data("standard_population")data("population_us") (Closes #58)sir_byfutime(): change output of integer columns to numeric to fix bug in summarize_sir_results() (Closes #59)vignette("introduction")reshape_wide_tt(), renumber_time_id_tt(), pat_status_tt(), vital_status_tt(), calc_futime_tt() –> the _tt variants usually have smaller memory use than tidyverse and data.table variants. Execution time is usually much faster than tidyverse and comparable to or a little slower than the data.table variant.sir_byfutime():race_var to optionally stratify SIR calculations by race.summarize_sir_results():sir_byfutime() functionsite_var_namesir_byfutime():
add_total_row and add_total_fu are replaced by calc_total_row and calc_total_fu. These are logical parameters now. The positioning of total rows and columns is completely handled by the summarize_sir_results() function now. There total rows can be set to top and bottom and total columns to left and right.expcount_src including related parameters stdpop_df, refpop_df, std_pop, truncate_std_pop and pyar_var have been removed. Function sir_byfutime() will only work calculating expected counts based on reference rates, not within the cohort of the dataset. To calculate expected based on the cohort, a new function create_refrates will be added in the future. (#41)collapse_ci has been removed and added to summarize_sir_results() instead.icdcat_var to site_varagegroup_var to age_varexpcount_src, futime_src, stdpop_df, refpop_df, std_pop, truncate_std_pop, pyar_var, icdcat_var, collapse_ci have been removed to simply the function –> make sure you remove these arguments from your sir_byfutime() function calls.sir():sir_byfutime(). To migrate your former sir() functions, you can simply use sir_byfutime(, futime_breaks = "none") that will yield the same results.summarize_sir_results():
summarize_icdcat to summarize_sitereshape_long_tidyr():var_selection is deprecated. Please select variables before running the reshape_long_* functions.asir():
agegroup_var to age_varicdcat_var to site_varpat_status(), pat_status_tt(), vital_status(), and vital_status_tt():
ir_crosstab_byfutime():
futime_breaks now uses breaks in years instead of months as previously.futime_var is now follow-up time in yearsicdcat_var to site_var. This need manual update of function calls of sir_byfutime() and asir(), if option is specified.t_icdcat to t_site. So the reference data frames used will need to have a t_site column.renumber_time_id_dt(), pat_status_dt(), reshape_long_dt(), reshape_wide_dt(), vital_status_dt()) have been removed for simplicity, please use tidytable variants, i.e. reshape_wide_tt(), renumber_time_id_tt(), pat_status_tt(), vital_status_tt(), calc_futime_tt(), instead. They will give the same data.table output and same performance.reshape_wide() with option chunks is used. Closes #1.reshape_wide_tidyr() and reshape_wide_tt() is now preserved. Closes #31.renumer_time_id() and make sure that new_time_id_var is returned as integer.pat_status_*(., check = TRUE)optionsir_byfutime() so that PYARs do not get lost before running summary functionsir_byfutime() now also gives correct results if range of futime_breaks is not 0-Inf but smallerrenumber_time_id() function; use sorting by date of diagnosis instead of old time_id_varreshape_wide_tidyr() functionreshape_wide_dt() function which is much faster now and uses data.table::dcast instead of stats::reshape nowpat_status() and pat_status_dt() functionssummarize_sir_results() is now functionalvignette("introduction")pat_status() and pat_status_dt() functionsrenumber_time_id() that broke functionspat_status() and calc_futime()tidyselect::all_of in summarize_sir_results()vignette("patstatus_futime")tidyselect::all_of for vector-based variable selectionvital_status_dt and pat_status_dtdata.tablereshape_long function work##New Features * new faster version of reshape_wide_dt function based on data.table and without problematic slices done by reshape_wide * new faster version of renumber_time_id function based on data.table
add_total_row work, even if option ybreak_vars = "none"NEWS.md file to track changes to the package.futime_breaks = "none" to sir_byfutime function