Merge pull request #26 from dwbapst/developmentBranch

paleotree v3.3.0 CRAN Release (06-04-19)

.Rbuildignore

@@ -5,3 +5,4 @@
 
 ^cran-comments\.md$
 
+^CRAN-RELEASE$

CHANGELOG

@@ -1,5 +1,8 @@
+Version - 3.3.0 - 06-03-19 
+
+
 Version - 3.2.8 - 06-02-19 (Not Released to CRAN)
-- Fixed bug communicated by user Armin Eisler in October 2018 in cal3TimePaleoPhy where if `dateTreatment = 'minMax'` was used, the output trees would have tips at the same absolute time, as the generating time-tree used for cal3 inference was generated using the input fixed first and last dates as if they were FAD and LAD, with the upper age constraint treated as fixed LAD and time of observation for each tip. This has the effect of making 'minMax' treatment with cal3 nearly identical to using 'firstLast'. This is now fixed by creating a new new basic-time-scaled tree using the randomly generated set of point occurrence times within each iteration under 'minMax', such that the resulting tip dates are always different.
+- Fixed bug communicated by user Armin Elsler in October 2018 in cal3TimePaleoPhy where if `dateTreatment = 'minMax'` was used, the output trees would have tips at the same absolute time, as the generating time-tree used for cal3 inference was generated using the input fixed first and last dates as if they were FAD and LAD, with the upper age constraint treated as fixed LAD and time of observation for each tip. This has the effect of making 'minMax' treatment with cal3 nearly identical to using 'firstLast'. This is now fixed by creating a new new basic-time-scaled tree using the randomly generated set of point occurrence times within each iteration under 'minMax', such that the resulting tip dates are always different.
 - Also fixed tests for variance in cal3 tree calculations that were not properly sorting time data before comparing it against the time-scaled tree.
 
 Version - 3.2.4 - 05-30-19 (Not Released to CRAN)
@@ -13,7 +16,7 @@ Version - 3.2.0 - 04-14-19 (Not Released to CRAN)
 -Numerous fixes to how making taxon trees are created.
 
 Version - 3.1.9 - 02-15-19 (Not Released to CRAN)
--Updates to timePaleoPhy and cal3 documentation for dateTreatment argument, thanks to Armin Eisler for pointing out some inaccuracies in the text.
+-Updates to timePaleoPhy and cal3 documentation for dateTreatment argument, thanks to Armin Elsler for pointing out some inaccuracies in the text.
 -Updated some (but not all) functions related to use of PBDB data to use the proper 1.2 API, and made sure usage was properly accounted for.
 -Added functions for getting taxonomic data for clades, or for a specific list of taxa from the PBDB, which previously had existed in proto form in examples.
 -Added a function for plotting a tree with phylopics from the PBDB - this function currently does not allow for a lot of flexibility and is a work in progress.

CRAN-RELEASE

@@ -0,0 +1,2 @@
+This package was submitted to CRAN on 2019-06-04.
+Once it is accepted, delete this file and tag the release (commit f6ddc4a1ba).

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: paleotree
 Type: Package
-Version: 3.2.8
+Version: 3.3.0
 Title: Paleontological and Phylogenetic Analyses of Evolution
-Date: 2019-05-30
+Date: 2019-06-04
 Author: David W. Bapst, Peter J. Wagner
 Depends:
 	R (>= 3.0.0),

R/binTimeData.R

@@ -33,26 +33,27 @@
 #' intervals giving in the output increases with time, as these are numbered
 #' relative to each other, from first to last.
 #' 
-#' As of version 1.7 of paleotree, taxa which are extant as indicated in timeData as being
-#' in a time interval bounded (0,0), unless time-bins are preset using
-#' argument int.times (prior to version 1.5 they were erroneously listed as
+#' As of version 1.7 of paleotree, taxa which are
+#' extant as indicated in timeData as being
+#' in a time interval bounded \code{(0, 0)}, unless time-bins are preset using
+#' argument \code{int.times} (prior to version 1.5 they were erroneously listed as
 #' NA).
 #' 
 #' @param timeData Two-column matrix of simulated first and last occurrences in
-#' absolute continuous time
+#' absolute continuous time.
 
-#' @param int.length Time interval length, default is 1 time unit
+#' @param int.length Time interval length, default is 1 time-unit.
 
 #' @param start Starting time for calculating the intervals.
 
 #' @param int.times A two column matrix with the start and end times of the
 #' intervals to be used.
 
