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/geiger/R/congruify.R

https://bitbucket.org/jonathaneastman/geiger
R | 389 lines | 270 code | 56 blank | 63 comment | 34 complexity | a994b24a62f009cd2acc80ba3ba693bc MD5 | raw file
    

  1. .build_classification=function(species){
    2. 

  2. 	.split_lab=function(label){
    3. 

  3. 		lab=gsub(".", "_", label, fixed=TRUE)
    4. 

  4. 		lab=gsub(" ", "_", lab, fixed=TRUE)
    5. 

  5. 		lab=unlist(strsplit(lab, "_", fixed=TRUE))
    6. 

  6. 		lab=lab[lab!=""]
    7. 

  7. 		lab
    8. 

  8. 	}
    9. 

  9. 	
    10. 

  10. 	data.frame(genus=sapply(species, function(s) .split_lab(s)[1]), species=species, stringsAsFactors=FALSE)
    11. 

  11. }
    12. 

  12. 

  13. 

  14. .build_calibrations=function(dat, scion, scion_desc=NULL, tol=0){
    15. 

  15. #	dat: branching times from stock; rows are 1:(Ntip(stock)+Nnode(stock))
    16. 

  16. #			time                             hash
    17. 

  17. #	1001 352.234677 3a4adb7cc0d4a51b9012dfb5615b3d71
    18. 

  18. #	1002 243.269677 33757769ee61bde8dd5574ae35b47053
    19. 

  19. 	
    20. 

  20. #	scion: phylo tree with 'hash' object -- to be scaled from stock
    21. 

  21. 	
    22. 

  22. 	fetch_spanning=function(phy, nd, desc){
    23. 

  23. 		# desc: a list from 1:(Ntip(phy)+Nnode(phy)) of tips descended from 'nd'
    24. 

  24. 		if(nd<=Ntip(phy)) return(NULL)
    25. 

  25. 		dd=.get.desc.of.node(nd,phy)[1:2]
    26. 

  26. 		tt=sapply(dd, function(x) return(desc[[x]][1]))
    27. 

  27. 		return(phy$tip.label[sort(tt)])		  
    28. 

  28. 	}
    29. 

  29. 	
    30. 

  30. 	if(is.null(scion_desc)) scion_desc=.cache.descendants(scion)$tips
    31. 

  31. 

  32. 	N=Ntip(scion)
    33. 

  33. 	stock_times=dat
    34. 

  34. 	scion_hash=scion$hash
    35. 

  35. 	df=data.frame(MRCA=scion_hash[(N+1):length(scion_hash)], MaxAge=NA, MinAge=NA, taxonA=NA, taxonB=NA, valid=FALSE, stringsAsFactors=FALSE)
    36. 

  36. 	for(i in 1:nrow(df)){
    37. 

  37. 		if(!is.na(hash.cur<-df$MRCA[i])){
    38. 

  38. 			if(hash.cur%in%stock_times$hash){
    39. 

  39. 				node.idx=i+N
    40. 

  40. 				df[i,c("MaxAge","MinAge")]<-age.idx<-stock_times$time[match(hash.cur, stock_times$hash)]
    41. 

  41. 				df[i,c("taxonA","taxonB")]<-taxa.idx<-fetch_spanning(scion, node.idx, scion_desc)
    42. 

  42. 				if(age.idx>tol & all(!is.na(taxa.idx))) df[i,"valid"]=TRUE
    43. 

  43. 			}
    44. 

  44. 		}
    45. 

  45. 	}
    46. 

  46. 	df=df[df$valid,]
    47. 

  47. 	return(df[,-which(names(df)=="valid")])
    48. 

  48. }
    49. 

  49. 

  50. congruify.phylo=function(reference, target, taxonomy=NULL, tol=0, scale=c(NA, "PATHd8")){
    51. 

  51.     ## adding requirement for ncbit
    52. 

  52.     require(ncbit)
    53. 

  53.     
    54. 

  54.     stock=reference
    55. 

