Use very early version to exclude introduced errors
For a better comparison of the two versions, I decided to use the earliest version of the our code with only one commit that fix the broken constructor (commit id - 78483b58). I also added two changes:
- remove duplicate Inputs in UnsortedAlignment
- ExcludablePrior from multitypetree
I started the computations and I think the results much closer to our current Lumiere version, then to .jar version.
Here is a results for NeutralFitModel:
earliest version:
Sample posterior prior BDMM TreeHeight origin birthRate.1 birthRate.2 birthRate.3 birthRate.4 birthRate.5 deathRate
0 -651.8700877357618 -651.8700877357618 -670.9475812165033 71.02702000000001 100.0 0.14 0.1 0.1 0.10632968411783428 0.1 0.05
100 -652.4256293181397 -652.4256293181397 -671.6918841684205 71.02702000000001 100.0 0.1260114874631196 0.11070469791733396 0.09568609065459042 0.12121739923249854 0.08019484946439305 0.05
200 -653.9042476537415 -653.9042476537415 -672.3263494306448 71.02702000000001 100.0 0.11052101269296302 0.12211576369948048 0.13569468250634814 0.14789574726509006 0.07860765301474872 0.05
300 -651.631593365216 -651.631593365216 -670.6372216723171 71.02702000000001 100.0 0.12524219590088603 0.09748966703727464 0.10792889112163057 0.129754692108322 0.09080621251796271 0.05
400 -652.0170616062171 -652.0170616062171 -671.3253502275666 71.02702000000001 100.0 0.11672346121651087 0.11091881717560152 0.08407806441243218 0.13797271672605377 0.08251638174912793 0.05
500 -652.1095193411564 -652.1095193411564 -670.9181370748997 71.02702000000001 100.0 0.10564751642254572 0.12759202453487806 0.08610024811676147 0.1494401959457569 0.09834046373091723 0.05
our version:
Sample posterior prior BDMM TreeHeight origin birthRate1 birthRate2 birthRate3 birthRate4 birthRate5 deathRate
0 -652.2114579142637 -652.2114579142637 -671.3828962612497 71.02702000000001 100.0 0.14 0.1 0.1 0.1 0.1 0.05
100 -654.5201845329851 -654.5201845329851 -674.1268431865124 71.02702000000001 100.0 0.16081588193694688 0.08475477594399952 0.08380863511746256 0.07983773916255658 0.10652401195484025 0.05
200 -654.731374918025 -654.731374918025 -675.0792216479654 71.02702000000001 100.0 0.15946725756990482 0.05454535608053485 0.06063736983810952 0.0905501119743065 0.10475440684070739 0.05
300 -652.1277598788464 -652.1277598788464 -672.0020625024281 71.02702000000001 100.0 0.13494290138870013 0.06260496242434298 0.07605633455606513 0.09722691280847236 0.12588005425071297 0.05
400 -652.8208908058607 -652.8208908058607 -671.9793276512291 71.02702000000001 100.0 0.1376179330419911 0.0605218156725193 0.10871053621695144 0.09068952929391921 0.14954273652521027 0.05
500 -653.1711223641565 -653.1711223641565 -672.704239631415 71.02702000000001 100.0 0.1609337844149245 0.07236184531733855 0.06751743818693373 0.09627838199576305 0.12603237452958607 0.05jar version:
Sample posterior prior BDMM TreeHeight origin birthRate1 birthRate2 birthRate3 birthRate4 birthRate5 deathRate
0 -694.4923609344356 -694.4923609344356 -713.678486455959 71.02702000000001 100.0 0.14 0.1 0.1 0.09902244766036372 0.1 0.05
100 -690.7993072157732 -690.7993072157732 -710.9463561405664 71.02702000000001 100.0 0.11392421851177002 0.0918813259910379 0.06247795482114177 0.0908958905673705 0.11635108984616528 0.05
200 -685.4492917444207 -685.4492917444207 -706.2758813924684 71.02702000000001 100.0 0.0760119850008318 0.09967908077856215 0.06809847841421704 0.07430104983953012 0.11285733497035072 0.05
300 -679.3948170014406 -679.3948170014406 -700.2898200958389 71.02702000000001 100.0 0.05593759955820535 0.07929959473777123 0.08755413600012123 0.08062788616296607 0.12443090529403848 0.05
400 -672.7464588032967 -672.7464588032967 -694.3556624166563 71.02702000000001 100.0 0.03243570335549547 0.05502145230966395 0.08346038775233022 0.0961324443494447 0.11430707067414504 0.05
500 -675.6752307726158 -675.6752307726158 -697.1577755832336 71.02702000000001 100.0 0.035500364862854204 0.0618694270091566 0.09321207503632573 0.10987523579300314 0.08884670650127169 0.05Same for ebola
Here is a results for ebola_makona_fitnessBD_9genos_exactP0s.xml:
earliest version:
Sample posterior prior BDMM birthRate migrationMatrix.1 migrationMatrix.2 samplingProportion.1 samplingProportion.2 mutFitEffects.1 mutFitEffects.2 mutFitEffects.3 mutFitEffects.4 mutFitEffects.5 mutFitEffects.6 mutFitEffects.7 mutFitEffects.8 mutFitEffects.9
0 5838.996939040244 5838.996939040244 5828.5677228434 60.0 0.002 0.002 0.0 0.056 1.0 1.0 1.0 1.0 1.0 1.0 0.9716881802715919 1.0 1.0
100 5861.025509279473 5861.025509279473 5851.6038290871 60.0 0.002091782774290086 0.003923289234651797 0.0 0.056 0.7660690842556591 1.0029290577893013 0.9618241869389083 1.01345264323589 0.9584273799233919 1.074946700273281 0.9733932190712875 1.0471534686010842 0.973521653199776