-#' @return A list containing: \item{int.times}{A 2 column matrix with the start
+#' @return A list containing: \item{\code{int.times}}{A 2-column matrix with the start
 #' and end times of the intervals used; time decreases relative to the
-#' present.} \item{taxon.times}{A 2 column matrix with the first and last
-#' occurrences of taxa in the intervals listed in int.times, with numbers
-#' referring to the row of int.times.}
+#' present.} \item{\code{taxon.times}}{A 2-column matrix with the first and last
+#' occurrences of taxa in the intervals listed in \code{int.times}, with numbers
+#' referring to the row of \code{int.times}.}
 
 #' @seealso \code{\link{simFossilRecord}}, \code{\link{sampleRanges}},
 #' \code{\link{taxicDivCont}}
@@ -63,38 +64,60 @@
 #' 
 #' #Simulate some fossil ranges with simFossilRecord
 #' set.seed(444)
-#' record <- simFossilRecord(p = 0.1, q = 0.1, nruns = 1,
-#' 	nTotalTaxa = c(30,40), nExtant = 0)
+#' record <- simFossilRecord(
+#'     p = 0.1, q = 0.1, nruns = 1,
+#'     nTotalTaxa = c(30,40), nExtant = 0)
 #' taxa <- fossilRecord2fossilTaxa(record)
-#' #simulate a fossil record with imperfect sampling with sampleRanges()
+#' #simulate a fossil record with imperfect sampling via sampleRanges
 #' rangesCont <- sampleRanges(taxa,r = 0.5)
 #' #Now let's use binTimeData() to bin in intervals of 1 time unit
 #' rangesDisc <- binTimeData(rangesCont,int.length = 1)
 #' #plot with taxicDivDisc()
 #' equalDiscInt <- taxicDivDisc(rangesDisc)
 #' 
 #' #example with pre-set intervals input (including overlapping)
-#' presetIntervals <- cbind(c(1000,990,970,940),c(980,970,950,930))
-#' rangesDisc1 <- binTimeData(rangesCont,int.times = presetIntervals)
+#' presetIntervals <- cbind(
+#'     c(1000, 990, 970, 940),
+#'     c(980, 970, 950, 930)
+#'     )
+#' rangesDisc1 <- binTimeData(rangesCont,
+#'     int.times = presetIntervals)
+#' 
+#' # plot the diversity curve with these uneven bins
 #' taxicDivDisc(rangesDisc1)
-#' #now let's plot diversity with (different) equal length intervals used above
-#' taxicDivDisc(rangesDisc1,int.times = equalDiscInt[,1:2])
+#'
+#' # now let's plot the diversity from these unequal-length bins
+#'    # with the original equal length intervals from above
+#' taxicDivDisc(rangesDisc1, int.times = equalDiscInt[,1:2])
+#' 
 #' 
+#' ####################################
 #' #example with extant taxa
 #' set.seed(444)
-#' record <- simFossilRecord(p = 0.1, q = 0.1, nruns = 1,
-#' 	nTotalTaxa = c(30,40))
+#' record <- simFossilRecord(
+#'    p = 0.1, q = 0.1, nruns = 1,
+#'    nTotalTaxa = c(30,40))
 #' taxa <- fossilRecord2fossilTaxa(record)
-#' #simulate a fossil record with imperfect sampling with sampleRanges()
-#' rangesCont <- sampleRanges(taxa,r = 0.5,,modern.samp.prob = 1)
-#' #Now let's use binTimeData() to bin in intervals of 1 time unit
-#' rangesDisc <- binTimeData(rangesCont,int.length = 1)
+#' #simulate a fossil record with imperfect sampling via sampleRanges
+#' rangesCont <- sampleRanges(
+#'     taxa, r = 0.5,
+#'     modern.samp.prob = 1)
+#' #Now let's use binTimeDat to bin into intervals of 1 time-unit
+#' rangesDisc <- binTimeData(rangesCont,
+#'     int.length = 1)
 #' #plot with taxicDivDisc()
 #' taxicDivDisc(rangesDisc)
 #' 
-#' #example with pre-set intervals input (including overlapping)
-#' presetIntervals <- cbind(c(40,30,20,10),c(30,20,10,0))
-#' rangesDisc1 <- binTimeData(rangesCont,int.times = presetIntervals)
+#' 
+#' #################################################
+#' #example with pre-set intervals input
+#'     # (including overlapping)
+#' presetIntervals <- cbind(
+#'     c(40, 30, 20, 10),
+#'     c(30, 20, 10, 0)
+#'     )