  55.     scion=target
    56. 

  56. #	stock: a time-calibrated phylogeny with tip-labels that can be treated as an exemplar for clades in 'scion'
    57. 

  57. #		-- e.g., tip.label in 'stock' might be "Pinus" while in 'scion' we might have "Pinus_cembra"
    58. 

  58. #		-- tips in 'stock' can be contained in 'scion' (FIXME: is this true?)
    59. 

  59. #	megaphylogeny: a rooted phylogeny that is to be time-scaled based on 'stock'
    60. 

  60. #	taxonomy: linkage table between tipsets for 'stock' and 'scion'; if empty, one is attempted to be built by 'scion' labels
    61. 

  61. #		-- if NULL, 'stock' tips must correspond to tips in 'scion'... e.g., A, B, C in 'stock'; A_sp1, B_sp2, C_sp3 in 'scion'
    62. 

  62. #		-- rownames of taxonomy must be tips in megaphylogeny
    63. 

  63. 	
    64. 

  64. 	## functions
    65. 

  65. 	method=match.arg(unname(sapply(scale, toString)), c("NA", "PATHd8"))
    66. 

  66. 	
    67. 

  67. 	hashes.mapping <- function (phy, taxa, mapping){
    68. 

  68. 	## GENERAL FUNCTION: find hash tag for every edge in tree (using phy$tip.label or predefined set of 'taxa')
    69. 

  69. 	# returns list of hash tags from node 1:(Nnode(phy)+Ntip(phy))
    70. 

  70. 	# taxa: set of species used to create hash keys
    71. 

  71. 	# mapping: named list -- names are tips in 'phy'; elements are tips represented by each tip in 'phy' (and should also be present in 'taxa')
    72. 

  72. 		mapping=mapping[names(mapping)%in%phy$tip.label]
    73. 

  73. 		if(is.null(taxa)) stop("Must supply 'tips'.")
    74. 

  74. 		if(!all(names(mapping)%in%phy$tip.label)) stop("'mapping' must be named list with names in tip labels of 'phy'.")
    75. 

  75. 		
    76. 

  76. 		mapping=mapping[match(names(mapping), phy$tip.label)]
    77. 

  77. 		descendants <- .cache.descendants(phy)$tips
    78. 

  78. 		hashes <- sapply(descendants, function(desc) .hash.tip(unlist(mapping[desc]), taxa))
    79. 

  79. 		empty=.md5(integer(length(taxa)))
    80. 

  80. 		hashes[hashes==empty]=NA
    81. 

  81. 		phy$hash=hashes
    82. 

  82. 		phy=.uniquify_hashes(phy)
    83. 

  83. 

  84. 		return(phy)
    85. 

  85. 	}
    86. 

  86. 	
    87. 

  87. 	times.mapping=function(phy, taxa, mapping){
    88. 

  88. 	#	mapping: named list -- names are tips in 'phy'; elements are tips represented by each tip in 'phy' (and should also be present in 'taxa')
    89. 

  89. 	#	taxa: species that are represented by tips in 'stock' 
    90. 

  90. 		
    91. 

  91. 		# find hash tags for stock 'phy'
    92. 

  92. 		stock=hashes.mapping(phy, taxa, mapping)
    93. 

  93. 		tmp=heights.phylo(stock)
    94. 

  94. 		tmp$hash=stock$hash
    95. 

  95. 		dat=data.frame(time=tmp[,"end"], hash=stock$hash, stringsAsFactors=FALSE)
    96. 

  96. 		dat$hash[1:Ntip(stock)]=NA 	# destroy keys that are associated with tips
    97. 

  97. 

  98. 		return(list(stock=stock,dat=dat))
    99. 

  99. 	}
    100. 

  100. 	
    101. 

  101. 	smooth_scion=function(stock, scion, scion_desc, taxa, spp, tol=0.01, method=c("PATHd8", NA)){
    102. 

  102. 		method=match.arg(toString(method), c("NA", "PATHd8"))
    103. 

