combine_runs: Make all women results from married and unmarried women FPEM...
In FPcounts/FPEMglobal: Estimation of Contraceptive Use for All Women

combine_runs

R Documentation

Make all women results from married and unmarried women FPEM runs

Description

Combines MCMC outputs from married and unmarried women FPEM runs to make MCMC outputs for all women. The MCMC outputs must have been produced by do_global_mcmc or do_global_run (the former is sufficient).

Usage

combine_runs(
  run_desc = "",
  output_folder_path = NULL,
  married_women_run_name = NULL,
  married_women_run_output_folder_path = NULL,
  unmarried_women_run_name = NULL,
  unmarried_women_run_output_folder_path = NULL,
  unmarried_women_run_data_folder_path =
    file.path(unmarried_women_run_output_folder_path, "data"),
  region_information_csv_filename = "country_and_area_classification.csv",
  special_aggregates_name = NULL,
  denominator_counts_csv_filename = NULL,
  countries_for_aggregates_csv_filename = "countries_mwra_195.csv",
  countries_in_CI_plots_csv_filename = "countries_mwra_195.csv",
  start_year = 1970.5,
  end_year = 2030.5,
  years_change = matrix(c(1990.5, 2000.5, 2000.5, 2019.5, 2019.5, 2030.5, 2012.5, 2019.5,
    2012.5, 2019.5, 2012.5, 2020.5), ncol = 2, byrow = TRUE),
  years_change2 = matrix(c(2005.5, 2010.5, 2015.5, 2000.5, 2005.5, 2010.5, 1995.5,
    2000.5, 2005.5, 1990.5, 1995.5, 2000.5, 1990.5, 2000.5, 2010.5, 2000.5, 2010.5,
    2019.5), ncol = 3, byrow = TRUE),
  make_any_aggregates = TRUE,
  adjust_medians = TRUE,
  age_ratios_age_total_unmarried_run_name = NULL,
  age_ratios_age_total_married_run_name = NULL,
  age_ratios_age_total_all_women_run_name = NULL,
  age_ratios_age_total_unmarried_output_folder_path = NULL,
  age_ratios_age_total_married_output_folder_path = NULL,
  age_ratios_age_total_all_women_output_folder_path = NULL,
  age_ratios_age_total_denominator_counts_csv_filename = "number_of_women_15-49.csv",
  age_ratios_age_total_denominator_counts_folder_path = NULL,
  run_name_override = NULL,
  verbose = FALSE
)

Arguments

`run_desc`	Character. Brief note to be appended to the auto-generated `run_name`. Ignored if `run_name_override` is non-`NULL`.
`output_folder_path`	Filepath to directory where outputs should be saved. If `NULL`, defaults to `file.path("output", run_name)`.
`married_women_run_name`	Run name of the married women run to be combined. Ignored if `married_women_run_output_folder_path` is `NULL`. Otherwise, the output folder will be assumed to be `file.path("output", married_women_run_name)`.
`married_women_run_output_folder_path`	Path to the folder containing results for the married women run to be combined.
`unmarried_women_run_name`	Same as `married_women_run_name` but for the unmarried women run.
`unmarried_women_run_output_folder_path`	Path to the folder containing results for the unmarried women run to be combined.
`unmarried_women_run_data_folder_path`	Path to the folder containing results for the unmarried women run to be combined. (Only used if `special_aggregates_name` is non-`NULL`).
`region_information_csv_filename`	Filename of the ‘.csv’ file containing classifications of countries in sub-regions, regions, etc. See “Details”.
`special_aggregates_name`	Character vector of names (not filenames) of any speical aggregates desired. There must be a corresponding file with name ‘`special_aggregates_name`.csv’ in `input_data_folder_path` that defines the special aggregates. See “Details”.
`denominator_counts_csv_filename`	Name of the ‘.csv’ file containing estimates and projections of the number of women by marital status, age, and year. See “Details”.
`countries_for_aggregates_csv_filename`	Name of the ‘.csv’ file listing countries that will be used in constructing country aggregates.
`countries_in_CI_plots_csv_filename`	Name of ‘.csv’ file that lists the countries to be included in the main country-level indicator plots. See `make_results` for further details. `combine_runs` will copy this file to ‘`output_folder_path`/data’ so it is available for `make_results`.
`start_year`	Estimates and projections are produced for a specified time interval. This is the start year of that interval.
`end_year`	Estimates and projections are produced for a specified time interval. This is the end year of that interval.
`years_change`	A two-column matrix giving the year pairs (as rows) between which probabilistic estimates of changes in the indicators are desired.
`years_change2`	A three-column matrix giving the year triples (as rows) among which to compute probabilistic estimates of change-in-changes.
`make_any_aggregates`	Logical. Should country aggregates of any kind (including default aggregates) be produced?
`adjust_medians`	Logical. Should adjusted medians outputs be produced in addition to unadjusted outputs?
`age_ratios_age_total_unmarried_run_name`	Run name of the unmarried 15–49 run to use as the denominator for age ratios.
`age_ratios_age_total_married_run_name`	Run name of the married 15–49 run to use as the denominator for age ratios.
`age_ratios_age_total_all_women_run_name`	Run name of the all women 15–49 run to use as the denominator for age ratios.
`age_ratios_age_total_unmarried_output_folder_path`	File path to output directory of the unmarried 15–49 run to use to make age ratios.
`age_ratios_age_total_married_output_folder_path`	File path to output directory of the married 15–49 run to use to make age ratios.
`age_ratios_age_total_all_women_output_folder_path`	File path to output directory of the all women 15–49 run to use to make age ratios.
`age_ratios_age_total_denominator_counts_csv_filename`	Name of the ‘.csv’ file containing estimates and projections of the number of women by marital status, age, and year, for the age group 15–49. Only used if `make_age_ratios` is `TRUE`. Searched for in `age_ratios_age_total_denominator_counts_folder_path`.
`age_ratios_age_total_denominator_counts_folder_path`	Path to `age_ratios_age_total_denominator_counts_csv_filename`. If `NULL`, defaults to `file.path(age_ratios_age_total_output_folder_path, "data")`.
`run_name_override`	Character. User defined run name to override default generation. `run_desc` is ignored if this is non-`NULL`.
`verbose`	Logical; print lots and lots of messages about progress?

Details

Married and unmarried women runs must have been produced previously by, e.g,. do_global_run. They are identified by their output directory filepaths (married_women_run_output_folder_path and unmarried_women_run_output_folder_path). Files from the married and unmarried runs that are needed to make all women results are copied to output_folder_path (and sub-directories) and noted in files called ‘log.txt’ in the respective directories. The file ‘output_folder_path/log.txt’ provides a record of which married and unmarried women runs were combined.