Nothing
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.dattype = NULL
and thus are more flexible to take other source data types (Closes #73)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.problems_missing_count_strata
and problems_missing_fu_strata
(Closes #80)sir_byfutime()
:results_df
tidytable
package have been replaced (Closes #71 and #74)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.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()
:sir_byfutime()
summarize_sir_results()
:summarize_site == TRUE
. Previously the results incorrectly counted each site multiple times. (Closes #62)pat_status()
:dattype = "zfkd"
data("standard_population")
data("population_us")
(Closes #58)sir_byfutime()
: change output of integer columns to numeric to fix bug in summarize_sir_results()
(Closes #59)vignette("introduction")
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()
:race_var
to optionally stratify SIR calculations by race.summarize_sir_results()
:sir_byfutime()
functionsite_var_name
sir_byfutime()
: 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.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)collapse_ci
has been removed and added to summarize_sir_results()
instead.icdcat_var
to site_var
agegroup_var
to age_var
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()
: 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()
: summarize_icdcat
to summarize_site
reshape_long_tidyr()
: var_selection
is deprecated. Please select variables before running the reshape_long_*
functions.asir()
:agegroup_var
to age_var
icdcat_var
to site_var
pat_status()
, pat_status_tt()
, vital_status()
, and vital_status_tt()
:ir_crosstab_byfutime()
: futime_breaks
now uses breaks in years instead of months as previously.futime_var
is now follow-up time in yearsicdcat_var
to site_var
. This need manual update of function calls of sir_byfutime()
and asir()
, if option is specified.t_icdcat
to t_site
. So the reference data frames used will need to have a t_site
column.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.reshape_wide()
with option chunks
is used. Closes #1.reshape_wide_tidyr()
and reshape_wide_tt()
is now preserved. Closes #31.renumer_time_id()
and make sure that new_time_id_var
is returned as integer.pat_status_*(., check = TRUE)
optionsir_byfutime()
so that PYARs do not get lost before running summary functionsir_byfutime()
now also gives correct results if range of futime_breaks
is not 0-Inf but smallerrenumber_time_id()
function; use sorting by date of diagnosis instead of old time_id_varreshape_wide_tidyr()
functionreshape_wide_dt()
function which is much faster now and uses data.table::dcast
instead of stats::reshape
nowpat_status()
and pat_status_dt()
functionssummarize_sir_results()
is now functionalvignette("introduction")
pat_status()
and pat_status_dt()
functionsrenumber_time_id()
that broke functionspat_status()
and calc_futime()
tidyselect::all_of
in summarize_sir_results()
vignette("patstatus_futime")
tidyselect::all_of
for vector-based variable selectionvital_status_dt
and pat_status_dt
data.table
reshape_long
function workadd_total_row
work, even if option ybreak_vars = "none"
NEWS.md
file to track changes to the package.futime_breaks = "none"
to sir_byfutime
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