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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 functionThese binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.