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")



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$new(file = ts_file)
is(ts)
ts
ts$num_nodes()
# Also
ts <- ts_load(ts_file)
is(ts)

## ------------------------------------------------
## 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()
ts

## ------------------------------------------------
## Method `TreeSequence$r_to_py`
## ------------------------------------------------

ts_file <- system.file("examples/test.trees", package = "RcppTskit")
ts_r <- ts_load(ts_file)
is(ts_r)
ts_r$num_samples() # 160

# Transfer the tree sequence to reticulate Python and use tskit Python API
tskit <- get_tskit_py()
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
}

## ------------------------------------------------
## Method `TreeSequence$num_provenances`
## ------------------------------------------------

ts_file <- system.file("examples/test.trees", package = "RcppTskit")
ts <- ts_load(ts_file)
ts$num_provenances()

## ------------------------------------------------
## Method `TreeSequence$num_populations`
## ------------------------------------------------

ts_file <- system.file("examples/test.trees", package = "RcppTskit")
ts <- ts_load(ts_file)
ts$num_populations()

## ------------------------------------------------
## Method `TreeSequence$num_migrations`
## ------------------------------------------------

ts_file <- system.file("examples/test.trees", package = "RcppTskit")
ts <- ts_load(ts_file)
ts$num_migrations()

## ------------------------------------------------
## Method `TreeSequence$num_individuals`
## ------------------------------------------------

ts_file <- system.file("examples/test.trees", package = "RcppTskit")
ts <- ts_load(ts_file)
ts$num_individuals()

## ------------------------------------------------
## Method `TreeSequence$num_samples`
## ------------------------------------------------

ts_file <- system.file("examples/test.trees", package = "RcppTskit")
ts <- ts_load(ts_file)
ts$num_samples()

## ------------------------------------------------
## Method `TreeSequence$num_nodes`
## ------------------------------------------------

ts_file <- system.file("examples/test.trees", package = "RcppTskit")
ts <- ts_load(ts_file)
ts$num_nodes()

## ------------------------------------------------
## Method `TreeSequence$num_edges`
## ------------------------------------------------

ts_file <- system.file("examples/test.trees", package = "RcppTskit")
ts <- ts_load(ts_file)
ts$num_edges()

## ------------------------------------------------
## Method `TreeSequence$num_trees`
## ------------------------------------------------

ts_file <- system.file("examples/test.trees", package = "RcppTskit")
ts <- ts_load(ts_file)
ts$num_trees()

## ------------------------------------------------
## Method `TreeSequence$num_sites`
## ------------------------------------------------

ts_file <- system.file("examples/test.trees", package = "RcppTskit")
ts <- ts_load(ts_file)
ts$num_sites()

## ------------------------------------------------
## Method `TreeSequence$num_mutations`
## ------------------------------------------------

ts_file <- system.file("examples/test.trees", package = "RcppTskit")
ts <- ts_load(ts_file)
ts$num_mutations()

## ------------------------------------------------
## Method `TreeSequence$sequence_length`
## ------------------------------------------------

ts_file <- system.file("examples/test.trees", package = "RcppTskit")
ts <- ts_load(ts_file)
ts$sequence_length()

## ------------------------------------------------
## Method `TreeSequence$time_units`
## ------------------------------------------------

ts_file <- system.file("examples/test.trees", package = "RcppTskit")
ts <- ts_load(ts_file)
ts$time_units()

## ------------------------------------------------
## Method `TreeSequence$min_time`
## ------------------------------------------------

ts_file <- system.file("examples/test.trees", package = "RcppTskit")
ts <- ts_load(ts_file)
ts$min_time()

## ------------------------------------------------
## Method `TreeSequence$max_time`
## ------------------------------------------------

ts_file <- system.file("examples/test.trees", package = "RcppTskit")
ts <- ts_load(ts_file)
ts$max_time()

## ------------------------------------------------
## Method `TreeSequence$metadata_length`
## ------------------------------------------------

ts_file <- system.file("examples/test.trees", package = "RcppTskit")
ts <- ts_load(ts_file)
ts$metadata_length()



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()
is(tskit)
if (check_tskit_py(tskit)) {
  tskit$ALLELES_01
}



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()



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)
ts
ts$num_nodes()
# Also
ts <- TreeSequence$new(file = ts_file)
is(ts)



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()
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
}



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()



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")
grDevices::dev.off()
###
### Local variables: ***
### mode: outline-minor ***
### outline-regexp: "\\(> \\)?### [*]+" ***
### End: ***
quit('no')