  103. 		if(!is.ultrametric(stock)) warning("Supplied 'stock' is non-ultrametric.")
    104. 

  104. 		stock_tmp=times.mapping(stock, taxa, spp)
    105. 

  105.         stock=stock_tmp$stock
    106. 

  106.         stock_dat=stock_tmp$dat
    107. 

  107. 		calibration=.build_calibrations(stock_dat, scion, scion_desc, tol=tol)
    108. 

  108. 		if(!nrow(calibration)) {
    109. 

  109. 			warning("No concordant branches reconciled between 'stock' and 'scion'; ensure that 'tax' involves rownames found as tip labels in 'scion'")
    110. 

  110. 			return(NA)
    111. 

  111. 		}
    112. 

  112. 		if(method=="PATHd8") {
    113. 

  113. 			phy=PATHd8.phylo(scion, calibration, base=".tmp_PATHd8", rm=FALSE)
    114. 

  114. 			phy$hash=c(rep("", Ntip(phy)), phy$node.label)
    115. 

  115. 			phy$hash[phy$hash==""]=NA
    116. 

  116. 		} else if(method=="NA"){
    117. 

  117. 			phy=NULL
    118. 

  118. 		}
    119. 

  119. 		
    120. 

  120. 		stock$node.label=stock$hash[(Ntip(stock)+1):max(stock$edge)]
    121. 

  121. 		stock$node.label[is.na(stock$node.label)]=""
    122. 

  122. 		return(list(phy=phy, calibrations=calibration, reference=stock, target=scion))
    123. 

  123. 	}
    124. 

  124. 	
    125. 

  125. 	## end functions
    126. 

  126. 	
    127. 

  127. 	## PROCESSING ##
    128. 

  128. 	classification=taxonomy
    129. 

  129. 	unfurl=FALSE
    130. 

  130. 	
    131. 

  131. 	if(class(stock)=="phylo") {
    132. 

  132. 		stock=list(stock)
    133. 

  133. 		unfurl=TRUE
    134. 

  134. 	}
    135. 

  135. 	if(is.null(classification)) {
    136. 

  136. 		classification=as.data.frame(unique(as.matrix(.build_classification(scion$tip.label)),MARGIN=2))
    137. 

  137. 	}
    138. 

  138. 	
    139. 

  139. 	tips=unique(unlist(lapply(stock, function(x) x$tip.label)))
    140. 

  140. 	spp=lapply(tips, function(o) {
    141. 

  141. 			   x=rownames(classification)[which(classification==o, arr.ind=TRUE)[,1]]
    142. 

  142. 			   x=x[x%in%scion$tip.label]
    143. 

  143. 	})
    144. 

  144. 	names(spp)=tips
    145. 

  145. 	taxa=unique(unlist(spp))
    146. 

  146. 	
    147. 

  147. 	scion=hashes.phylo(scion, taxa)
    148. 

  148. 	scion_desc=.cache.descendants(scion)$tips
    149. 

  149.     if(is.null(scion$edge.length)) scion$edge.length=numeric(nrow(scion$edge)) ## JME 01302013
    150. 

  150. 	
    151. 

  151. 	f=lapply
    152. 

  152. 	results=f(1:length(stock), function(i) {
    153. 

  153. 			  phy=stock[[i]]
    154. 

  154. 			  smooth_scion(phy, scion, scion_desc, taxa, spp, tol=tol, method=method)
    155. 

  155. 	})
    156. 

  156. 	
    157. 

  157. 	if(unfurl) results=results[[1]]
    158. 

  158. 	return(results)
    159. 

  159. }
    160. 

  160. 

  161. ## END CONGRUIFICATION FUNCTIONS ##
    162. 

  162. 

  163. 

  164. write.treePL=function(phy, calibrations, nsites, min=1e-4, base="", opts=list(smooth=100, nthreads=8, optad=0, opt=1, cvstart=1000, cviter=3, cvend=0.1, thorough=TRUE)){
    165. 

