get_rates_and_fractions: Get rate and fraction data

In ki-tools/champs-mortality: Calculate mortality fractions and rates for CHAMPS sites

Get rate and fraction data

Description

Get rate and fraction data

Usage

get_rates_and_fractions(
  x,
  sites = NULL,
  catchments = NULL,
  condition = NULL,
  icd10_regex = NULL,
  maternal = FALSE,
  cond_name_short = condition[1],
  causal_chain = TRUE,
  adjust_vars_override = NULL,
  factor_groups = NULL,
  pval_cutoff = 0.1,
  pct_na_cutoff = 20,
  per = 10000
)

Arguments

x	Processed CHAMPS dataset.
sites	A vector of site names to include in the calculations. If NULL, all sites with data will be used.
catchments	A vector of catchments to include in the calculations. If NULL, all catchments with data will be used.
condition	CHAMPS group specifying the condition
icd10_regex	An optional regular expression specifying ICD10 codes that define a condition.
maternal	Are we searching for a maternal condition or ICD10 specification? Default is FALSE.
cond_name_short	The name of the condition to use in outputs (e.g. if the condition is "Congenital birth defects", cond_name_short could be "CBD"). Defaults to condition if not specified.
causal_chain	if TRUE, the causal chain is searched, if FALSE, the underlying cause is searched
adjust_vars_override	An optional vector of adjustment variables that will override the automatic adjustment. Cannot be more than two variables and must include age.
factor_groups	A named list that specifies how to group factors
pval_cutoff	P-value for which variables are considered for adjustment. Ignored if adjust_vars_override is specified.
pct_na_cutoff	Proportion of missingness for which variables are considered for adjustment. Ignored if adjust_vars_override is specified.
per	Calculate rates and fractions per how many births. 10k is the default.

Note

One or both of icd10_regex and condition must be specified

ki-tools/champs-mortality documentation built on Oct. 9, 2022, 6:32 a.m.