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R helper functions for Second Primary Cancer analyses

Home Page: http://marianschmidt.github.io/msSPChelpR

License: GNU General Public License v3.0

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msspchelpr's Issues

implement option 'inclusion_restrictions' to asir function

Currently, the asir function assumes that for all regions the same period of data registration was applied. However, in case you included regional registries that have collected data for different time periods, this should be defined in the function call and the calculations should take this into account.

Prepare for dplyr 1.0.0

group_by --> change add to .add

mutate_at/_if/_all --> use new dplyr::across function

see https://www.tidyverse.org/blog/2020/03/dplyr-1-0-0-is-coming-soon/

Checklist

  • bind_cols() should not be expected to convert to tibble
  • n() and row_number() need dplyr:: prefix
  • all.equal.tbl_df() should not be used
  • funs() should be replaced by list()
  • group_by(add = ) needs to be replaced by .add
  • sample_n() and sample_frac() need to be replaced by slice_sample(n = ) and slice_sample(prop = )
  • mutate_*, group_by_*, select_* and rename_* sections need to bee rewritten using across()

create new filter_long function

Function should be constructed as

filter_long(long_df, keep_cond="", reverse = FALSE){
1 create new dummy variable keep that is 1 if keep_cond == TRUE
2 filter based on keep == 1 or on keep= 0, if reverse ==TRUE
}

keep_condition could be tidyverse filter expression (capture 3 dots?)

[pat_status] old tidyverse function produces bug on zfkd lung cancer data

  • check if it still occurs with as_tibble()
  • check what changes in pat_status_tt() have not been adapted in tidyverse variant [if changes are too severe, consider replacing with tidytable function

Error code

kein nicht-fehlendes Argument f�r min; gebe Inf zur�ckkein nicht-fehlendes Argument f�r max; gebe -Inf zur�ckCan't set value labels for "p_status". Infinite value range.

new function to recode tumor id

aim give a new sequence in numbering tumor ids per patient in long dataset version

  • option 1a: consecutive numbering of all primary tumors (SEER-definition) in long dataset irrespective of predating malignancies not covered by the registry
  • option 1b: consecutive numbering of all primary tumors (IARC-definition) in long dataset irrespective of predating malignancies not covered by the registry

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