  165. #	calibrations: dataframe with minimally 'MRCA' 'MaxAge' 'MinAge' 'taxonA' and 'taxonB' from .build_calibrations
    166. 

  166. #	MRCA							MaxAge     MinAge                                  taxonA                                  taxonB 
    167. 

  167. #	c65bacdf65aa29635bec90f3f0447c6e 352.234677 352.234677                          Inga_chartacea             Encephalartos_umbeluziensis
    168. 

  168. #	d4bc6557dccbd4e8e18b867979f34f8e 243.269677 243.269677                          Inga_chartacea                     Nuphar_sagittifolia
    169. 

  169. #	5e30c16531694aff7d94da3b35806677 217.632627 217.632627                          Inga_chartacea                  Schisandra_glaucescens
    170. 

  170. 	
    171. 

  171. 	if(file.exists(inp<-paste(base,"infile",sep="."))) unlink(inp)
    172. 

  172. 	if(file.exists(int<-paste(base,"intree",sep="."))) unlink(inp)
    173. 

  173. 	
    174. 

  174. 	poss=list(
    175. 

  175. 			  cv="numeric",
    176. 

  176. 			  collapse="boolean",
    177. 

  177. 			  checkconstraints="boolean",
    178. 

  178. 			  cvstart="numeric",
    179. 

  179. 			  cvstop="numeric",
    180. 

  180. 			  cvmultstep="numeric",
    181. 

  181. 			  verbose="boolean",
    182. 

  182. 			  lftemp="numeric",
    183. 

  183. 			  pltemp="numeric",
    184. 

  184. 			  plcool="numeric",
    185. 

  185. 			  lfstoptemp="numeric",
    186. 

  186. 			  plstoptemp="numeric",
    187. 

  187. 			  lfrtstep="numeric",
    188. 

  188. 			  plrtstep="numeric",
    189. 

  189. 			  thorough="boolean",
    190. 

  190. 			  lfiter="integer",
    191. 

  191. 			  pliter="integer",
    192. 

  192. 			  cviter="integer",
    193. 

  193. 			  ldfsimaniter="integer",
    194. 

  194. 			  plsimaniter="integer",
    195. 

  195. 			  cvsimaniter="integer",
    196. 

  196. 			  calcgrad="numeric",
    197. 

  197. 			  paramverbose="boolean",
    198. 

  198. 			  prime="boolean",
    199. 

  199. 			  opt="boolean",
    200. 

  200. 			  optad="boolean",
    201. 

  201. 			  optcvad="boolean",
    202. 

  202. 			  moredetail="boolean",
    203. 

  203. 			  moredetailad="boolean",
    204. 

  204. 			  moredetailcvad="boolean",
    205. 

  205. 			  randomcv="boolean",
    206. 

  206. 			  ftol="numeric",
    207. 

  207. 			  xtol="numeric",
    208. 

  208. 			  mapspace="boolean",
    209. 

  209. 			  nthreads="integer"
    210. 

  210. 	)
    211. 

  211. 	if(length(opts)==0) {
    212. 

  212. 		print(poss)
    213. 

  213. 		stop("No 'opts' specified")
    214. 

  214. 	}
    215. 

  215. 	
    216. 

  216. # correct small branch lengths
    217. 

  217. 	z=phy$edge.length[which(phy$edge.length>0)]
    218. 

  218. 	if(any(z<min)){
    219. 

  219. 		scl=min/min(z)
    220. 

  220. 		phy$edge.length=phy$edge.length*scl
    221. 

  221. 	}
    222. 

  222. 	write.tree(phy, file=int)
    223. 

  223. 	
    224. 

  224. ##	check appropriateness of constraints ##
    225. 

  225. #	check for 'calibrations' and 'phy' congruence
    226. 

  226. #	if(!is.null(phy)){
    227. 

  227. #		check=function(t, phy) all(t%in%phy$tip.label)
    228. 

