msSPChelpR (version 0.8.7)

summarize_sir_results: Summarize detailed SIR results

Description

Summarize detailed SIR results

Usage

summarize_sir_results(
  sir_df,
  summarize_groups,
  summarize_site = FALSE,
  output = "long",
  output_information = "full",
  add_total_row = "no",
  add_total_fu = "no",
  collapse_ci = FALSE,
  shorten_total_cols = FALSE,
  fubreak_var_name = "fu_time",
  ybreak_var_name = "yvar_name",
  xbreak_var_name = "none",
  site_var_name = "t_site",
  alpha = 0.05
)

Arguments

sir_df

dataframe with stratified sir results created using the sir or sir_byfutime functions

summarize_groups

option to define summarizing stratified groups. Default is "none". If you want to define variables that should be summarized into one group, you can chose from age, sex, region, year. Define multiple summarize variables e.g. by summarize_groups = c("region", "sex", "year")

summarize_site

If TRUE results will be summarized over all t_site categories. Default is FALSE.

output

Define the format of the output. Can be either "nested" for nested dataframe with fubreak_var and xbreak_var in separate sub_tables (purrr). Or "wide" for wide format where fubreak_var and xbreak_var are appended as columns. Or "long" for long format where sir_df is not reshaped, but just summarized (ybreak_var, xbreak_var and fubreak_var remain in rows). Default is "long".

output_information

option to define information to be presented in final output table. Default is "full" information, i.e. all variables from from sir_df. "reduced" is observed, expected, sir, sir_ci / sir_lci+sir_uci, pyar, n_base. "minimal" is observed, expected, sir, sir_ci. Default is "full".

add_total_row

option to add a row of totals. Can be either "no" for not adding such a row or "start" or "end" for adding it at the first or last row or "only" for only showing totals and no yvar. Default is "no".

add_total_fu

option to add totals for follow-up time. Can be either "no" for not adding such a column or "start" or "end" for adding it at the first or last column or "only" for only showing follow-up time totals. Default is "no".

collapse_ci

If TRUE upper and lower confidence interval will be collapsed into one column separated by "-". Default is FALSE.

shorten_total_cols

Shorten text in all results columns that start with "Total". Default == FALSE.

fubreak_var_name

Name of variable with futime stratification. Default is "fu_time".

ybreak_var_name

Name of variable with futime stratification. Default is "yvar_name".

xbreak_var_name

Name of variable with futime stratification. Default is "xvar_name".

site_var_name

Name of variable with site stratification. Default is "t_site".

alpha

significance level for confidence interval calculations. Default is alpha = 0.05 which will give 95 percent confidence intervals.

Examples

# NOT RUN {
#There are various preparation steps required, before you can run this function.
#Please refer to the Introduction vignette to see how to prepare your data
# }
# NOT RUN {
summarize_sir_results(.,
    summarize_groups = c("region", "age", "year", "race"),
    summarize_site = TRUE,
    output = "long",  output_information = "minimal",
    add_total_row = "only",  add_total_fu = "no",
    collapse_ci = FALSE,  shorten_total_cols = TRUE,
    fubreak_var_name = "fu_time", ybreak_var_name = "yvar_name",
    xbreak_var_name = "none", site_var_name = "t_site",
    alpha = 0.05
    )
    
# }
# NOT RUN {
    
# }