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lonelyjoeparker / befi-bats-gui

Java software to analyse phylogeny-trait correlations in discrete traits, accounting for phylogenetic uncertainty via posterior sampling.
http://science.lonelyjoeparker.com
GNU General Public License v3.0
9 stars 3 forks source link

Strange 95%CI results #5

Closed psperez07 closed 8 years ago

psperez07 commented 9 years ago

I write to ask advice about some troublesome results I have obtained with BaTS software. The problem is that the upper and lower 95%CI limits are the same and strangely round numbers. What is more, the observed mean is not included in the 95%CI reported. This has occurred in repeated occasions and for all the statistics. I could not attached here the input trees file due to its size. I hope you could please help me to understand what the problem with this data is. Thank you very much in advanced.

Command input:

BaTS_beta_build2.jar single 04_Core.input.trees 1000 3 >04.Core.txt

Output: Performing single analysis. File: 04_Core.input.trees Null replicates: 1000 Maximum number of discrete character states: 3

analysing... 9000 trees, with 3 states analysing observed (using obs state data) 9000 8550 9000 8550 9000 8550 9000 8550 9000 8550 Statistic observed mean lower 95% CI upper 95% CU null mean lower 95% CI upper 95% CI significance AI 2.3106416847440414E-5 5.4800979726321586E-11 1.2207391591800842E-5 3.849498748779297 3.307699680328369 4.338315963745117 0.0 PS 2.003000020980835 2.0 2.0 22.962961196899414 20.796443939208984 24.84433364868164 0.0 MC (state 0) 15.991777420043945 16.0 16.0 2.470072031021118 2.0306665897369385 3.2673332691192627 9.999871253967285E-4
MC (state 1) 17.884666442871094 18.0 18.0 2.3556597232818604 1.9315555095672607 3.0166666507720947 9.999871253967285E-4
MC (state 2) 11.960222244262695 12.0 12.0 1.7799134254455566 1.374333381652832 2.3259999752044678 9.999871253967285E-4
done

Done.

lonelyjoeparker commented 9 years ago

Hi @psperez07 - can you please attach the head of the .trees file (the STATES block and first few trees, about 10 lines, of the TREES block) please? This should be less than the attachment limit.

psperez07 commented 9 years ago

Yes of course, here it is. Thank you very much.

NEXUS

begin states; 1 NT 2 NT 3 NT 4 NT 5 NT 6 NT 7 NT 8 NT 9 NT 10 NT 11 NT 12 NT 13 NT 14 NT 15 NT 16 NT 17 NT 18 NT 19 NT 20 S 21 S 22 S 23 S 24 S 25 S 26 S 27 S 28 S 29 S 30 S 31 S 32 S 33 S 34 S 35 S 36 S 37 S 38 T 39 T 40 T 41 T 42 T 43 T 44 T 45 T 46 T 47 T 48 T 49 T End; begin trees; tree STATE_10010000= &R; tree STATE_10020000= &R; tree STATE_10030000= &R; tree STATE_10040000= &R; tree STATE_10050000= &R; tree STATE_10060000= &R; tree STATE_10070000= &R; tree STATE_10080000= &R; tree STATE_10090000= &R; tree STATE_10100000= &R; End;

lonelyjoeparker commented 9 years ago

@psperez07 - there's no trees in those tree lines, did you paste correctly? For example (see the package files): 

#NEXUS

begin states;
1 black
2 black
3 black
4 black
5 white
6 white
7 white
8 white
End;

begin trees;
tree STATE_1011000 = [&R] (1,2,3,4,5,6,7,8);
tree STATE_1011000 = [&R] ((1,2,3,4):1,(5,6,7,8):1);
tree STATE_1011000 = [&R] (((1,2):1,(3,4):1):1,((5,6):1,(7,8):1):1);
tree STATE_1011000 = [&R] (((1,2):1,(5,6):1):1,((3,4):1,(7,8):1):1);
tree STATE_1011000 = [&R] (((1:0.5,2:0.5):1,(5:0.5,6:0.5):1):1,((3:0.5,4:0.5):1,(7:0.5,8:0.5):1):1);
tree STATE_1011000 = [&R] (((1:1.5,2:0.5):1,(5:0.5,6:0.5):1):1,((3:0.5,4:0.5):1,(7:0.5,8:0.5):1):1);
tree STATE_1011000 = [&R] (((1,5):1,(2,6):1):1,((3,7):1,(4,8):1):1);
tree STATE_1011000 = [&R] (((1:0.5,5:0.5):1,(2:0.5,6:0.5):1):1,((3:0.5,7:0.5):1,(4:0.5,8:0.5):1):1);
tree STATE_1011000 = [&R] (((1:1.5,5:0.5):1,(2:0.5,6:0.5):1):1,((3:0.5,7:0.5):1,(4:0.5,8:0.5):1):1);
End;
psperez07 commented 9 years ago