  228. #		a=check(calibrations$taxonA, phy)
    229. 

  229. #		b=check(calibrations$taxonB, phy)
    230. 

  230. 	
    231. 

  231. #		if(!all(c(a,b))) stop("Some calibrations not encountered in tree.")		
    232. 

  232. #	}
    233. 

  233. 	
    234. 

  234. ##	build r8s file
    235. 

  235. #	calibrations$fixage=ifelse(calibrations$MinAge==calibrations$MaxAge, TRUE, FALSE)
    236. 

  236. 	constraints<-constraintnames<-character(nrow(calibrations))
    237. 

  237. 	for(i in 1:nrow(calibrations)){
    238. 

  238. 		cal=calibrations[i,]
    239. 

  239. 		taxon=cal$MRCA
    240. 

  240. 		desc=c(cal$taxonA, cal$taxonB)
    241. 

  241. 		
    242. 

  242. 		txt1=ifelse(!is.na(cal$MinAge), paste("min =", taxon, cal$MinAge, sep=" "), "")
    243. 

  243. 		txt2=ifelse(!is.na(cal$MaxAge), paste("max =", taxon, cal$MaxAge, sep=" "), "")
    244. 

  244. 		txt=paste(txt1,txt2,sep="\n")
    245. 

  245. 		
    246. 

  246. 		constraints[i]=txt
    247. 

  247. 		constraintnames[i]=paste("mrca =", taxon, desc[1], desc[2], sep=" ")
    248. 

  248. 	}
    249. 

  249. 	infile=list(
    250. 

  250. 				tree=paste("treefile = ", int, sep=""),
    251. 

  251. 				ns=paste("numsites = ", nsites, sep=""),
    252. 

  252. 				names=paste(unlist(constraintnames), collapse="\n"),
    253. 

  253. 				mrca=paste(unlist(constraints), collapse="\n"),
    254. 

  254. 				out=paste("outfile = ", paste(base, "dated", "tre", sep="."), sep=""),
    255. 

  255. 				opt=paste(names(opts), opts, sep="=", collapse="\n")
    256. 

  256. 				)
    257. 

  257. 	
    258. 

  258. 	inp=paste(base,"infile",sep=".")
    259. 

  259. 	writeLines(paste(infile,collapse="\n\n"), con=inp)	
    260. 

  260. 	attr(inp, "method")="treePL"
    261. 

  261. 	return(inp)
    262. 

  262. }
    263. 

  263. 

  264. write.r8s=function(phy=NULL, calibrations, base="", blformat=c(lengths="persite", nsites=1, ultrametric="no", round="yes"), divtime=c(method="NPRS", algorithm="POWELL"), describe=c(plot="chrono_description")){
    265. 

  265. #	calibrations: dataframe with minimally 'MRCA' 'MaxAge' 'MinAge' 'taxonA' and 'taxonB' from .build_calibrations
    266. 

  266. #	MRCA							MaxAge     MinAge                                  taxonA                                  taxonB 
    267. 

  267. #	c65bacdf65aa29635bec90f3f0447c6e 352.234677 352.234677                          Inga_chartacea             Encephalartos_umbeluziensis
    268. 

  268. #	d4bc6557dccbd4e8e18b867979f34f8e 243.269677 243.269677                          Inga_chartacea                     Nuphar_sagittifolia
    269. 

  269. #	5e30c16531694aff7d94da3b35806677 217.632627 217.632627                          Inga_chartacea                  Schisandra_glaucescens
    270. 

  270. 	
    271. 

  271. 	if(file.exists(inp<-paste(base,"infile",sep="."))) unlink(inp)
    272. 

  272. 	
    273. 

  273. ##	check appropriateness of constraints ##
    274. 

  274. #	check for 'calibrations' and 'phy' congruence
    275. 

  275. #	if(!is.null(phy)){
    276. 

  276. #		check=function(t, phy) all(t%in%phy$tip.label)
    277. 

  277. #		a=check(calibrations$taxonA, phy)
    278. 

