| arm |
Arm that patient is in |
character |
|
Arm 1 ; Arm 2 ; Arm 3 [str_extract(redcap_event_name, "Arm \\d")] |
| arm_n |
Number arm that patient is in |
character |
|
1 ; 2 ; 3 [str_extract(arm, "\\d")] |
| onset2admission |
Onset to admission in days |
numeric |
Onset to admission (days) |
hostdat - cestdat |
| anydat |
Available form date |
date |
|
Uses date from source in order of precendence: hostdat, daily_dsstdat, cestdat, dsstdat |
| age |
Age |
numeric |
Age on admission (years) |
Uses/calculates age in order of precendence: calc_age, age_estimateyears, (anydat - agedat)/365 |
| age.factor |
Age, grouped into factors |
factor |
Age on admission (years) |
<50 ; 50-69 ; 70-79 ; 80+ |
| daily_fio2c_lborres_converted |
Daily FiO2 converted into L/min |
numeric |
|
If > 15, then value is assumed to be FiO2%, otherwise values converted from x to y: 0 ~ 0 ; <= 2 ~ 0.24 ; <= 3 ~ 0.28 ; <= 4 ~ 0.32 ; <= 5 ~ 0.36 ; <= 6 ~ 0.40 ; <= 10 ~ 0.50 ; <= 15 ~ 0.70 |
| daily_fio2_combined |
Combined FiO2 variables |
numeric |
|
!is.na(daily_fio2_lborres) ~ daily_fio2_lborres,is.na(daily_fio2_lborres) & !is.na(daily_fio2b_lborres) ~ daily_fio2b_lborres / 100,is.na(daily_fio2_lborres) & !is.na(daily_fio2c_lborres) ~ daily_fio2c_lborres_converted |
| ethnicity |
Ethnicity checkbox summary |
factor |
Ethnicity |
NOTE! If multiple ethnicities have been ticked, only the first (in numerical order of ethnic___X) will be identified in the ethnicity variable. Value will be: ethnic___1 == "Checked" ~ "Arab", ethnic___2 == "Checked" ~ "Black", ethnic___3 == "Checked" ~ "East Asian", ethnic___4 == "Checked" ~ "South Asian", ethnic___5 == "Checked" ~ "West Asian", ethnic___6 == "Checked" ~ "Latin American", ethnic___7 == "Checked" ~ "White", ethnic___8 == "Checked" ~ "Aboriginal/First Nations", ethnic___9 == "Checked" ~ "Other" |
| smoking_mhyn_2levels |
Smoking variable, grouped into 2 factors |
factor |
Smoking |
NO = "Never Smoked" or "Former Smoker" ; YES = "Yes" ; N/K = "N/K" |
| daily_pt_lborres_add_inr |
Where PT is missing, replace with INR calculation |
numeric |
PT |
If daily_pt_lborres is missing, replace with (daily_inr_lborres * 12) |
| any_daily_hoterm |
Any daily admission to ICU/ITU/IMC/HDU across events |
factor |
|
Any daily_hoterm == "Yes" across events then "Yes", otherwise "No" |
| any_daily_nasaloxy_cmtrt |
Any daily high flow nasal canula across events |
factor |
|
Any daily_nasaloxy_cmtrt == "Yes" across events then "Yes", otherwise "No" |
| any_daily_noninvasive_prtrt |
Any daily non-invasive ventilation (NIV, BIPAP, CPAP) across events |
factor |
|
Any daily_noninvasive_prtrt == "Yes" across events then "Yes", otherwise "No" |
| any_daily_invasive_prtrt |
Any daily invasive ventilation across events |
factor |
|
Any daily_invasive_prtrt == "Yes" across events then "Yes", otherwise "No" |
| any_daily_fio2_21 |
Any daily FiO2 greater than 0.211 across events |
factor |
|
Any daily_fio2_combined > 0.211 across events then "Yes", otherwise "No" |
| any_daily_fio2_28 |
Any daily FiO2 greater than 0.281 across events |
factor |
|
Any daily_fio2_combined > 0.281 across events then "Yes", otherwise "No" |
| any_icu_hoterm |
Any admission to ICU/HDU at any point during hospitalisation across events |
factor |
|
Any icu_hoterm == "Yes" across events then "Yes", otherwise "No" |
| any_oxygen_cmoccur |
Any oxygen at any point during hospitalisation across events |
factor |
|
Any oxygen_cmoccur == "Yes" across events then "Yes", otherwise "No" |
|
any_oxygenhf_cmoccur |
Any high flow nasal canula at any point during hospitalisation across events |
factor |
|
| any_noninvasive_proccur |
Any non-invasive ventilation at any point during hospitalisation across events |
factor |
|
Any noninvasive_proccur == "Yes" across events then "Yes", otherwise "No" |
| any_invasive_proccur |
Any invasive ventilation at any point during hospitalisation across events |
factor |
|
Any icu_hoterm == "Yes" across events then "Yes", otherwise "No" |
| any_trach |
Any tracheostomy inserted at any point during hospitalisation across events |
factor |
|
Any daily_trach_prperf == "Yes" across events then "Yes", otherwise "No" |
| any_icu |
Summary of "any ICU admission" variables |
factor |
|
Any any_daily_hoterm OR any_icu_hoterm == "Yes" then "Yes", otherwise "No" |
| any_oxygen |
Summary of "any oxygen" variables |
factor |
|
Any any_daily_nasaloxy_cmtrt OR any_oxygen_cmoccur OR any_daily_fio2_21 == "Yes" then "Yes", otherwise "No" |
| any_noninvasive |
Summary of "any noninvasive ventilation" variables |
factor |
|
Any any_daily_noninvasive_prtrt OR any_noninvasive_proccur == "Yes" then "Yes", otherwise "No" |
| any_invasive |
Summary of "any invasive ventilation" variables |
factor |
|
Any any_daily_invasive_prtrt OR any_invasive_proccur == "Yes" then "Yes", otherwise "No" |
| status |
Summary of final outcome into 3 factors, "Discharged alive", "On-going care" or "Died" |
factor |
|
any(dsterm == "Discharged alive") ~ "Discharged alive", any(dsterm == "Hospitalization") ~ "On-going care", any(dsterm == "Transfer to other facility") ~ "On-going care", any(dsterm == "Death") ~ "Died", any(dsterm == "Palliative discharge") ~ "Died", any(dsterm == "Unknown") ~ NA_character_, all(is.na(dsterm)) & any(grepl("Discharge/Death", redcap_event_name)) ~ "On-going care") |
| place_name |
Hospital name (matches redcap_data_access_group for majority of cases) |
character |
|
Taken from full NHS hospital list across Scotland and linked by dag_id |
| postcode_e |
Hospital level postcode |
character |
|
Taken from full NHS hospital list across Scotland and linked by dag_id |
| redcap_data_access_group_e |
Hospital level redcap data access group |
character |
|
|
| country |
Country |
character |
|
Deduced from hospital level postcode |
| imd |
Index of multiple deprivation (IMD) |
numeric |
|
IMD produced from postcode lookup (look at 03_prep.R for more further information) |
| imd_quintile |
Index of multiple deprivation (IMD) |
factor |
|
IMD grouped into 5 levels based on deprivation, 1 ; 2 ; 3 ; 4 ; 5. |