+#' rangesDisc1 <- binTimeData(rangesCont,
+#'     int.times = presetIntervals)
 #' taxicDivDisc(rangesDisc1)
 #' 
 #' @export binTimeData
@@ -108,41 +131,69 @@ binTimeData <- function(timeData,int.length = 1,start = NA,int.times = NULL){
 			#the last bin is cut off at zero (present day)
 	#x <- c(0,runif(99));timeData <- cbind(x+rexp(100),x);int.length = 1;start = NA;int.times = NULL
 	timeData <- timeData[!is.na(timeData[,1]),]
-	if(any(is.na(timeData))){stop("Weird NAs in Data?")}
-	if(any(timeData[,1]<timeData[,2])){stop("timeData is not in time relative to modern (decreasing to present)")}
-	if(any(timeData[,2]<0)){stop("Some dates in timeData <0 ?")}
+	if(any(is.na(timeData))){
+		stop("Weird NAs in Data?")
+			}
+	if(any(timeData[,1]<timeData[,2])){
+		stop("timeData is not in time relative to modern (decreasing to present)")
+		}
+	if(any(timeData[,2]<0)){
+		stop("Some dates in timeData <0 ?")
+		}
 	if(is.null(int.times)){
-		if(is.na(start)){start <- max(timeData)+int.length}else{if(start<max(timeData)){stop("Error:Start<max(timeData)?")}}
+		if(is.na(start)){
+			start <- max(timeData)+int.length
+		}else{
+			if(start<max(timeData)){
+				stop("Error:Start<max(timeData)?")
+				}
+			}
 		end <- start-(ceiling((start-min(timeData))/int.length)+1)*int.length
 		bins <- seq(start,end,by = -int.length)
-		bins <- unique(ifelse(bins<0,0,bins))	#get rid of any extra zeroes or negative numbers
+		#get rid of any extra zeroes or negative numbers
+		bins <- unique(ifelse(bins<0,0,bins))	
 		fads <- sapply(timeData[,1],function(x) which(bins<x)[1]-1)
 		lads <- sapply(timeData[,2],function(x) which(bins<x)[1]-1)
 		if(any(timeData[,1] == 0) | any(timeData[,2] == 0)){
 			bins <- c(bins,0)
 			fads[timeData[,1] == 0] <- length(bins)-1
 			lads[timeData[,2] == 0] <- length(bins)-1
 			}
-		res <- list(int.times = cbind(int.start = bins[1:(length(bins)-1)],int.end = bins[2:length(bins)]),
-			taxon.times = cbind(first.int = fads,last.int = lads))
+		res <- list(
+			int.times = cbind(int.start = bins[1:(length(bins)-1)],
+			int.end = bins[2:length(bins)]),
+			taxon.times = cbind(first.int = fads,last.int = lads)
+			)
 	}else{
 		int.durs <- int.times[,1]-int.times[,2]
-		if(any(int.durs <= 0)){stop("Some input time intervals have zero or negative durations?")}
+		if(any(int.durs <= 0)){
+			stop("Some input time intervals have zero or negative durations?")
+			}
 		int.times <- int.times[order(int.durs),]
-		Fint <- sapply(timeData[,1],function(x) which(apply(int.times,1,function(y) y[1] >= x & y[2]<x))[1])
-		Lint <- sapply(timeData[,2],function(x) which(apply(int.times,1,function(y) y[1] >= x & y[2]<x))[1])
+		Fint <- sapply(timeData[,1],function(x)
+			which(apply(int.times,1,function(y) y[1] >= x & y[2]<x))[1]
+			)
+		Lint <- sapply(timeData[,2],function(x)
+			which(apply(int.times,1,function(y) y[1] >= x & y[2]<x))[1]
+			)
 		if(any(int.times[,2] == 0)){
 			Fint[timeData[,1] == 0] <- which(int.times[,2] == 0)[1]
 			Lint[timeData[,2] == 0] <- which(int.times[,2] == 0)[1]
 			}
 		taxon.times <- cbind(first.int = Fint,last.int = Lint)
 		rownames(taxon.times) <- rownames(timeData)
-		taxon.times <- taxon.times[!apply(taxon.times,1,function(x) any(is.na(x))),]
+		taxon.times <- taxon.times[
+			!apply(taxon.times,1, function(x) any(is.na(x))),
+			]
 		new.order <- rank(-int.times[,1])	
 		taxon.times[,1] <- new.order[taxon.times[,1]]
 		taxon.times[,2] <- new.order[taxon.times[,2]]
 		int.times <- int.times[order(-int.times[,1]),]
-		res <- list(int.times = int.times,taxon.times = taxon.times)
+		res <- list(
+			int.times = int.times,
+			taxon.times = taxon.times
+			)
 		}
+	#
 	return(res)
 	}