NEWS

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msSPChelpR 2020-09-28

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/age group 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  • is superseded by the use of sir_byfutime().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/age group 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

msSPChelpR 2020-05-21

New Features

• add timevar_max option to renumber_time_id() function; use sorting by date of diagnosis instead of old time_id_var
• various improvements to reshape_wide_tidyr() function
• various improvements to reshape_wide_dt() function which is much faster now and uses data.table::dcast instead of stats::reshape now
• various improvements to pat_status() and pat_status_dt() functions
• option summarize_icdcat in summarize_sir_results() is now functional
• update vignette vignette("introduction")

Bug Fixes

• fix incomplete check for required variables in pat_status() and pat_status_dt() functions
• fix error in check for required variables in renumber_time_id() that broke functions
• fix bug in check for end of FU time in pat_status() and calc_futime()
• implement new tidyselect routine using tidyselect::all_of in summarize_sir_results()

msSPChelpR 0.9.1.9000

msSPChelpR 0.9.1 (2024-01-23)

New Features

• new function histgroup_iarc() to create variable for groups of malignant neoplasms considered to be histologically 'different' for the purpose of defining multiple tumors, ICD-O-3 (see #100)
• some functions gain new quiet argument to suppress rlang::warn() and rlang::inform() messages. You can use this when you have checked your results for correctness and want to reduce message output, but keep the progress bars.
• asir(): add World Standard Population 2000-2025 for function with option std_pop=="WHO2000" as described here: https://seer.cancer.gov/stdpopulations/world.who.html
• sir_byfutime() gains new argument expect_missing_refstrata_df. You can define another dataframe that contains strata expected to be missing from refrates_df (because they are not explicitly coded with incidence = 0). This can be helpful, if refrates_df has a lot of strata and 0 incidence strata have been removed to save storage space. Internally, the rows of expect_missing_refstrata_df will be appended to refrates_df. This reduces the number of lines reported in attribute problems_missing_ref_strata. Default setting is expect_missing_refstrata_df = NULL.
• sample data set for data("us_second_cancer") gains new variable t_hist on histology, i.e. ICD-O-3-Code on tumor morphology (4 digits)

Breaking Changes

• no breaking changes in this version

Bug fixes

• make calc_refrates() more robust for missing race_var (Closes #89)
• fix bug in calc_refrates() using calc_totals == TRUE (Closes #90)
• fix bug in calc_refrates() using numeric versions of fill_sites (Closes #92)
• fix bug in asir() that throws error for variable not needed (Closes #95)

Internal

• replace progress bars by cli
• deprecate verb.()syntax from tidytable (Closes #94)

msSPChelpR 0.9.0 (2022-06-10)

New Features

• new function calc_refrates() to calculate age-, sex-, region-, year-specific reference rates from a long format dataframe with cancer cases that are counted for incident cases and then matched with a reference population. The resulting reference rates dataframe can directly be used with sir_byfutime() function.
• functions gain new default dattype = NULL and thus are more flexible to take other source data types (Closes #73)

Breaking Changes

• functions asir, calc_futime*, calc_refrates, ir_crosstab_byfutime, pat_status*, renumber_time_id*, and sir_byfutime now by default are set to dattype = NULL. If you relied on automatic variable naming feature, you need to add dattype = "seer"or dattype = "zfkd" to your function call.
• fix typo in attribute names: attributes are now correctly named problems_missing_count_strata and problems_missing_fu_strata (Closes #80)

Bug fixes

• sir_byfutime():
  • attributes with notes and problems are now correctly saved to results_df

Internal

• deprecated functions from tidytable package have been replaced (Closes #71 and #74)

msSPChelpR 0.8.7 (2021-07-01)

New Features

• new function sir_ratio() and related sir_ratio_lci() and sir_ratio_uci() to calculate ratio of two SIRs/SMRs to get relative risk and confidence limits for this ratio.
• tidytable variant of reshape_long function, i.e. reshape_long_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.
• summarize_sir_results():
  • add ability to summarize by different site_var than the one used in sir_byfutime()

Bug fixes

• summarize_sir_results():
  • PYARs are now correctly calculated when using summarize_site == TRUE. Previously the results incorrectly counted each site multiple times. (Closes #62)
• pat_status():
  • update default values for dattype = "zfkd"

Internal

• add R-CMD-Check to github actions

msSPChelpR 0.8.6 (2020-11-04)

New Features

• new sample data set for standard populations ⇒ data("standard_population")
• new sample data set for us population ⇒ data("population_us") (Closes #58)

Bug fixes

• sir_byfutime(): change output of integer columns to numeric to fix bug in summarize_sir_results() (Closes #59)

Other changes

• add examples to function documentation (Closes #56)
• remove "R" from package title (Closes #57)
• update package description (Closes #54)
• update introduction vignette vignette("introduction")

msSPChelpR 0.8.3

New Features

• new faster version of reshape_long based on data.table
• start new vignette on workflow from filtered long dataset to follow-up times vignette("patstatus_futime")

Bug Fixes

• implement new tidyselect routine using tidyselect::all_of for vector-based variable selection
• implement correct referencing in vital_status_dt and pat_status_dt
• add exports from data.table
• update documentation for sir and sir_byfutime functions
• make reshape_long function work

msSPChelpR 0.8.2

msSPChelpR 0.8.1

New Features

• new faster version of vital_status function using data.table
• new faster version of pat_status function using data.table

msSPChelpR 0.8.0

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

msSPChelpR 0.7.4

New Features

• new function renumber_time_id

msSPChelpR 0.7.3

Bug Fixes

• add check to revert status_var to numeric in case it was created with option as_labelled_factor
• fix label bug in life_var_new

msSPChelpR 0.7.2

• add option as_labelled_factor to vital_status function
• fix newly introduced error in vital_status function

msSPChelpR 0.7.1

• fix error in vital_status function by replacing sjlabelled::get_label function

msSPChelpR 0.7.0

• fix error in pat_status and vital_status functions due to change in sjlabelled package

msSPChelpR 0.6.10

• rebuild description file and manual

msSPChelpR 0.6.9

• remove nest_legacy functions and use new tidyr syntax, close #19

msSPChelpR 0.6.8

• make summarize_sir_results function work without break variables

msSPChelpR 0.6.7

• for function sir_byfutime ⇒ make option add_total_row work, even if option ybreak_vars = "none"

msSPChelpR 0.6.6

• Make use of time_id_var and case_id_var use coherent across reshape functions

msSPChelpR 0.6.5

• Fixed issue in Namespace

msSPChelpR 0.6.4

• Added a NEWS.md file to track changes to the package.

msSPChelpR 0.6.3

• add option futime_breaks = "none" to sir_byfutime function

msSPChelpR 0.6.0

• includes a new function to calculate crude (absolute) incidence rates a tabulate them by whatever number of grouping variables and it can be used as a Table 1 for publications ⇒ The function is called msSPChelpR::ir_crosstab
• includes a new function to calculate SIRs (standardized incidence ratios) by whatever strata you desire (unlimited ybreak_vars; one xbreak_var) and additionally customized breaks for follow-up times (default is: to 6 months, .5-1 year, 1-5 years, 5-10 years, >10 years) ⇒ attention, it only makes sense to stratify results (ybreak_vars or xbreak_var) by variables measured at baseline and not for variables that are dependent on the occurrence of an SPC) ⇒ function msSPChelpR::sir_byfutime ⇒ depending on the number of stratification variables you are using, this function may result in a very long results data.frame. So please use it together with the new function msSPChelpR::summarize_sir_results
• includes a new function to summarize results dataframes from SIR calculations
• New reshape functions that are faster and are using less memory