I’m sorry. Is it correct now? Thank you.

    #NEXUS
    begin states;
    1 NT
    2 NT
    3 NT
    4 NT
    5 NT
    6 NT
    7 NT
    8 NT
    9 NT
    10 NT
    11 NT
    12 NT
    13 NT
    14 NT
    15 NT
    16 NT
    17 NT
    18 NT
    19 NT
    20 S
    21 S
    22 S
    23 S
    24 S
    25 S
    26 S
    27 S
    28 S
    29 S
    30 S
    31 S
    32 S
    33 S
    34 S
    35 S
    36 S
    37 S
    38 T
    39 T
    40 T
    41 T
    42 T
    43 T
    44 T
    45 T
    46 T
    47 T
    48 T
    49 T
    End;
    begin trees;
    tree STATE_10010000= [&R] ((((((5:6.585894854216533E-4,7:6.585894854216533E-4):0.0013065640636305575,15:0.0019651535490522107):0.0027203272906577564,((16:0.002815922226667739,(19:2.5993339172098915E-5,12:2.5993339172098915E-5):0.00278992888749564):2.3591839412692413E-4,((18:9.484319167224474E-4,((4:2.432010706755679E-4,(14:2.430248667337635E-5,8:2.430248667337635E-5):2.1889858400219155E-4):4.1335888365470795E-5,2:2.845369590410387E-4):6.638949576814087E-4):0.0016590175217583514,(((6:4.300747810337065E-4,(3:4.033224843253775E-4,17:4.033224843253775E-4):2.675229670832897E-5):3.654308997128869E-4,11:7.955056807465934E-4):6.505940446799791E-4,13:0.0014460997254265725):0.0011613497130542264):4.4439118231386424E-4):0.0016336402189153039):0.0015170073765403943,((((36:6.930723315379454E-4,22:6.930723315379454E-4):0.0021923626827362657,(21:0.0027320927575655925,(29:6.190409867649042E-5,35:6.190409867649042E-5):0.002670188658889102):1.5334225670861866E-4):0.0015380947312263293,((((20:1.492981666773891E-5,25:1.492981666773891E-5):8.519958065721502E-4,27:8.669256232398891E-4):0.0014163414041543933,(24:0.0012247003125022795,34:0.0012247003125022795):0.001058566714892003):7.272527716802851E-4,((23:1.655720467513638E-4,32:1.655720467513638E-4):0.00221056947129284,(((30:5.80715932961561E-4,37:5.80715932961561E-4):4.932750404885737E-4,(28:1.6356133933721827E-4,31:1.6356133933721827E-4):9.104296341129164E-4):6.002688275220686E-4,26:0.0016742598009722033):7.018817170720006E-4):6.343782810303636E-4):0.001413009946425973):5.776567686189855E-4,33:0.005001186514119526):0.0012013017021308353):3.557257238624252E-4,((1:0.0015304135941012114,9:0.0015304135941012114):0.0029109311670295172,10:0.004441344761130729):0.002116869178982058):9.282655295714693E-5,((((41:0.0027077880378332357,(38:0.001666151298209164,39:0.001666151298209164):0.0010416367396240717):3.9942984229457976E-4,(48:0.0026708810404647196,(43:3.4790224741633024E-4,44:3.4790224741633024E-4):0.0023229787930483894):4.3633683966309584E-4):0.001601805367698945,(47:0.002233868940058117,45:0.002233868940058117):0.0024751543077686437):1.6829454856969687E-4,((46:0.0041777462463708885,49:0.0041777462463708885):6.032620926497432E-4,(42:5.388610659184093E-4,40:5.388610659184093E-4):0.004242147273102222):9.630945737582573E-5):0.001773722696673476);
