full SHA for c53aae8

• Merge in testing changes

  emilydolson

  committed
  f728a3f

  Copy full SHA for f728a3f

• Swap in updated systematics tests

  emilydolson

  committed
  4898614

  Copy full SHA for 4898614

• Add additional tests that didn't transfer over; fix resource tests

  emilydolson

  committed
  c33e776

  Copy full SHA for c33e776

• Add more tests

  emilydolson

  committed
  0885e50

  Copy full SHA for 0885e50

• Merge branch 'master' into memic_merge

  emilydolson

  authored
  cd675dd

  Copy full SHA for cd675dd

Commits on May 31, 2020

• Add more vecter_utils tests

  emilydolson

  committed
  351b8cb

  Copy full SHA for 351b8cb

• Add tests for new DataNode features

  emilydolson

  committed
  56ad817

  Copy full SHA for 56ad817

• Add skew, kurtosis, and stdev tests

  emilydolson

  committed
  bcd70e0

  Copy full SHA for bcd70e0

• Merge branch 'memic_merge' of github.com:emilydolson/Empirical into memic_merge

  emilydolson

  committed
  7c18a0c

  Copy full SHA for 7c18a0c

• Fix missing template

  emilydolson

  authored
  85401ee

  Copy full SHA for 85401ee

• Removed duplicate count function

  emilydolson

  committed
  54a8c79

  Copy full SHA for 54a8c79

• Add more tests

  emilydolson

  committed
  9ad6112

  Copy full SHA for 9ad6112

• fix tempalte

  emilydolson

  committed
  f9a434b

  Copy full SHA for f9a434b

• fix tempalte

  emilydolson

  committed
  3a424d3

  Copy full SHA for 3a424d3

• GetNodes should be in base graph class

  emilydolson

  committed
  0b182dc

  Copy full SHA for 0b182dc

• Rename get site-specific fitness function to avoid conflict

  emilydolson

  committed
  94055a7

  Copy full SHA for 94055a7

• Add more tests

  emilydolson

  committed
  173eee1

  Copy full SHA for 173eee1

Commits on Jun 4, 2020

• adding systematics documentation

  abbywlsn

  committed
  e0a54c2

  Copy full SHA for e0a54c2

Commits on Jun 16, 2020

• miniphylotrees makes very simple trees, still needs to incorporate systematics tools and record runs

  abbywlsn

  committed
  1c14505

  Copy full SHA for 1c14505

Commits on Jun 18, 2020

• miniphylotrees prints data to csv file now

  abbywlsn

  committed
  2824062

  Copy full SHA for 2824062

• added systematics manager tools, still broken though

  abbywlsn

  committed
  d0b9be3

  Copy full SHA for d0b9be3

Commits on Jun 22, 2020

• new changes to miniphylotrees

  abbywlsn

  committed
  01e3808

  Copy full SHA for 01e3808

Commits on Jun 25, 2020

• miniphylotrees works and generates data, concerned about compiler differences though

  abbywlsn

  committed
  5b47ce7

  Copy full SHA for 5b47ce7

Commits on Jun 26, 2020

• new csv with percentile data and miniphylotrees is correctly outputting phylodiversity

  abbywlsn

  committed
  10ff45e

  Copy full SHA for 10ff45e

• original file with no systematics implementation for example purposes

  abbywlsn

  committed
  cf2bbe7

  Copy full SHA for cf2bbe7

Commits on Jul 1, 2020

• new miniphylo changes

  abbywlsn

  committed
  7e22970

  Copy full SHA for 7e22970

• changes made to systematics with percentile functions

  abbywlsn

  committed
  c9ad62a

  Copy full SHA for c9ad62a

Commits on Jul 23, 2020

• new improvements and updated systematics functions

  abbywlsn

  committed
  1836ef4

  Copy full SHA for 1836ef4

Commits on Jul 28, 2020

• cleaned up miniphylotrees

  abbywlsn

  committed
  14dcc46

  Copy full SHA for 14dcc46

Commits on Jul 30, 2020

• updated systematics function, still needs work

  abbywlsn

  committed
  28294af

  Copy full SHA for 28294af

Commits on Jul 31, 2020

• cleaning up directories

  abbywlsn

  committed
  72c442e

  Copy full SHA for 72c442e

• more directory cleaning

  abbywlsn

  committed
  516735b

  Copy full SHA for 516735b

• cleaned up systematics.h

  abbywlsn

  committed
  f1c61a3

  Copy full SHA for f1c61a3

• cleaning up some stuff in GenTrees

  abbywlsn

  committed
  d0aca02

  Copy full SHA for d0aca02