Usage: cox-ipw:[version] [options]


Options:
--df_input=FILENAME.CSV
Input dataset. csv, csv.gz, rds, arrow, or a feather filename (this is assumed
to be within the output directory but can be within a subdirectory) [default
input.csv]

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

--sample_exposed=TRUE/FALSE
Logical, indicating whether exposed individuals should be sampled [default
FALSE]

--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;... OR COVARIATE-OTHER.TXT
Semi-colon separated list of other covariates or filename of text file
containing 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. Note that if you are including only a single covariate
please include the semi-colon after it [default
cov_cat_ethnicity;cov_num_consultation_rate;cov_bin_healthcare_worker;cov_bin_carehome_status]

--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;...
Semi-colon 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]

--controls_per_case=INTEGER
Number of controls to retain per case in the analysis [default 20]

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

--covariate_threshold=INTEGER
Minimum number of individuals per covariate level for covariate to be retained
[default 5]

--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=FILENAME.CSV
Output data csv filename (this is assumed to be within the output directory but
can be within a subdirectory) [default results.csv]

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

--save_analysis_ready=FILENAME.DTA
If provided, analysis ready Stata dataset filename (this is assumed to be
within the output directory but can be within a subdirectory) [default ]

--run_analysis=TRUE/FALSE
Logical, if analysis should be run [default TRUE]

--config=
Config parsed from the YAML

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