    tree STATE_10020000= [&R] ((((13:0.0014878641390446952,((((18:5.834278453779008E-5,2:5.834278453779008E-5):6.50201835259841E-5,5:1.2336296806377418E-4):1.889983599715805E-4,6:3.1236132803535467E-4):1.970143961833793E-4,19:5.09375724218734E-4):9.784884148259614E-4):0.0011897296959262672,14:0.0026775938349709624):0.0014169090149208714,((((4:0.0012382571708777583,(7:9.895780702969116E-4,8:9.895780702969116E-4):2.4867910058084673E-4):5.656025497497157E-4,(15:9.384727506705477E-4,16:9.384727506705477E-4):8.653869699569263E-4):6.632508274104034E-4,(12:2.85002317913444E-4,(11:7.249005959987959E-5,17:7.249005959987959E-5):2.1251225831356443E-4):0.0021821082301244333):0.0015773855890129185,3:0.004044496137050796):5.000671284103794E-5):0.0028164345613682093,(((1:0.0022414442454036245,9:0.0022414442454036245):0.0029822515618319685,(10:0.004869314288161104,((41:0.0031908196639026357,(38:0.0031163433525663565,39:0.0031163433525663565):7.447631133627921E-5):4.6530301587766314E-4,((48:0.003397815808008078,(49:0.002948658261406716,(40:0.0018953644318378566,45:0.0018953644318378566):0.0010532938295688594):4.491575466013622E-4):1.1785667130871733E-4,((47:0.0014178665121549572,44:0.0014178665121549572):0.0020846099229097003,((46:0.002314884188142302,42:0.002314884188142302):1.3806232058713626E-4,43:0.0024529465087294385):0.001049529926335219):1.319604425213802E-5):1.404502004635033E-4):0.0012131916083808051):3.543815190744891E-4):0.0010089414476608036,((32:0.003676668702690447,(((25:3.971061433524497E-5,27:3.971061433524497E-5):0.00167550909781333,24:0.001715219712148575):9.810212101507825E-5,(20:3.448116437513091E-4,34:3.448116437513091E-4):0.001468510189412344):0.001863346869526794):0.0015671722022708658,((29:0.002269761156772447,35:0.002269761156772447):0.0024185742019397164,(((23:9.635305508343574E-4,(33:9.245463283973765E-4,(22:5.42857714318777E-4,21:5.42857714318777E-4):3.8168861407859953E-4):3.898422243698088E-5):8.489209542857772E-4,36:0.0018124515051201346):0.0013758824803580135,((28:9.726837166678555E-4,(31:3.942628324947102E-4,(30:4.2675593660173674E-5,37:4.2675593660173674E-5):3.515872388345365E-4):5.784208841731454E-4):8.020440569254132E-4,26:0.0017747277735932687):0.0014136062118848794):0.0015000013732340152):5.555055462491496E-4):9.887963499350836E-4):6.783001563636466E-4);
    tree STATE_10030000= [&R] ((((((37:1.1556257410416943E-4,31:1.1556257410416943E-4):0.0016485524084599824,(28:3.6023014738977813E-4,30:3.6023014738977813E-4):0.0014038848351743737):0.002071928709488395,26:0.0038360436920525467):0.0014019019587515323,((22:0.003933779695932185,((24:0.001214874175877673,20:0.001214874175877673):1.3558746908498695E-5,((25:2.3353801016622866E-4,34:2.3353801016622866E-4):6.284064307341262E-4,27:8.619444409003549E-4):3.6648848188581683E-4):0.0027053467731460133):6.965214184570679E-4,((23:0.0025362209214151777,(((36:4.763798883386593E-4,32:4.763798883386593E-4):4.2992154189589723E-4,33:9.063014302345565E-4):0.0010590784696246373,21:0.001965379899859194):5.708410215559839E-4):5.381527223526071E-4,(29:0.0016532520435930122,35:0.0016532520435930122):0.0014211216001747725):0.0015559274706214684):6.076445364148258E-4):3.6964613851508954E-4,((6:0.003012645184987808,13:0.003012645184987808):2.8724072853343824E-4,(((17:0.002412606643840947,2:0.002412606643840947):4.108976842600123E-4,11:0.0028235043281009593):7.679711166641264E-5,((7:6.279308582858038E-4,16:6.279308582858038E-4):0.0018620404522622137,(((((12:3.9160703181325936E-4,8:3.9160703181325936E-4):1.9542245267