R Under development (unstable) (2026-01-30 r89357 ucrt) -- "Unsuffered Consequences"
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> pkgname <- "RcppTskit"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> options(pager = "console")
> base::assign(".ExTimings", "RcppTskit-Ex.timings", pos = 'CheckExEnv')
> base::cat("name\tuser\tsystem\telapsed\n", file=base::get(".ExTimings", pos = 'CheckExEnv'))
> base::assign(".format_ptime",
+ function(x) {
+   if(!is.na(x[4L])) x[1L] <- x[1L] + x[4L]
+   if(!is.na(x[5L])) x[2L] <- x[2L] + x[5L]
+   options(OutDec = '.')
+   format(x[1L:3L], digits = 7L)
+ },
+ pos = 'CheckExEnv')
> 
> ### * </HEADER>
> library('RcppTskit')
> 
> base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
> base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
> cleanEx()
> nameEx("RcppTskit-package")
> ### * RcppTskit-package
> 
> flush(stderr()); flush(stdout())
> 
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RcppTskit-package
> ### Title: RcppTskit: R Access to the Tskit C API
> ### Aliases: RcppTskit RcppTskit-package
> ### Keywords: internal
> 
> ### ** Examples
> 
> vignette(package="RcppTskit")
Vignettes in package 'RcppTskit':

RcppTskit_intro         RcppTskit: Working with tree sequences in R
                        (source, html)
> 
> 
> 
> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
> base::cat("RcppTskit-package", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("TreeSequence")
> ### * TreeSequence
> 
> flush(stderr()); flush(stdout())
> 
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: TreeSequence
> ### Title: Succinct tree sequence R6 class (TreeSequence)
> ### Aliases: TreeSequence
> 
> ### ** Examples
> 
> 
> ## ------------------------------------------------
> ## Method `TreeSequence$new`
> ## ------------------------------------------------
> 
> ts_file <- system.file("examples/test.trees", package = "RcppTskit")
> ts <- TreeSequence$new(file = ts_file)
> is(ts)
[1] "TreeSequence"
> ts
Object of class 'TreeSequence'
$ts
         property            value
1     num_samples              160
2 sequence_length            10000
3       num_trees               26
4      time_units      generations
5        min_time                0
6        max_time 7.47028168974859
7    has_metadata            FALSE

$tables
        table number has_metadata
1 provenances      2           NA
2 populations      1         TRUE
3  migrations      0        FALSE
4 individuals     80        FALSE
5       nodes    344        FALSE
6       edges    414        FALSE
7       sites   2376        FALSE
8   mutations   2700        FALSE

> ts$num_nodes()
[1] 344
> # Also
> ts <- ts_load(ts_file)
> is(ts)
[1] "TreeSequence"
> 
> ## ------------------------------------------------
> ## Method `TreeSequence$dump`
> ## ------------------------------------------------
> 
> ts_file <- system.file("examples/test.trees", package = "RcppTskit")
> ts <- ts_load(ts_file)
> dump_file <- tempfile()
> ts$dump(dump_file)
> ts$write(dump_file) # alias
> 
> ## ------------------------------------------------
> ## Method `TreeSequence$print`
> ## ------------------------------------------------
> 
> ts_file <- system.file("examples/test.trees", package = "RcppTskit")
> ts <- ts_load(ts_file)
> ts$print()
Object of class 'TreeSequence'
$ts
         property            value
1     num_samples              160
2 sequence_length            10000
3       num_trees               26
4      time_units      generations
5        min_time                0
6        max_time 7.47028168974859
7    has_metadata            FALSE

$tables
        table number has_metadata
1 provenances      2           NA
2 populations      1         TRUE
3  migrations      0        FALSE
4 individuals     80        FALSE
5       nodes    344        FALSE
6       edges    414        FALSE
7       sites   2376        FALSE
8   mutations   2700        FALSE

> ts
Object of class 'TreeSequence'
$ts
         property            value
1     num_samples              160
2 sequence_length            10000
3       num_trees               26
4      time_units      generations
5        min_time                0
6        max_time 7.47028168974859
7    has_metadata            FALSE

$tables
        table number has_metadata
1 provenances      2           NA
2 populations      1         TRUE
3  migrations      0        FALSE
4 individuals     80        FALSE
5       nodes    344        FALSE
6       edges    414        FALSE
7       sites   2376        FALSE
8   mutations   2700        FALSE

