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 t1 1 971.9145 971.9145
## 2 t1 1 973.3466 973.3466
## 3 t1 1 987.4003 987.4003
## 4 t1 33 989.7576 989.7576
## 5 t3 2 966.6233 966.6233
## 6 t4 28 949.1969 949.1969
## 7 t4 60 964.0159 964.0159
## 8 t4 60 970.8105 970.8105
## 9 t5 27 971.4643 971.4643
## 10 t5 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 t1 1 t0 988.7071 971.8536 r FALSE t1
## 2 t1 33 t0 990.2402 988.7071 r FALSE t1
## 3 t1 32 t0 1000.0000 990.2402 r FALSE t1
## 4 t2 31 t1 990.2402 987.1709 b FALSE t2
## 5 t3 2 t1 970.5744 965.5648 b FALSE t3
## 6 t3 37 t1 972.4283 970.5744 b FALSE t3
## 7 t3 36 t1 973.6627 972.4283 b FALSE t3
## 8 t3 35 t1 974.2120 973.6627 b FALSE t3
## 9 t3 34 t1 988.7071 974.2120 b FALSE t3
## 10 t4 28 t3 956.5642 941.7118 b FALSE t4
## 11 t4 61 t3 960.3618 956.5642 b FALSE t4
## 12 t4 60 t3 974.2120 960.3618 b FALSE t4
## 13 t5 27 t3 973.6627 961.2136 b FALSE t5
## 14 t6 26 t3 972.4283 968.7297 b FALSE t6
## 15 t7 3 t3 962.3386 952.6071 b FALSE t7
## 16 t7 40 t3 967.5172 962.3386 b FALSE t7
## 17 t7 39 t3 969.0815 967.5172 b FALSE t7
## 18 t7 38 t3 970.5744 969.0815 b FALSE t7
## 19 t8 17 t7 940.4658 940.4620 b FALSE t8
## 20 t8 53 t7 962.4451 940.4658 b FALSE t8
## 21 t8 52 t7 969.0815 962.4451 b FALSE t8
## 22 t9 5 t7 959.9962 959.2716 b FALSE t9
## 23 t9 41 t7 967.5172 959.9962 b FALSE t9
## 24 t10 19 t8 954.3532 953.3409 b FALSE t10
## 25 t10 56 t8 956.8053 954.3532 b FALSE t10
## 26 t10 55 t8 958.6901 956.8053 b FALSE t10
## 27 t10 54 t8 962.4451 958.6901 b FALSE t10
## 28 t11 4 t7 962.3386 955.0158 b FALSE t11
## 29 t12 30 t4 960.3618 956.9353 b FALSE t12
## 30 t13 6 t9 958.4771 954.6815 b FALSE t13
## 31 t13 42 t9 959.9962 958.4771 b FALSE t13
## 32 t14 25 t10 958.6901 958.4241 b FALSE t14
## 33 t15 7 t13 953.7851 951.0418 b FALSE t15
## 34 t15 46 t13 953.8828 953.7851 b FALSE t15
## 35 t15 45 t13 957.5866 953.8828 b FALSE t15
## 36 t15 44 t13 957.8415 957.5866 b FALSE t15
## 37 t15 43 t13 958.4771 957.8415 b FALSE t15
## 38 t16 16 t15 957.8415 949.9326 b FALSE t16
## 39 t17 15 t15 957.5866 950.6253 b FALSE t17
## 40 t18 21 t10 951.5603 947.1416 b FALSE t18
## 41 t18 57 t10 956.8053 951.5603 b FALSE t18
## 42 t19 29 t4 956.5642 956.0796 b FALSE t19
## 43 t20 20 t10 954.3532 940.6825 b FALSE t20
## 44 t21 9 t15 950.7111 942.7013 b FALSE t21
## 45 t21 47 t15 953.8828 950.7111 b FALSE t21
## 46 t22 8 t15 953.7851 946.9731 b FALSE t22
## 47 t23 22 t18 948.6775 942.2671 b FALSE t23
## 48 t23 58 t18 951.5603 948.6775 b FALSE t23
## 49 t24 10 t21 946.9941 944.0227 b FALSE t24
## 50 t24 49 t21 949.1859 946.9941 b FALSE t24
## ...
## 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"