306722E-4,5:5.870294844863266E-4):3.685571704668451E-4,(18:5.181206158290491E-4,19:5.181206158290491E-4):4.3746603912412263E-4):1.7497127129992914E-4,(4:6.176352574671319E-4,14:6.176352574671319E-4):5.12922668785969E-4):1.3125110202426076E-5,(15:9.770282080771269E-5,3:9.770282080771269E-5):0.0010459802156478142):0.0013462882740924906):4.103301292193544E-4):3.995844737538744E-4):0.002307705875797922):4.5657171483918634E-4,(((45:0.004332823944035173,((41:0.003027889849766074,48:0.003027889849766074):3.767950208027741E-4,(38:0.0020505387046740775,39:0.0020505387046740775):0.0013541461658947707):9.281390734663252E-4):2.1921739759876366E-4,((47:0.003972525832812303,(46:0.0010560438726687697,42:0.0010560438726687697):0.002916481960143533):2.64246854506078E-4,(43:0.0031198066097120466,(44:0.00201422866014553,(49:0.0015517442234608664,40:0.0015517442234608664):4.624844366846637E-4):0.0011055779495665165):0.0011169660776063342):3.152686543155562E-4):5.269667377739698E-4,((1:0.0013399621979836506,9:0.0013399621979836506):0.002858393942331971,10:0.004198356140315621):8.806519390922854E-4):9.85155424750448E-4);
    tree STATE_10040000= [&R] ((((3:3.1720086807273106E-4,4:3.1720086807273106E-4):0.0024382926357744807,(6:9.317926505598796E-4,17:9.317926505598796E-4):0.001823700853287332):8.228637225637706E-4,((((14:4.818359898573045E-4,(11:4.368413705880857E-4,2:4.368413705880857E-4):4.499461926921877E-5):6.278809689663403E-4,12:0.0011097169588236448):0.0020514270862076003,(15:0.00211571247156647,7:0.00211571247156647):0.0010454315734647751):2.467078207268906E-4,(((5:1.5667312736238114E-4,19:1.5667312736238114E-4):6.579416810706143E-4,8:8.146148084329954E-4):0.0013377654787092744,(16:0.001714230749387526,(18:0.0016211187553472242,13:0.0016211187553472242):9.311199404030178E-5):4.381495377547438E-4):0.001255471578615866):1.705053606528466E-4):0.001533661100583786,((((((45:0.002815817780036909,44:0.002815817780036909):9.649954486832136E-5,42:0.0029123173249052305):3.688532437892515E-4,(46:4.855586239449346E-4,40:4.855586239449346E-4):0.0027956119447495476):1.4601569428351934E-4,((49:0.0010788538463177514,(43:7.088707941962655E-4,47:7.088707941962655E-4):3.699830521214859E-4):0.002050160412883619,((48:0.0020328809916080413,41:0.0020328809916080413):0.0010464664737940069,(38:0.0026859702710805757,39:0.0026859702710805757):3.933771943214724E-4):4.966679379932214E-5):2.981720037766311E-4):6.951607439909485E-4,((1:0.001484433850534152,9:0.001484433850534152):0.0016955627817623305,10:0.0031799966322964826):9.423503746724673E-4):6.308721199845243E-4,((((32:0.0012787586969379167,36:0.0012787586969379167):0.0011219064117236632,(29:2.8670963066046304E-4,35:2.8670963066046304E-4):0.002113955478001117):8.598057215756377E-4,((33:0.002991228659521922,(21:3.681824307862088E-4,22:3.681824307862088E-4):0.0026230462287357135):1.7170939695686097E-4,(((28:8.648599440285777E-5,31:8.648599440285777E-5):0.0018096224925695649,(30:2.788705168248124E-4,37:2.788705168248124E-4):0.0016172379701476104):7.591861808164725E-4,26:0.0026552946677888952):5.076433886898879E-4):9.75327737584345E-5):3.4527461195348443E-4,(((25:0.001338597533271955,((34:3.3185704170119503E-4,20:3.3185704170119503E-4):3.974878009998704E-4,24:7.293448427010654E-4):6.092526905708895E-4):2.138524924080907E-4,27:0.0015524500256800457):0.0015118990742591385,23:0.003064349099939184):5.413963422515179E-4):0.001147473684762772):3.587992000412942E-4);