> 
> ## ------------------------------------------------
> ## Method `TreeSequence$r_to_py`
> ## ------------------------------------------------
> 
> ts_file <- system.file("examples/test.trees", package = "RcppTskit")
> ts_r <- ts_load(ts_file)
> is(ts_r)
[1] "TreeSequence"
> ts_r$num_samples() # 160
[1] 160
> 
> # Transfer the tree sequence to reticulate Python and use tskit Python API
> tskit <- get_tskit_py()
Python module tskit is not available. Attempting to install it ...
> if (check_tskit_py(tskit)) {
+   ts_py <- ts_r$r_to_py()
+   is(ts_py)
+   ts_py$num_samples # 160
+   ts2_py <- ts_py$simplify(samples = c(0L, 1L, 2L, 3L))
+   ts2_py$num_samples # 4
+ }
object must be a reticulate Python module object!
> 
> ## ------------------------------------------------
> ## Method `TreeSequence$num_provenances`
> ## ------------------------------------------------
> 
> ts_file <- system.file("examples/test.trees", package = "RcppTskit")
> ts <- ts_load(ts_file)
> ts$num_provenances()
[1] 2
> 
> ## ------------------------------------------------
> ## Method `TreeSequence$num_populations`
> ## ------------------------------------------------
> 
> ts_file <- system.file("examples/test.trees", package = "RcppTskit")
> ts <- ts_load(ts_file)
> ts$num_populations()
[1] 1
> 
> ## ------------------------------------------------
> ## Method `TreeSequence$num_migrations`
> ## ------------------------------------------------
> 
> ts_file <- system.file("examples/test.trees", package = "RcppTskit")
> ts <- ts_load(ts_file)
> ts$num_migrations()
[1] 0
> 
> ## ------------------------------------------------
> ## Method `TreeSequence$num_individuals`
> ## ------------------------------------------------
> 
> ts_file <- system.file("examples/test.trees", package = "RcppTskit")
> ts <- ts_load(ts_file)
> ts$num_individuals()
[1] 80
> 
> ## ------------------------------------------------
> ## Method `TreeSequence$num_samples`
> ## ------------------------------------------------
> 
> ts_file <- system.file("examples/test.trees", package = "RcppTskit")
> ts <- ts_load(ts_file)
> ts$num_samples()
[1] 160
> 
> ## ------------------------------------------------
> ## Method `TreeSequence$num_nodes`
> ## ------------------------------------------------
> 
> ts_file <- system.file("examples/test.trees", package = "RcppTskit")
> ts <- ts_load(ts_file)
> ts$num_nodes()
[1] 344
> 
> ## ------------------------------------------------
> ## Method `TreeSequence$num_edges`
> ## ------------------------------------------------
> 
> ts_file <- system.file("examples/test.trees", package = "RcppTskit")
> ts <- ts_load(ts_file)
> ts$num_edges()
[1] 414
> 
> ## ------------------------------------------------
> ## Method `TreeSequence$num_trees`
> ## ------------------------------------------------
> 
> ts_file <- system.file("examples/test.trees", package = "RcppTskit")
> ts <- ts_load(ts_file)
> ts$num_trees()
[1] 26
> 
> ## ------------------------------------------------
> ## Method `TreeSequence$num_sites`
> ## ------------------------------------------------
> 
> ts_file <- system.file("examples/test.trees", package = "RcppTskit")
> ts <- ts_load(ts_file)
> ts$num_sites()
[1] 2376
> 
> ## ------------------------------------------------
> ## Method `TreeSequence$num_mutations`
> ## ------------------------------------------------
> 
> ts_file <- system.file("examples/test.trees", package = "RcppTskit")
> ts <- ts_load(ts_file)
> ts$num_mutations()
[1] 2700
> 
> ## ------------------------------------------------
> ## Method `TreeSequence$sequence_length`
> ## ------------------------------------------------
> 
> ts_file <- system.file("examples/test.trees", package = "RcppTskit")
> ts <- ts_load(ts_file)
> ts$sequence_length()
[1] 10000
> 
> ## ------------------------------------------------
> ## Method `TreeSequence$time_units`
> ## ------------------------------------------------
> 
> ts_file <- system.file("examples/test.trees", package = "RcppTskit")
> ts <- ts_load(ts_file)
> ts$time_units()
[1] "generations"
> 
> ## ------------------------------------------------
> ## Method `TreeSequence$min_time`
> ## ------------------------------------------------
> 
> ts_file <- system.file("examples/test.trees", package = "RcppTskit")
> ts <- ts_load(ts_file)
> ts$min_time()
[1] 0
> 
> ## ------------------------------------------------
> ## Method `TreeSequence$max_time`
> ## ------------------------------------------------
> 
> ts_file <- system.file("examples/test.trees", package = "RcppTskit")
> ts <- ts_load(ts_file)
> ts$max_time()
[1] 7.470282
> 
> ## ------------------------------------------------
> ## Method `TreeSequence$metadata_length`
> ## ------------------------------------------------
> 
> ts_file <- system.file("examples/test.trees", package = "RcppTskit")
> ts <- ts_load(ts_file)
> ts$metadata_length()
$ts
[1] 0