200 5869.573198607359 5869.573198607359 5860.725826763832 60.0 0.002956804320193256 0.004206884386441171 0.0 0.056 0.7646557140656745 0.9921776218353849 0.8724298163072073 1.0337578897829476 1.029376622620967 1.1004914389782097 0.9620336655301502 0.9513076346744725 0.9777476826426915
300 5866.536688988686 5866.536688988686 5857.833449391001 60.0 0.0026082016404317806 0.00484375155788562 0.0 0.056 0.7613692612982887 0.9921776218353849 0.8848787020390946 1.0055731943512727 1.1345932144243538 1.0089653035883865 0.9670092903312565 0.9707998632156619 0.9691629342502144
400 5869.926148245505 5869.926148245505 5861.072507145851 60.0 0.002927410643284225 0.004223739551096085 0.0 0.056 0.7879716415514709 0.9921776218353849 0.9874024416484793 0.9982632221194399 1.0442881039143581 1.0723133336965784 0.9940524883703008 0.9720162253780512 0.9966117939846607
500 5872.993948103002 5872.993948103002 5864.615397705398 60.0 0.0038775920473841175 0.004223739551096085 0.0 0.056 0.7832732473689985 0.9949739681851785 0.8825466394022072 1.0291006695087475 1.050273373855802 1.044753177651041 0.9665851087381722 1.0152102072067881 0.959409872104546our version:
Sample posterior prior BDMM birthRate migrationMatrix1 migrationMatrix2 samplingProportion1 samplingProportion2 mutFitEffects1 mutFitEffects2 mutFitEffects3 mutFitEffects4 mutFitEffects5 mutFitEffects6 mutFitEffects7 mutFitEffects8 mutFitEffects9
0 5839.254085912977 5839.254085912977 5828.8248697161325 60.0 0.002 0.002 0.0 0.056 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
100 5860.422557417332 5860.422557417332 5850.506918546031 60.0 0.0026881448011871695 0.002339009849898732 0.0 0.056 0.7829076736984679 1.0 0.7645734018368442 0.9789768036593017 0.947693841488871 1.1022956065801834 1.0023892962421022 0.9923602597321513 0.9737889302399262
200 5865.070527634538 5865.070527634538 5855.740908549451 60.0 0.0035529161643024286 0.0026462780592124437 0.0 0.056 0.7887230882528057 1.0 0.8743529727216022 1.0117007810090246 0.9333426754149925 1.0191720133198943 0.9899184110466538 0.9369855883623858 0.9706894392212835
300 5864.023931366746 5864.023931366746 5854.502126717882 60.0 0.0034048954646422698 0.0024099276313171896 0.0 0.056 0.8083388643042084 1.009814524765242 0.86951744334544 0.9804572389443407 1.009903006514433 1.2086636945311426 0.9993355819093426 0.9654167446861993 1.0077200094814467
400 5866.471926203697 5866.471926203697 5857.3408921369555 60.0 0.004319780650103226 0.002276583610102749 0.0 0.056 0.7412994063235615 0.9872708692447795 0.8050582178259135 1.0321088600496546 1.0731785999191932 1.0360171226013466 0.9388498534389988 1.0564382657602074 0.9997798644598997
500 5866.325843733324 5866.325843733324 5857.472666371235 60.0 0.004644091406559338 0.002507986262951078 0.0 0.056 0.777175612759779 0.982061187216584 0.9536482504700852 0.9967041786307216 1.0211550524495487 1.0926835286563379 0.9126490522609487 1.045642356802149 1.0457229628702485jar version:
Sample posterior prior BDMM birthRate migrationMatrix1 migrationMatrix2 samplingProportion1 samplingProportion2 mutFitEffects1 mutFitEffects2 mutFitEffects3 mutFitEffects4 mutFitEffects5 mutFitEffects6 mutFitEffects7 mutFitEffects8 mutFitEffects9
0 5908.037569842589 5908.037569842589 5897.6083536457445 60.0 0.002 0.002 0.0 0.056 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0
100 5928.607667245489 5928.607667245489 5918.398340229658 60.0 0.002070126479476124 0.002369651882550757 0.0 0.056 0.8056488227950465 1.0 0.8493536586521234 1.0141882829661593 1.0202483263864235 1.0273713565391753 1.0355592163937728 0.9444772359250415 0.9534216813932193
200 5937.681872759152 5937.681872759152 5927.587623875115 60.0 0.002622408534112489 0.002047526091503548 0.0 0.056 0.73653437148505 1.0 0.9020518669175078 0.9844366267996254 1.0685935557257598 1.1836713121682525 1.0847826750938485 1.0266985505590165 0.9768319522150926
300 5931.934360410506 5931.934360410506 5921.737268121229 60.0 0.0023037875391783355 0.0021604602759560856 0.0 0.056 0.7778782004783722 1.0 0.8595417581917585 0.9951624717782397 0.9789204732572111 1.158442363529131 0.9963260905644143 1.0199964847191643 1.026606597791423
400 5934.568362243192 5934.568362243192 5924.660923953423 60.0 0.0028490669726816374 0.002194488841468847 0.0 0.056 0.7050312412368308 0.9906445136114276 0.9174737342148644 0.9899769478000059 1.1921722737353664 1.1355749579377246 1.0437610912184532 0.988206471299841 0.9711655502356127
500 5944.269290032404 5944.269290032404 5934.81358856806 60.0 0.0035948121430202577 0.0023522173219812023 0.0 0.056 0.7469018806815167 0.9906445136114276 0.8901848557630985 1.0129478296899042 0.9800238884091664 1.0286845947870962 1.061530906817821 1.0163182037172465 1.002991205080869Edited by Maria Del