    tree STATE_10050000= [&R] ((((8:0.0026141036728366623,(15:0.0020418523461119844,(((16:8.445640472999962E-4,2:8.445640472999962E-4):3.1806402012668326E-4,4:0.0011626280674266794):7.963015708570336E-4,19:0.001958929638283713):8.292270782827129E-5):5.722513267246779E-4):0.002507004256273616,((5:0.0012181568452066921,14:0.0012181568452066921):0.0028346138199004793,(((12:1.3959025478026387E-4,(11:3.235319453503407E-5,17:3.235319453503407E-5):1.072370602452298E-4):0.003004162865020552,(6:4.7511928786563376E-4,(7:2.194618054288223E-4,13:2.194618054288223E-4):2.556574824368115E-4):0.0026686338319351823):8.029180326653024E-4,(3:0.002107213442512817,18:0.002107213442512817):0.0018394577099533015):1.06099512641053E-4):0.0010683372640031066):0.0015464365309949494,(23:0.005708551645543851,(((29:0.001243981411850331,35:0.001243981411850331):0.0013642295721521518,((21:0.0018963143216494602,(((30:7.548984654310855E-4,31:7.548984654310855E-4):4.2956162266807657E-4,(28:1.957294131018423E-4,37:1.957294131018423E-4):9.8873067499732E-4):4.0104415315582323E-4,26:0.0015855042412549853):3.1081008039447484E-4):4.5445703938667504E-4,(36:0.00195432098030103,((32:5.056455871940087E-4,33:5.056455871940087E-4):1.838197538114513E-4,22:6.8946534100546E-4):0.0012648556392955699):3.9645038073510535E-4):2.574396229663477E-4):0.002105818076594512,(((20:1.9298174499428206E-4,25:1.9298174499428206E-4):6.425416892384852E-4,34:8.355234342327673E-4):0.0012188627567937685,(24:4.7668704117621375E-4,27:4.7668704117621375E-4):0.001577699149850322):0.0026596428695704593):9.94522584946856E-4):9.589928145613763E-4):6.596887685229392E-4,((10:0.0064342539956786255,(1:0.0019764889391000805,9:0.0019764889391000805):0.004457765056578545):6.236166827576061E-4,(((43:0.0028109763957062965,42:0.0028109763957062965):0.0014812396444283645,(40:0.0036372078471977693,45:0.0036372078471977693):6.550081929368916E-4):3.596658644325545E-4,(((44:0.002417172501687922,49:0.002417172501687922):4.85067332871892E-4,(47:0.0014806372556501618,(48:2.3535050581453324E-4,46:2.3535050581453324E-4):0.0012452867498356284):0.0014216025789096523):0.0014414817076545245,((38:0.0010846547735562776,39:0.0010846547735562776):9.226862194161539E-4,41:0.0020073409929724315):0.002336380549241907):3.081603623528769E-4):0.002405988773869016):2.6936255019193497E-4);
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    tree STATE_10080000= [&R] ((((((12:0.0016916467428928265,4:0.0016916467428928265):7.630207808066018E-4,(19:0.0022348492722708124,((2:0.001853670197656263,3:0.001853670197656263):3.2218560784859677E-4,(5:0.0016826849505322424,((7:3.4980575060816613E-4,13:3.4980575060816613E-4):0.0012840968297315658,(16:5.933653005763271E-4,15:5.933653005763271E-4):0.001040537279763405):4.878237019251036E-5):4.931708549726175E-4):5.899346676595252E-5):2.1981825142861587E-4):5.541191074890221E-4,((8:0.0023665125833198693,14:0.0023665125833198693):4.786629045533657E-5,((11:6.409782600057166E