$populations
[1] 33

$migrations
[1] 0

$individuals
[1] 0

$nodes
[1] 0

$edges
[1] 0

$sites
[1] 0

$mutations
[1] 0

> 
> 
> 
> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
> base::cat("TreeSequence", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("get_tskit_py")
> ### * get_tskit_py
> 
> flush(stderr()); flush(stdout())
> 
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_tskit_py
> ### Title: Get the reticulate 'tskit' Python module
> ### Aliases: get_tskit_py check_tskit_py
> 
> ### ** Examples
> 
> tskit <- get_tskit_py()
Python module tskit is not available. Attempting to install it ...
> is(tskit)
[1] "python.builtin.ModuleNotFoundError"
> if (check_tskit_py(tskit)) {
+   tskit$ALLELES_01
+ }
object must be a reticulate Python module object!
> 
> 
> 
> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
> base::cat("get_tskit_py", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("kastore_version")
> ### * kastore_version
> 
> flush(stderr()); flush(stdout())
> 
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: kastore_version
> ### Title: Report the version of the installed kastore C API
> ### Aliases: kastore_version
> 
> ### ** Examples
> 
> kastore_version()
major minor patch 
    2     1     1 
> 
> 
> 
> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
> base::cat("kastore_version", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("ts_load")
> ### * ts_load
> 
> flush(stderr()); flush(stdout())
> 
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ts_load
> ### Title: Load a tree sequence from a file
> ### Aliases: ts_load ts_read
> 
> ### ** Examples
> 
> ts_file <- system.file("examples/test.trees", package = "RcppTskit")
> ts <- ts_load(ts_file)
> is(ts)
[1] "TreeSequence"
> ts
Object of class 'TreeSequence'
$ts
         property            value
1     num_samples              160
2 sequence_length            10000
3       num_trees               26
4      time_units      generations
5        min_time                0
6        max_time 7.47028168974859
7    has_metadata            FALSE

$tables
        table number has_metadata
1 provenances      2           NA
2 populations      1         TRUE
3  migrations      0        FALSE
4 individuals     80        FALSE
5       nodes    344        FALSE
6       edges    414        FALSE
7       sites   2376        FALSE
8   mutations   2700        FALSE

> ts$num_nodes()
[1] 344
> # Also
> ts <- TreeSequence$new(file = ts_file)
> is(ts)
[1] "TreeSequence"
> 
> 
> 
> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
> base::cat("ts_load", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("ts_py_to_r")
> ### * ts_py_to_r
> 
> flush(stderr()); flush(stdout())
> 
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ts_py_to_r
> ### Title: Transfer a tree sequence from reticulate Python to R
> ### Aliases: ts_py_to_r
> 
> ### ** Examples
> 
> ts_file <- system.file("examples/test.trees", package = "RcppTskit")
> 
> # Use the tskit Python API to work with a tree sequence (via reticulate)
> tskit <- get_tskit_py()
Python module tskit is not available. Attempting to install it ...
> if (check_tskit_py(tskit)) {
+   ts_py <- tskit$load(ts_file)
+   is(ts_py)
+   ts_py$num_samples # 160
+   ts2_py <- ts_py$simplify(samples = c(0L, 1L, 2L, 3L))
+   ts2_py$num_samples # 4
+ 
+   # Transfer the tree sequence to R and use RcppTskit
+   ts2_r <- ts_py_to_r(ts2_py)
+   is(ts2_r)
+   ts2_r$num_samples() # 4
+ }
object must be a reticulate Python module object!
> 
> 
> 
> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
> base::cat("ts_py_to_r", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("tskit_version")
> ### * tskit_version
> 
> flush(stderr()); flush(stdout())
> 
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tskit_version
> ### Title: Report the version of the installed tskit C API
> ### Aliases: tskit_version
> 
> ### ** Examples
> 
> tskit_version()
major minor patch 
    1     3     0 
> 
> 
> 
> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
> base::cat("tskit_version", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  3 0.44 17.75 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')