Objects produced by FossilSim contain all the
information required by the paleotree format and
vice-versa, thus these two packages are fully compatible.
Converting from paleotree is done using the
paleotree.record.to.fossils function, which returns a list
of the corresponding phylo, taxonomy and
fossils objects.
record = paleotree::simFossilRecord(p = 0.1, q = 0.1, r = 0.1, nruns = 1, nTotalTaxa = c(30,40),
nExtant = 0, nSamp = c(5,25))
converted_record = paleotree.record.to.fossils(record = record)
converted_record## $tree
##
## Phylogenetic tree with 31 tips and 30 internal nodes.
##
## Tip labels:
## t1, t3, t7, t11, t9, t13, ...
## Node labels:
## 32, 33, 34, 35, 36, 37, ...
##
## Rooted; includes branch length(s).
##
## $fossils
## sp edge hmin hmax
## 1 1 32 971.9145 971.9145
## 2 1 32 973.3466 973.3466
## 3 1 32 987.4003 987.4003
## 4 1 32 989.7576 989.7576
## 5 2 32 966.6233 966.6233
## 6 28 32 949.1969 949.1969
## 7 28 32 964.0159 964.0159
## 8 28 32 970.8105 970.8105
## 9 27 32 971.4643 971.4643
## 10 27 32 971.6289 971.6289
## ...
## Fossil record with 29 occurrences representing 15 species
## Fossils record simulated from or assigned to an existing taxonomy
##
## $taxonomy
## sp edge parent start end mode cryptic cryptic.id
## 1 1 1 NA 58.075735 971.853629 r FALSE 1
## 2 1 33 NA 59.608890 58.075735 r FALSE 1
## 3 1 32 NA 1000.000000 59.608890 r FALSE 1
## 4 31 31 1 59.608890 987.170861 b FALSE 31
## 5 2 2 1 39.943035 965.564845 b FALSE 2
## 6 2 37 1 41.797001 39.943035 b FALSE 2
## 7 2 36 1 43.031361 41.797001 b FALSE 2
## 8 2 35 1 43.580711 43.031361 b FALSE 2
## 9 2 34 1 58.075735 43.580711 b FALSE 2
## 10 2 33 1 59.608890 58.075735 b FALSE 2
## 11 2 32 1 988.707069 59.608890 b FALSE 2
## 12 28 28 2 25.932899 941.711849 b FALSE 28
## 13 28 61 2 29.730503 25.932899 b FALSE 28
## 14 28 60 2 43.580711 29.730503 b FALSE 28
## 15 28 34 2 58.075735 43.580711 b FALSE 28
## 16 28 33 2 59.608890 58.075735 b FALSE 28
## 17 28 32 2 974.212045 59.608890 b FALSE 28
## 18 27 27 2 43.031361 961.213641 b FALSE 27
## 19 27 35 2 43.580711 43.031361 b FALSE 27
## 20 27 34 2 58.075735 43.580711 b FALSE 27
## 21 27 33 2 59.608890 58.075735 b FALSE 27
## 22 27 32 2 973.662695 59.608890 b FALSE 27
## 23 26 26 2 41.797001 968.729698 b FALSE 26
## 24 3 3 2 31.707225 952.607144 b FALSE 3
## 25 3 40 2 36.885853 31.707225 b FALSE 3
## 26 3 39 2 38.450125 36.885853 b FALSE 3
## 27 3 38 2 39.943035 38.450125 b FALSE 3
## 28 3 37 2 41.797001 39.943035 b FALSE 3
## 29 3 36 2 43.031361 41.797001 b FALSE 3
## 30 3 35 2 43.580711 43.031361 b FALSE 3
## 31 3 34 2 58.075735 43.580711 b FALSE 3
## 32 3 33 2 59.608890 58.075735 b FALSE 3
## 33 3 32 2 970.574368 59.608890 b FALSE 3
## 34 17 17 3 9.834472 940.462046 b FALSE 17
## 35 17 53 3 31.813778 9.834472 b FALSE 17
## 36 17 52 3 38.450125 31.813778 b FALSE 17
## 37 17 38 3 39.943035 38.450125 b FALSE 17
## 38 17 37 3 41.797001 39.943035 b FALSE 17
## 39 17 36 3 43.031361 41.797001 b FALSE 17
## 40 17 35 3 43.580711 43.031361 b FALSE 17
## 41 17 34 3 58.075735 43.580711 b FALSE 17
## 42 17 33 3 59.608890 58.075735 b FALSE 17
## 43 17 32 3 969.081459 59.608890 b FALSE 17
## 44 5 5 3 29.364906 959.271553 b FALSE 5
## 45 5 41 3 36.885853 29.364906 b FALSE 5
## 46 5 39 3 38.450125 36.885853 b FALSE 5
## 47 5 38 3 39.943035 38.450125 b FALSE 5
## 48 5 37 3 41.797001 39.943035 b FALSE 5
## 49 5 36 3 43.031361 41.797001 b FALSE 5
## 50 5 35 3 43.580711 43.031361 b FALSE 5
## ...