  278. #		b=check(calibrations$taxonB, phy)
    279. 

  279. 	
    280. 

  280. #		if(!all(c(a,b))) stop("Some calibrations not encountered in tree.")		
    281. 

  281. #	}
    282. 

  282. 	
    283. 

  283. ##	build r8s file
    284. 

  284. #	calibrations$fixage=ifelse(calibrations$MinAge==calibrations$MaxAge, TRUE, FALSE)
    285. 

  285. 	constraints<-constraintnames<-character(nrow(calibrations))
    286. 

  286. 	for(i in 1:nrow(calibrations)){
    287. 

  287. 		cal=calibrations[i,]
    288. 

  288. 		taxon=cal$MRCA
    289. 

  289. 		desc=c(cal$taxonA, cal$taxonB)
    290. 

  290. 		
    291. 

  291. 		txt=paste(paste("\tfixage taxon=", taxon,sep=""), paste("age=", cal$MinAge, ";\n", sep=""), sep=" ")
    292. 

  292. 		
    293. 

  293. 		constraints[i]=txt
    294. 

  294. 		constraintnames[i]=paste("\tMRCA", taxon, desc[1], paste(desc[2], ";\n", sep=""), sep=" ")
    295. 

  295. 	}
    296. 

  296. 	#	phy$node.label=NULL
    297. 

  297. 	infile=paste(c(
    298. 

  298. 				"#nexus\n",
    299. 

  299. 				"begin trees;\n",
    300. 

  300. 				paste("tree r8s = ", write.tree(phy), "\n", sep=""),
    301. 

  301. 				"end;\n",
    302. 

  302. 				"begin r8s;\n", 
    303. 

  303. 				paste("\tblformat ", paste(names(blformat), blformat, collapse=" ", sep="="), ";\n", sep=""),
    304. 

  304. 				names=paste(unlist(constraintnames), collapse=""),
    305. 

  305. 				mrca=paste(unlist(constraints), collapse=""),
    306. 

  306. 				"\tcollapse;\n",
    307. 

  307. 				paste("\tdivtime ", paste(names(divtime), divtime, collapse=" ", sep="="), ";\n", sep=""),
    308. 

  308. 				paste("\tdescribe ", paste(names(describe), describe, sep="="), ";\n", sep="", collapse=""),
    309. 

  309. 				"end;"
    310. 

  310. 			),collapse="")
    311. 

  311. 	
    312. 

  312. 	inp=paste(base,"infile",sep=".")
    313. 

  313. 	writeLines(paste(infile,collapse="\n\n"), con=inp)	
    314. 

  314. 	attr(inp, "method")="r8s"
    315. 

  315. 	return(inp)
    316. 

  316. }
    317. 

  317. 

  318. 

  319. write.pathd8=function(phy, calibrations, base=""){
    320. 

  320. #	calibrations: dataframe with minimally 'MRCA' 'MaxAge' 'MinAge' 'taxonA' and 'taxonB' 
    321. 

  321. 	
    322. 

  322. 	if(file.exists(inp<-paste(base,"infile",sep="."))) unlink(inp)
    323. 

  323. 	
    324. 

  324. 	##	check appropriateness of constraints ##
    325. 

  325. 	#	check for 'calibrations' and 'phy' congruence
    326. 

  326. 	check=function(t, phy) all(t%in%phy$tip.label)
    327. 

  327. 	a=check(calibrations$taxonA, phy)
    328. 

  328. 	b=check(calibrations$taxonB, phy)
    329. 

  329. 	
    330. 

  330. 	if(!all(c(a,b))) stop("Some calibrations not encountered in tree.")
    331. 

  331. 	
    332. 

  332. 	##	build PATHd8 file
    333. 

  333. 	calibrations$fixage=ifelse(calibrations$MinAge==calibrations$MaxAge, TRUE, FALSE)
    334. 

  334. 	constraints<-constraintnames<-character(nrow(calibrations))
    335. 

