calc_futime | R Documentation |
Calculate follow-up time per case until end of follow-up depending on pat_status - tidyverse version
calc_futime( wide_df, futime_var_new = "p_futimeyrs", fu_end, dattype = NULL, check = TRUE, time_unit = "years", status_var = "p_status", lifedat_var = NULL, fcdat_var = NULL, spcdat_var = NULL )
wide_df |
dataframe in wide format |
futime_var_new |
Name of the newly calculated variable for follow-up time. Default is p_futimeyrs. |
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. |
check |
Check newly calculated variable p_status by printing frequency table. Default is TRUE. |
time_unit |
Unit of follow-up time (can be "days", "weeks", "months", "years"). Default is "years". |
status_var |
Name of the patient status variable that was previously created. Default is p_status. |
lifedat_var |
Name of variable containing Date of Death. Will override dattype preset. |
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. |
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)) #prep step - create patient status variable usdata_wide <- usdata_wide %>% msSPChelpR::pat_status(., fu_end = "2017-12-31", dattype = "seer", status_var = "p_status", life_var = "p_alive.1", birthdat_var = "datebirth.1", lifedat_var = "datedeath.1") #now we can run the function msSPChelpR::calc_futime(usdata_wide, futime_var_new = "p_futimeyrs", fu_end = "2017-12-31", dattype = "seer", time_unit = "years", status_var = "p_status", lifedat_var = "datedeath.1", fcdat_var = "t_datediag.1", spcdat_var = "t_datediag.2")
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