## Taxonomy representing 31 species across 61 edges.If the paleotree record is fully extinct, i.e contains
no extant samples, the age of the record will be encoded in the field
origin.time of the tree.
## [1] 1000Similarly, converting from the FossilSim objects to
paleotree format is done using the
fossils.to.paleotree.record function, which requires a
fossils object and either a phylo or
taxonomy object. If no taxonomy is provided, all speciation
events in the tree will be assumed to be symmetric (bifurcating).
t = ape::rtree(6)
f = sim.fossils.poisson(rate = 2, tree = t)
converted_record = fossils.to.paleotree.record(fossils = f, tree = t)
converted_record## $t8
## $t8$taxa.data
## taxon.id ancestor.id orig.time ext.time still.alive looks.like
## 1.0000000 NA 1.3951422 0.9213295 0.0000000 1.0000000
##
## $t8$sampling.times
## numeric(0)
##
##
## $t6
## $t6$taxa.data
## taxon.id ancestor.id orig.time ext.time still.alive looks.like
## 2.0000000 1.0000000 0.9213295 0.5870906 0.0000000 2.0000000
##
## $t6$sampling.times
## numeric(0)
##
##
## $t5
## $t5$taxa.data
## taxon.id ancestor.id orig.time ext.time still.alive looks.like
## 3.0000000 1.0000000 0.9213295 0.4150379 0.0000000 3.0000000
##
## $t5$sampling.times
## numeric(0)
##
##
## $t9
## $t9$taxa.data
## taxon.id ancestor.id orig.time ext.time still.alive looks.like
## 4.000000 NA 1.395142 1.052488 0.000000 4.000000
##
## $t9$sampling.times
## [1] 1.169976 1.062755
##
##
## $t4
## $t4$taxa.data
## taxon.id ancestor.id orig.time ext.time still.alive looks.like
## 5.0000000 4.0000000 1.0524875 0.3692032 0.0000000 5.0000000
##
## $t4$sampling.times
## [1] 0.9279696 0.4424305
##
##
## $t10
## $t10$taxa.data
## taxon.id ancestor.id orig.time ext.time still.alive looks.like
## 6.000000 4.000000 1.052488 1.040256 0.000000 6.000000
##
## $t10$sampling.times
## numeric(0)
##
##
## $t3
## $t3$taxa.data
## taxon.id ancestor.id orig.time ext.time still.alive looks.like
## 7.0000000 6.0000000 1.0402556 0.4318103 0.0000000 7.0000000
##
## $t3$sampling.times
## [1] 0.6594577
##
##
## $t11
## $t11$taxa.data
## taxon.id ancestor.id orig.time ext.time still.alive looks.like
## 8.0000000 6.0000000 1.0402556 0.6050447 0.0000000 8.0000000
##
## $t11$sampling.times
## [1] 0.9238745
##
##
## $t1
## $t1$taxa.data
## taxon.id ancestor.id orig.time ext.time still.alive looks.like
## 9.0000000 8.0000000 0.6050447 0.3302180 0.0000000 9.0000000
##
## $t1$sampling.times
## numeric(0)
##
##
## $t2
## $t2$taxa.data
## taxon.id ancestor.id orig.time ext.time still.alive looks.like
## 10.0000000 8.0000000 0.6050447 0.0000000 1.0000000 10.0000000
##
## $t2$sampling.times
## [1] 0.4005886 0.3860503 0.0000000
##
##
## attr(,"class")
## [1] "fossilRecordSimulation"