pat_status | R Documentation |
Calculate patient status at specific end of follow-up - tidyverse version
pat_status( wide_df, fu_end = NULL, dattype = NULL, status_var = "p_status", life_var = NULL, spc_var = NULL, birthdat_var = NULL, lifedat_var = NULL, lifedatmin_var = NULL, fcdat_var = NULL, spcdat_var = NULL, life_stat_alive = NULL, life_stat_dead = NULL, spc_stat_yes = NULL, spc_stat_no = NULL, lifedat_fu_end = NULL, use_lifedatmin = FALSE, check = TRUE, as_labelled_factor = FALSE )
wide_df |
dataframe in wide format |
fu_end |
end of follow-up in time format YYYY-MM-DD. |
dattype |
can be "zfkd" or "seer" or NULL. Will set default variable names if dattype is "seer" or "zfkd". Default is NULL. |
status_var |
Name of the newly calculated variable for patient status. Default is p_status. |
life_var |
Name of variable containing life status. Will override dattype preset. |
spc_var |
Name of variable containing SPC status. Will override dattype preset. |
birthdat_var |
Name of variable containing Date of Birth. Will override dattype preset. |
lifedat_var |
Name of variable containing Date of Death. Will override dattype preset. |
lifedatmin_var |
Name of variable containing the minimum Date of Death when true DoD is missing. Will override dattype preset. Will only be used if use_lifedatmin = TRUE. |
fcdat_var |
Name of variable containing Date of Primary Cancer diagnosis. Will override dattype preset. |
spcdat_var |
Name of variable containing Date of SPC diagnosis Will override dattype preset. |
life_stat_alive |
Value for alive status in life_var. Will override dattype preset. |
life_stat_dead |
Value for dead status in life_var. Will override dattype preset. |
spc_stat_yes |
Value for SPC occurred in spc_var. Will override dattype preset. |
spc_stat_no |
Value for no SPC in spc_var. Will override dattype preset. |
lifedat_fu_end |
Date of last FU of alive status in registry data. Will override dattype preset (2017-03-31 for zfkd; 2018-12-31 for seer). |
use_lifedatmin |
If TRUE, option to use Date of Death from lifedatmin_var when DOD is missing. Default is FALSE. |
check |
Check newly calculated variable p_status. Default is TRUE. |
as_labelled_factor |
If TRUE, output status_var as labelled factor variable. Default is FALSE. |
wide_df
#load sample data data("us_second_cancer") #prep step - make wide data as this is the required format usdata_wide <- us_second_cancer %>% msSPChelpR::reshape_wide_tidyr(case_id_var = "fake_id", time_id_var = "SEQ_NUM", timevar_max = 10) #prep step - calculate p_spc variable usdata_wide <- usdata_wide %>% dplyr::mutate(p_spc = dplyr::case_when(is.na(t_site_icd.2) ~ "No SPC", !is.na(t_site_icd.2) ~ "SPC developed", TRUE ~ NA_character_)) %>% dplyr::mutate(count_spc = dplyr::case_when(is.na(t_site_icd.2) ~ 1, TRUE ~ 0)) #now we can run the function msSPChelpR::pat_status(usdata_wide, fu_end = "2017-12-31", dattype = "seer", status_var = "p_status", life_var = "p_alive.1", spc_var = NULL, birthdat_var = "datebirth.1", lifedat_var = "datedeath.1", use_lifedatmin = FALSE, check = TRUE, as_labelled_factor = FALSE)
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