msSPChelpR 0.8.5

This release is the first alpha pre-release. It has not been accepted by CRAN yet

NOTE

• This release has not been accepted by CRAN due to incomplete documentation.

New Features

• tidytable variants of functions, i.e. 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():
• is much faster using tidytable package
• gained the option race_var to optionally stratify SIR calculations by race.
• summarize_sir_results():
• new function that increases functionality in summarizing results from sir_byfutime() function
• new option to define custom site_var_name
• new package website https://marianschmidt.github.io/msSPChelpR
• new sample datasets included in the package to demonstrate examples (#36)

Breaking Changes

• sir_byfutime():
  • options 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.
  • option 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)
  • option collapse_ci has been removed and added to summarize_sir_results() instead.
  • option name for tumor site variable changed from icdcat_var to site_var
  • option name for age/agegroup variable changed from agegroup_var to age_var
  • in total the parameters expcount_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():
• is superseded by the use of sir_byfutime().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():
  • option name for tumor site variable changed from summarize_icdcat to summarize_site
• reshape_long_tidyr():
• option var_selection is deprecated. Please select variables before running the reshape_long_* functions.
• asir():
  • option name for age/agegroup variable changed from agegroup_var to age_var
  • option name for tumor site variable changed from icdcat_var to site_var
• pat_status(), pat_status_tt(), vital_status(), and vital_status_tt():
  • Capitalized default variable labelling.
  • This might break code that relied on using the labels coming out of these functions in later filter or mutate functions.
• ir_crosstab_byfutime():
  • option futime_breaks now uses breaks in years instead of months as previously.
  • default futime_var is now follow-up time in years
• now requires dplyr version 1.0.0
• now requires tidytable package
• the default option name for tumor site variable changed from icdcat_var to site_var. This need manual update of function calls of sir_byfutime() and asir(), if option is specified.
• the default variable name for tumor site in all functions has been changed from t_icdcat to t_site. So the reference data frames used will need to have a t_site column.
• the data.table variants of functions (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.

Bug Fixes

• implement new reliable routine to split df when reshape_wide() with option chunks is used. Closes #1.
• Sorting of columns in wide datasets by reshape_wide_tidyr() and reshape_wide_tt() is now preserved. Closes #31.
• ensure sorting in renumer_time_id() and make sure that new_time_id_var is returned as integer.
• fix bug in pat_status_*(., check = TRUE)option
• improve internal tests in sir_byfutime() so that PYARs do not get lost before running summary function
• sir_byfutime() now also gives correct results if range of futime_breaks is not 0-Inf but smaller