  335. 	for(i in 1:nrow(calibrations)){
    336. 

  336. 		cal=calibrations[i,]
    337. 

  337. 		taxon=cal$MRCA
    338. 

  338. 		desc=c(cal$taxonA, cal$taxonB)
    339. 

  339. 		if(cal$fixage) {
    340. 

  340. 			txt=paste("mrca:", paste(desc[1], ", ", desc[2], ", ", sep=""), paste("fixage=", cal$MinAge, ";", sep=""), sep=" ")
    341. 

  341. 		} else {
    342. 

  342. 			txt1=paste("mrca:", paste(desc[1], ", ", desc[2], ", ", sep=""), paste("minage=", cal$MinAge, ";", sep=""), sep=" ")
    343. 

  343. 			txt2=paste("mrca:", paste(desc[1], ", ", desc[2], ", ", sep=""), paste("maxage=", cal$MaxAge, ";", sep=""), sep=" ")
    344. 

  344. 			txt=paste(txt1,txt2,sep="\n")
    345. 

  345. 		}
    346. 

  346. 		constraints[i]=txt
    347. 

  347. 		constraintnames[i]=paste("name of mrca: ", paste(desc[1], ", ", desc[2], ", ", sep=""), paste("name=", cal$MRCA, ";", sep=""), sep=" ")
    348. 

  348. 	}
    349. 

  349. 	phy$node.label=NULL
    350. 

  350. 	infile=list(tree=write.tree(phy),
    351. 

  351. 				mrca=paste(unlist(constraints), collapse="\n"),
    352. 

  352. 				names=paste(unlist(constraintnames), collapse="\n")
    353. 

  353. 				)
    354. 

  354. 	
    355. 

  355. 	inp=paste(base,"infile",sep=".")
    356. 

  356. 	writeLines(paste(infile,collapse="\n\n"), con=inp)	
    357. 

  357. 	attr(inp, "method")="pathd8"
    358. 

  358. 	return(inp)
    359. 

  359. }
    360. 

  360. 

  361. PATHd8.phylo=function(phy, calibrations=NULL, base="", rm=TRUE){
    362. 

  362. #	calibrations: dataframe with minimally 'MRCA' 'MaxAge' 'MinAge' 'taxonA' and 'taxonB' 
    363. 

  363. #		-- if NULL, simple ultrametricization of 'phy' is performed
    364. 

  364. 	
    365. 

  365. 	phy$node.label=NULL
    366. 

  366. 	if(!is.null(calibrations)){
    367. 

  367. 		infile=write.pathd8(phy, calibrations, base)
    368. 

  368. 	} else {
    369. 

  369. 		infile=paste(base, "infile", sep=".")
    370. 

  370. 		write.tree(phy, infile)
    371. 

  371. 	}
    372. 

  372. 	smooth.file=paste(base, "smoothed.tre", sep=".")
    373. 

  373. 	parsed.outfile=paste(base, "pathd8.out", sep=".")
    374. 

  374. 	outfile=paste(base, "pathd8.orig.out", sep=".")
    375. 

  375. 	if(file.exists(outfile)) unlink(outfile)
    376. 

  376. 	if(!system("which PATHd8", ignore.stdout=TRUE)==0) stop("Install 'PATHd8' before proceeding.")
    377. 

  377. 	system(paste("PATHd8 -n", infile, "-pn >", outfile, sep=" "))
    378. 

  378. 	system(paste("grep \"d8 tree\" ", outfile, ">", parsed.outfile, sep=" "))
    379. 

  379. 	smoothed=read.tree(parsed.outfile)
    380. 

  380. 	if(rm & base=="") {
    381. 

  381. 		unlink(parsed.outfile)
    382. 

  382. 		unlink(smooth.file)
    383. 

  383. 		unlink(outfile)
    384. 

  384. 		unlink(infile)
    385. 

  385. 	}
    386. 

  386. 	return(smoothed)
    387. 

  387. }
    388. 

  388. 

  389. 

  390.