-4,6:6.409782600057166E-4):9.779521052494056E-4,17:0.0016189303652551221):7.954485085200837E-4):5.944077574132445E-4):0.0012279225122828704,18:0.004236709143471321):8.911368816405321E-4,(((22:0.0034992896993916783,(36:0.002305333010535406,33:0.002305333010535406):0.0011939566888562723):0.0011463556701892096,((((24:0.0026632612598470233,(20:1.6155190024184972E-4,34:1.6155190024184972E-4):0.0025017093596051737):1.5487518464766398E-4,(25:0.0013838921930726122,27:0.0013838921930726122):0.001434244251422075):9.739882713176531E-4,(29:2.41340596025023E-4,35:2.41340596025023E-4):0.0035507841197873176):1.3115946261668112E-4,(((37:5.652934914625491E-5,31:5.652934914625491E-5):0.0019254938996469042,(30:6.01578268118723E-4,28:6.01578268118723E-4):0.001380444980674436):0.0017849375252543187,26:0.0037669607740474778):1.5632340438154375E-4):7.223611911518664E-4):9.928160334084831E-5,(23:0.0032683412807151977,(21:0.0020662271883182715,32:0.0020662271883182715):0.0012021140923969263):0.0014765856922065385):3.829190521901166E-4):2.3306490784061676E-4,((10:0.0031306769735328726,(1:0.0012727201510507088,9:0.0012727201510507088):0.0018579568224821638):0.002001013010075221,(((38:0.0020992411980673693,39:0.0020992411980673693):2.8347753367179065E-4,41:0.00238271873173916):0.0017186757405164414,((42:0.0030125766407459406,((49:0.001329751439094009,45:0.001329751439094009):9.457435904015946E-4,(44:0.0014544761464522526,((47:8.580212258071752E-4,(46:6.484572857694769E-6,43:6.484572857694769E-6):8.515366529494805E-4):2.4048950837552905E-4,40:0.0010985107341827042):3.5596541226954833E-4):8.210188830433511E-4):7.370816112503369E-4):3.662499276110894E-4,48:0.00337882656835703):7.225679038985714E-4):0.0010302955113524921):2.2922094934437615E-4);
    tree STATE_10090000= [&R] ((((13:0.003216551627400266,8:0.003216551627400266):3.3235570158137015E-4,((14:0.0010944738117500056,5:0.0010944738117500056):0.0019812870064047964,(((((2:8.855863608043482E-4,3:8.855863608043482E-4):3.103918195954974E-4,11:0.0011959781803998456):2.006077051060868E-4,6:0.0013965858855059324):5.443524197693277E-4,17:0.00194093830527526):0.001084150856702468,(((19:3.6928587894609E-4,16:3.6928587894609E-4):0.002237449593950125,(7:0.002474188566743832,((15:2.3691581323154998E-4,4:2.3691581323154998E-4):0.001621470375512109,18:0.0018583861887436588):6.158023780001732E-4):1.3254690615238304E-4):1.648351901048042E-4,12:0.002771570663001019):2.535184989767088E-4):5.067165617707401E-5):4.731465108268342E-4):0.00154082681301101,((29:5.65669108740497E-4,35:5.65669108740497E-4):0.003340883063529869,((((((30:2.475813277580219E-4,(31:3.650617110093709E-5,28:3.650617110093709E-5):2.1107515665708484E-4):4.8086387599310525E-4,37:7.284452037511272E-4):6.481844582389368E-4,26:0.001376629661990064):0.0011747395576452828,((36:3.2132336594976603E-4,22:3.2132336594976603E-4):0.0012381044565795529,21:0.001559427822529319):9.919413971060278E-4):0.0011091258729819479,(32:0.0034008365855010157,(((27:0.0016346056987472301,24:0.0016346056987472301):1.8812751953167913E-4,20:0.0018227332182789093):6.082929507132428E-4,(34:6.641907491724936E-4,25:6.641907491724936E-4):0.0017668354198196584):9.698104165088636E-4):2.5965850711627