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 lengths.
##
## $fossils
## sp edge hmin hmax
## 1 1 1 971.9145 971.9145
## 2 1 1 973.3466 973.3466
## 3 1 1 987.4003 987.4003
## 4 1 33 989.7576 989.7576
## 5 2 2 966.6233 966.6233
## 6 28 28 949.1969 949.1969
## 7 28 60 964.0159 964.0159
## 8 28 60 970.8105 970.8105
## 9 27 27 971.4643 971.4643
## 10 27 27 971.6289 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 988.7071 971.8536 r FALSE 1
## 2 1 33 NA 990.2402 988.7071 r FALSE 1
## 3 1 32 NA 1000.0000 990.2402 r FALSE 1
## 4 31 31 1 990.2402 987.1709 b FALSE 31
## 5 2 2 1 970.5744 965.5648 b FALSE 2
## 6 2 37 1 972.4283 970.5744 b FALSE 2
## 7 2 36 1 973.6627 972.4283 b FALSE 2
## 8 2 35 1 974.2120 973.6627 b FALSE 2
## 9 2 34 1 988.7071 974.2120 b FALSE 2
## 10 28 28 2 956.5642 941.7118 b FALSE 28
## 11 28 61 2 960.3618 956.5642 b FALSE 28
## 12 28 60 2 974.2120 960.3618 b FALSE 28
## 13 27 27 2 973.6627 961.2136 b FALSE 27
## 14 26 26 2 972.4283 968.7297 b FALSE 26
## 15 3 3 2 962.3386 952.6071 b FALSE 3
## 16 3 40 2 967.5172 962.3386 b FALSE 3
## 17 3 39 2 969.0815 967.5172 b FALSE 3
## 18 3 38 2 970.5744 969.0815 b FALSE 3
## 19 17 17 3 940.4658 940.4620 b FALSE 17
## 20 17 53 3 962.4451 940.4658 b FALSE 17
## 21 17 52 3 969.0815 962.4451 b FALSE 17
## 22 5 5 3 959.9962 959.2716 b FALSE 5
## 23 5 41 3 967.5172 959.9962 b FALSE 5
## 24 19 19 17 954.3532 953.3409 b FALSE 19
## 25 19 56 17 956.8053 954.3532 b FALSE 19
## 26 19 55 17 958.6901 956.8053 b FALSE 19
## 27 19 54 17 962.4451 958.6901 b FALSE 19
## 28 4 4 3 962.3386 955.0158 b FALSE 4
## 29 30 30 28 960.3618 956.9353 b FALSE 30
## 30 6 6 5 958.4771 954.6815 b FALSE 6
## 31 6 42 5 959.9962 958.4771 b FALSE 6
## 32 25 25 19 958.6901 958.4241 b FALSE 25
## 33 7 7 6 953.7851 951.0418 b FALSE 7
## 34 7 46 6 953.8828 953.7851 b FALSE 7
## 35 7 45 6 957.5866 953.8828 b FALSE 7
## 36 7 44 6 957.8415 957.5866 b FALSE 7
## 37 7 43 6 958.4771 957.8415 b FALSE 7
## 38 16 16 7 957.8415 949.9326 b FALSE 16
## 39 15 15 7 957.5866 950.6253 b FALSE 15
## 40 21 21 19 951.5603 947.1416 b FALSE 21
## 41 21 57 19 956.8053 951.5603 b FALSE 21
## 42 29 29 28 956.5642 956.0796 b FALSE 29
## 43 20 20 19 954.3532 940.6825 b FALSE 20
## 44 9 9 7 950.7111 942.7013 b FALSE 9
## 45 9 47 7 953.8828 950.7111 b FALSE 9
## 46 8 8 7 953.7851 946.9731 b FALSE 8
## 47 22 22 21 948.6775 942.2671 b FALSE 22
## 48 22 58 21 951.5603 948.6775 b FALSE 22
## 49 10 10 9 946.9941 944.0227 b FALSE 10
## 50 10 49 9 949.1859 946.9941 b FALSE 10
## ...
## 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.
converted_record$tree$origin.time## [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"