Usage: cox-ipw: [options]


Options:
--df_input=FILEPATH/FILENAME.CSV
Input dataset filename, including filepath [default input.csv]

--ipw=TRUE/FALSE
Logical, indicating whether sampling and IPW are to be applied [default TRUE]

--exposure=EXPOSURE_VARNAME
Exposure variable name [default exp_date_covid19_confirmed]

--outcome=OUTCOME_VARNAME
Outcome variable name [default out_date_vte]

--strata=VARNAME_1;VARNAME_2;...
Semi-colon separated list of variable names to be included as strata in the
regression model [default cov_cat_region]

--covariate_sex=SEX_VARNAME
Variable name for the sex covariate; specify argument as NULL to model without
sex covariate [default cov_cat_sex]

--covariate_age=AGE_VARNAME
Variable name for the age covariate; specify argument as NULL to model without
age covariate [default cov_num_age]

--covariate_other=VARNAME_1;VARNAME_2;...
Semi-colon separated list of other covariates to be included in the regression
model; specify argument as NULL to run age, age squared, sex adjusted model
only [default
cov_cat_ethnicity;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_carehome_status]

--covariate_protect=VARNAME_1;VARNAME_2;...
Semi-colon separated list of protected covariates - if checks indicate one of
these variables is to be removed from the regression model then an error is
returned [default cov_cat_ethnicity;cov_cat_region;cov_cat_sex;cov_num_age]

--cox_start=VARNAME_1;VARNAME_2;...
Semi-colon separated list of variable names used to define start of patient
follow-up or single variable if already defined [default pat_index_date]

--cox_stop=VARNAME_1;VARNAME_2;...
semicolon separated list of variable names used to define end of patient
follow-up or single variable if already defined [default
death_date;out_date_vte;vax_date_covid_1]

--study_start=YYYY-MM-DD
Study start date; this is used to remove events outside study dates [default
2021-06-01]

--study_stop=YYYY-MM-DD
Study end date; this is used to remove events outside study dates [default
2021-12-14]

--cut_points=CUTPOINT_1;CUTPOINT_2
Semi-colon separated list of cut points to be used to define time post exposure
[default 28;197]

--cut_points_reduced=CUTPOINT_1;CUTPOINT_2
Semi-colon separated list of cut points to be used to define time post exposure
if insufficient events prevent first choice [default 28;197]

--controls_per_case=INTEGER
Number of controls to retain per case in the analysis [default 10]

--total_event_threshold=INTEGER
Number of events that must be present for any model to run [default 50]

--episode_event_threshold=INTEGER
Number of events that must be present in a time period; if threshold is not
met, time periods are collapsed [default 5]

--covariate_threshold=INTEGER
Minimum number of individuals per covariate level for covariate to be retained
[default 2]

--age_spline=TRUE/FALSE
Logical, if age should be included in the model as a spline with knots at 0.1,
0.5, 0.9 [default TRUE]

--df_output=FILEPATH/FILENAME.CSV
Filename with filepath for output data [default results.csv]

--seed=INTEGER
Random number generator seed passed to IPW sampling [default 137]

-h, --help
Show this help message and exit