msSPChelpR - msSPChelpR 0.9.1

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 refratesdf (because they are not explicitly coded with incidence = 0). This can be helpful, if refratesdf has a lot of strata and 0 incidence strata have been removed to save storage space. Internally, the rows of expectmissingrefstratadf will be appended to refratesdf. 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)

- R
Published by marianschmidt over 2 years ago

msSPChelpR - msSPChelpR 0.9.0

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)

- R
Published by marianschmidt about 4 years ago

msSPChelpR - msSPChelpR 0.8.7

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 reshapelong function, i.e. `reshapelong_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 sitevar than the one used in `sirbyfutime()`

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

- R
Published by marianschmidt about 5 years ago

msSPChelpR - msSPChelpR 0.8.6

This is the first CRAN release for the msSPChelpR package.

New Features

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

Breaking Changes

• for breaking changes, please see release notes for version 0.8.5 https://github.com/marianschmidt/msSPChelpR/releases/tag/0.8.5

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")

- R
Published by marianschmidt over 5 years ago

msSPChelpR - 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

- R
Published by marianschmidt almost 6 years ago