894E-4):5.254652030140753E-5,(23:4.361837720895225E-4,33:4.361837720895225E-4):0.0032768578408291795):1.9351055935166398E-4):0.00118318196972228):6.601693432484743E-4,((10:0.004082929982045352,(1:0.00234911056811035,9:0.00234911056811035):0.0017338194139350019):3.77693663916487E-4,(((44:0.002283673658988063,((49:0.0010853006049377756,40:0.0010853006049377756):0.0010895100325359467,48:0.0021748106374737224):1.088630215143405E-4):8.018989348840527E-4,((46:9.234331541955103E-4,43:9.234331541955103E-4):0.0019173977705626703,45:0.0028408309247581805):2.44741669113935E-4):2.21633340091551E-4,((47:0.002118097694049335,42:0.002118097694049335):0.001145082729249443,((39:0.0019060008168429955,38:0.0019060008168429955):0.0010895966018651603,41:0.002995597418708156):2.675830045906222E-4):4.402551066488847E-5):0.0011534177119981726):0.0012892798392792814);
    tree STATE_10100000= [&R] ((((((43:0.0018810162283308415,((44:6.446574427618623E-4,45:6.446574427618623E-4):6.44757050487934E-4,47:0.0012894144932497963):5.916017350810453E-4):4.828419668155863E-5,(40:2.1140214519852643E-4,46:2.1140214519852643E-4):0.0017178982798138737):3.586156107922829E-4,(42:0.0015696584480736373,48:0.0015696584480736373):7.182575877310458E-4):0.0028892089843047357,49:0.005177125020109419):3.942685978163517E-5,((39:0.003863337970844518,38:0.003863337970844518):7.044400863270095E-4,41:0.004567778057171528):6.487738227195262E-4):8.043822183711469E-4,((10:0.004591790435882514,(1:0.0016870405896996653,9:0.0016870405896996653):0.002904749846182849):0.0013880194273921832,((((15:0.0016114695659565277,(11:7.360272916921066E-4,(4:6.658664209410281E-4,2:6.658664209410281E-4):7.016087075107844E-5):8.754422742644211E-4):0.0022062247519953593,(8:0.002209167437583083,(5:8.342296495231505E-4,16:8.342296495231505E-4):0.0013749377880599328):0.0016085268803688038):1.9715321899634996E-4,((((7:0.0017117552570775382,14:0.0017117552570775382):7.110141906857318E-4,(19:0.0013402948523010062,3:0.0013402948523010062):0.0010824745954622639):2.578921445135808E-4,((17:6.503918401327513E-4,12:6.503918401327513E-4):9.843208714394925E-4,(18:2.1592876835617753E-4,13:2.1592876835617753E-4):0.0014187839432160663):0.001045948880704607):0.0012077941721713972,6:0.003888455764448248):1.263917724999889E-4):0.0010873117203755705,((24:0.003831645504426705,((20:0.0020813285729342464,25:0.0020813285729342464):6.042717714924671E-5,(27:0.0014377128306506176,34:0.0014377128306506176):7.040429194328755E-4):0.001689889754343212):8.074783799797728E-4,((((28:0.0023347391737778837,(30:0.002066504900291491,(31:0.0019140419897094967,37:0.0019140419897094967):1.5246291058199427E-4):2.6823427348639283E-4):0.0012798826903855603,26:0.003614621864163444):3.867983264140796E-4,23:0.004001420190577524):3.041306120385428E-4,((32:0.0015236832727727441,(33:5.158258444959128E-4,21:5.158258444959128E-4):0.0010078574282768313):0.002675577177870752,((22:1.4020889127335552E-5,36:1.4020889127335552E-5):0.0014906132339115759,(29:2.9623220792960827E-4,35:2.9623220792960827E-4):0.0012084019151093032):0.002694626327604585):1.0629035197257022E-4):3.3357308179041145E-4):4.630353729173295E-4):8.776506059508899E-4):4.1124234987503436E-5);
    End;

