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Import effective population size history

import_ne_history.Rd

Import demographic history outputs from PSMC, MSMC2, SMC++, or Stairway Plot 2 into a typed tidy object for plot_ne_history() or ggpop() + geom_ne_history().

Usage

import_ne_history(
  dir = NULL,
  ...,
  type = c("auto", "psmc", "msmc2", "smcpp", "stairway"),
  sample_id = NULL,
  mutation_rate = NULL,
  generation_time = 1,
  bin_size = 100
)

import_demographic_history(
  dir = NULL,
  ...,
  type = c("auto", "psmc", "msmc2", "smcpp", "stairway"),
  sample_id = NULL,
  mutation_rate = NULL,
  generation_time = 1,
  bin_size = 100
)

Arguments

dir

Directory containing Ne history result files, or a single file path.

...

Optional named file paths. Relative paths are resolved inside dir.

type

Input type. Supports "psmc", "msmc2", "smcpp", and "stairway".

sample_id

Optional sample or population labels for input files.

mutation_rate

Optional per-site mutation rate. Required to convert PSMC/MSMC2 scaled values to absolute time and Ne. For SMC++ outputs, the value is retained as metadata when supplied.

generation_time

Generation time multiplier for absolute PSMC/MSMC2 time. For SMC++ CSV files with generation-scale time values, values are multiplied by this number and reported as years. If the input contains a time_unit column with years, time values are left unchanged.

bin_size

PSMC bin size used for theta scaling.

Value

A ggpop_ne_history tidy S3 data frame with standardized columns including method, sample_id, time, ne, time_unit, and scale. Common SMC++ columns such as plot_type, plot_num, type, and replicate are retained, as are supplied SMC++ mutation_rate and generation_time assumptions.

Details

PSMC and MSMC2 outputs are scaled unless mutation_rate is supplied. SMC++ and Stairway Plot 2 examples are expected to contain absolute effective population size columns. SMC++ time values are treated as generations unless a time_unit column says they are years. Stairway Plot 2 confidence intervals are retained when lower and upper Ne columns are present.

Examples

smcpp <- import_ne_history(
  system.file("extdata", "ne_history", "SMC++", "model.csv", package = "ggpop"),
  type = "smcpp"
)
#> Error: `dir` must point to an existing directory or file.
smcpp |> plot_ne_history()
#> Error: object 'smcpp' not found