High-Performance Open-Source Archive
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)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.htmlsir_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.data("us_second_cancer") gains new
variable t_hist on histology, i.e. ICD-O-3-Code on tumor
morphology (4 digits)calc_refrates() more robust for missing
race_var (Closes #89)calc_refrates() using
calc_totals == TRUE (Closes #90)calc_refrates() using numeric versions of
fill_sites (Closes #92)asir() that throws error for variable not
needed (Closes #95)cliverb.()syntax from tidytable (Closes
#94)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_dftidytable 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_namesir_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_varagegroup_var to age_varexpcount_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_sitereshape_long_tidyr():
var_selection is deprecated. Please select
variables before running the reshape_long_* functions.asir():
agegroup_var to age_varicdcat_var to site_varpat_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_dtdata.tablereshape_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 function
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