marianschmidt / msspchelpr Goto Github PK

check that all changes in calculations for asir_results with futime_src="refpop" are also reflected in "cohort" calculations (first half of 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.

NAs should appear in final results table. Expected would be 0.

so far summarize_group = c("region", "year", "sex") have been implemented as they are distinct and we can simply add up observed counts and PYARs.
Does it make sense to summarize asir over multiple icdcat and how could that be implemented into asir function?

make a new function ir_crosstab_futime and include this new function to be optionally called from ir_crosstab

.shallow(x, cols = cols, retain.key = TRUE) :
can't set ALTREP truelength

Check if some unclean version of data is returned by _dt() functions or whether key needs to be reset at beginning.

https://docs.ropensci.org/assertr/

tidyr release: check all functions whether they use nest() or unnest(); check whether existing functions can profit from new vignette("rectangle")

Check functions *_byfutime for bug where pyar can temporarily be negative and thus sum(i_pyar) is wrongly calculated

--> may apply to crosstab_byfutime

(function sir_byfutime was developed after bug was identified)

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()

• remove "cohort" option from sir_byfutime
• implement new function create_refrates_df

• add_total_fu

• add_total_row

• output_information

• output = "nested"

finalize checks of options and expected errors in function implementation

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?)

• 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.

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

• output = "wide" does not work with add_total_row (fu_time_sort needs to be filled before reshaping)

• check that add_total_row works with add_total_futime

https://guides.github.com/activities/citable-code/

check if year futime_breaks are correctly handled in all functions