De: Joe Parker [mailto:notifications@github.com] Enviado el: miércoles, 03 de junio de 2015 12:19 p.m. Para: lonelyjoeparker/befi-bats-gui CC: psperez07 Asunto: Re: [befi-bats-gui] Strange 95%CI results (#5)

@psperez07 https://github.com/psperez07 - there's no trees in those tree lines, did you paste correctly? For example (see the package files):

NEXUS

begin states; 1 black 2 black 3 black 4 black 5 white 6 white 7 white 8 white End;

begin trees; tree STATE_1011000 = &R; tree STATE_1011000 = &R; tree STATE_1011000 = &R; tree STATE_1011000 = &R; tree STATE_1011000 = &R; tree STATE_1011000 = &R; tree STATE_1011000 = &R; tree STATE_1011000 = &R; tree STATE_1011000 = &R;

tree STATE_1011000 = &R; tree STATE_1011000 = &R; tree STATE_1011000 = &R; tree STATE_1011000 = &R; End;

— Reply to this email directly or view it on GitHub https://github.com/lonelyjoeparker/befi-bats-gui/issues/5#issuecomment-108480154 . Web Bug from https://github.com/notifications/beacon/AMH_UTl6XLM9qSrfbwome_wHZ7CHAFgIks5oPxJ4gaJpZM4E0jEp.gif http://www.mailscanner.tv/1x1spacer.gif

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lonelyjoeparker commented 9 years ago

Thanks, that looks better.

psperez07 commented 9 years ago

Dear Dr. Parker, I would like to know if you could find an answer to this matter.

Thank you very much in advanced. Kind regards.

lonelyjoeparker commented 9 years ago

Hi @psperez07 - I've just been having a look at this.

The output you're referring to concerns only the empirical/observed statistics, not the simulated/null/expected ones as far as I can see. The 'round numbers' you see occur in because the statistics calculated (PS and MC are integer counts - numbers of state changes or members of a clade, respectively. Therefore every observation will be an integer and, when these are binned into an emprical cumulative density function, this will give slightly odd-appearing results if every observation is identical. In this case it seems that every tree in the PST has the same MC and PS. This is being reported correctly, I think.

There is a worrying thing here, which is that the mean observed values for these statistics (sum of observed values in each tree / number of trees) are not behaving correctly, as you point out. I think this is to do with how these numbers are stored in Java (we're storing two integers as doubles, then dividing one by the other). Since this process introduces small '0.0000000001' type errors all over the place, the large number of observations are throwing the averages out slightly by the time they are printed to the screen. In most datasets previously reported the 95% CIs for the observed stats have been wider than a single value so this issue hasn't come to light - but in your case clearly this isn't correct.

For now, you can assume that:

I hope this helps. I won't be closing this issue yet until I think about how best to re-cast the PS and MC variables in the package.

cheers joe

psperez07 commented 9 years ago

Thank you very much.

Your answer has been very helpful.

Kind regards

Paula

De: Joe Parker [mailto:notifications@github.com] Enviado el: jueves, 30 de julio de 2015 12:34 p.m. Para: lonelyjoeparker/befi-bats-gui befi-bats-gui@noreply.github.com CC: psperez07 psperez@ffyb.uba.ar Asunto: Re: [befi-bats-gui] Strange 95%CI results (#5)

Hi @psperez07 https://github.com/psperez07 - I've just been having a look at this.

The output you're referring to concerns only the empirical/observed statistics, not the simulated/null/expected ones as far as I can see. The 'round numbers' you see occur in because the statistics calculated (PS and MC are integer counts - numbers of state changes or members of a clade, respectively. Therefore every observation will be an integer and, when these are binned into an emprical cumulative density function, this will give slightly odd-appearing results if every observation is identical. In this case it seems that every tree in the PST has the same MC and PS. This is being reported correctly, I think.

There is a worrying thing here, which is that the mean observed values for these statistics (sum of observed values in each tree / number of trees) are not behaving correctly, as you point out. I think this is to do with how these numbers are stored in Java (we're storing two integers as doubles, then dividing one by the other). Since this process introduces small '0.0000000001' type errors all over the place, the large number of observations are throwing the averages out slightly by the time they are printed to the screen. In most datasets previously reported the 95% CIs for the observed stats have been wider than a single value so this issue hasn't come to light - but in your case clearly this isn't correct.

For now, you can assume that:

I hope this helps. I won't be closing this issue yet until I think about how best to re-cast the PS and MC variables in the package.

cheers joe

— Reply to this email directly or view it on GitHub https://github.com/lonelyjoeparker/befi-bats-gui/issues/5#issuecomment-126372026 . http://www.mailscanner.tv/1x1spacer.gif

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