Hi all,
I seem to have found a combination of topology and characters that causes
ancestral.pars in phangorn to hard crash, at least in Windows7 with R v3.03
and phangorn v1.99-7.
This issue seems to have been introduced recently; the code works fine in
phangorn v1.99-5 with R v3.02.
I have a reproducible example below; as I said, it does hard crash the R
console, so BEWARE when trying it out. I'm not entirely certain what about
this particular dataset is causing the crash: the below is a big graptolite
phylogeny (...as I'm sure some of you guessed). The tree has polytomies,
but multi2di()-ing the tree doesn't stop the hard crash.
Cheers,
-Dave
library(phangorn)
char<-c(5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,
5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,5,3,3,3,3,3,
3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,
3,4,3,3,3,3,3,3,3,3,3,3,3,3,3,4,3,3,3,3,3,3,3,3,3,3,3,3,
3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,4,3,3,3,3,3,3,4,3,
3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,3,5,5,3,3,3,3,3,
3,3,3,3,3,3,3,3,3,2,1,1,1,3,1,1,3,3,3,3,3,3,3,5,3,3,3,0,
0,0,0,0,0,0,0,0,0,0,0,0,0,3,3,4,3,3,3,0,0,1,3,3,3,3,0,3,
3,3,0,3,0,0,0,0,3,4,3,0,0,0,2,0,0,3,0,0,0,0,0,0,0)
tree<-read.tree(file="",text="((((((((((((((((((((((t1,t2,t3,t4,t5,t6,t7,t8,t9,t10,t11,t12,t13,t14,t15,t16,t17,t18,t19,t20,t21,t22,t23,t24,t25,t26,t27,t28,t29,t30,t31,t32,t33,t34,t35,t36,t37,t38,t39,t40,t41,t42,t43,t44,t45,t46,t47),t48),t49,t50),t51),((((((((((((((((t52,t53),t54,t55,t56,t57,t58),((t59,t60),t61)),t62),(t63,t64)),t65),t66,t67),t68,t69,t70),t71,t72),t73),t74,t75),(t76,t77),t78,t79,t80,t81),(t82,t83),t84,t85,t86),t87,t88),t89),t90,t91,t92,t93,t94),t95,t96,t97,t98,t99,t100,t101,t102),t103),t104),t105),(((((((((((((t106,t107),t108,t109,t110,t111),t112),t113),(t114,t115)),t116),t117),t118),((((((((t119,t120),t121),((t122,t123),t124)),(t125,t126)),t127),t128,t129),t130),t131)),t132),t133),t134),((((t135,t136,t137,t138),t139,t140,t141,t142),t143),t144),(((((t145,t146),t147),t148),t149),t150,t151))),t152,t153),t154),t155),t156),t157),((((t158,t159),t160),t161,t162,t163,t164,t165),t166,t167,t168)),t169),((t170,t171,t172),t173)),(((t174,t175,t176),t177),(t178,t179)),t18!
0),(((t181,t182),t183),t184,t185),(t186,t187,t188,t189),t190,t191),t192,t193,t194,t195,t196,t197,t198,t199,t200,t201,t202,t203,t204,t205),(((t206,t207,t208,t209,t210,t211),t212,t213,t214),(t215,t216,t217,t218,t219,t220,t221),(t222,t223,t224),t225,t226,t227,t228,t229,t230,t231,t232,t233,t234)),t235,t236,t237,t238,t239,t240,t241,t242,t243,t244,t245);")
char<-matrix(char,,1)
rownames(char)<-tree$tip.label
char<-phyDat(char,type="USER",levels=sort(unique(char)))
anc<-ancestral.pars(tree,char,type="MPR") #here's the crash!
--
David W. Bapst, PhD
Adjunct Asst. Professor, Geology and Geol. Eng.
South Dakota School of Mines and Technology
501 E. St. Joseph
Rapid City, SD 57701
http://webpages.sdsmt.edu/~dbapst/
http://cran.r-project.org/web/packages/paleotree/index.html
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