Ventilation Variation

Objective

• Explore low tidal volume ventilation variation between males and females
• Identify risk factors for length of mechanical ventilation. Specific variables of interest:
  • ltvv
  • sex
  • oxygenation_index
  • hospital

Required CLIF tables and fields

Please refer to the online CLIF data dictionary, ETL tools, and specific table contacts for more information on constructing the required tables and fields. List all required tables for the project here, and provide a brief rationale for why they are required.

The following tables are required:

1. patient: patient_id, race_category, ethnicity_category, sex_category, death_date
2. hospitalization: hospitalization_id, admission_dttm, discharge_dttm, age_at_admission, patient_id, admission_type_name, admission_type_category, discharge_name, discharge_category
3. vitals: hospitalization_id, recorded_dttm, vital_category, vital_value - vital_category = 'heart_rate', 'resp_rate', 'sbp', 'dbp', 'resp_rate', 'spo2'
4. labs: hospitalization_id, lab_result_dttm, lab_order_dttm, lab_collect_dttm, lab_category, lab_name, lab_value_numeric, reference_unit, lab_category = 'sodium', 'albumin', 'bilirubin_total', 'bun', 'carbon_dioxide', 'creatinine', 'glucose_serum', 'hemoglobin', 'lactate', 'pco2_arterial', 'po2_arterial', 'ph_arterial', 'platelet_count', 'so2_arterial', 'sodium', 'troponin_i', 'wbc'
5. adt: hospitalization_id, in_dttm, out_dttm, location_name, location_category
6. respiratory_support: hospitalization_id, recorded_dttm, device_name, device_category, mode_name, mode_category, fio2_set, lpm_set, tidal_volume_set, resp_rate_set, pressure_support_set, peep_set, tidal_volume_obs (optional), plateau_pressure_obs, peak_inspiratory_pressure_obs, mean_airway_pressure_obs (optional), tracheostomy
7. patient_assessments: hospitalization_id, recorded_dttm, numerical_value, assessment_category = "gcs_total"

Cohort identification

Inclusion

1. Adults (age >= 18 years old)
2. Mechanical Ventilation within 72 hours of admission
3. Admission from 2018-2024 (anytime between these years is acceptable... does not need to be the entire time frame)
4. Volume control with a set tidal volume within 24 hours of mechanical ventilation

Exclusion

1. Patient that died within 24 hours of mechanical ventilation

Expected Results

Table 1 - descriptive data by hospital aggregated data 1 - male vs. female LTVV aggregated data 2 - odds ratios for regression of ventilator days

project results will be saved in the output/final directory.

Detailed Instructions for running the project

1. Setup Project Environment (Script Developer Only)

This has been completed by Nick when making this script already (SKIP)
Describe the steps to set up the project environment.

# Install renv if not already installed:
if (!require("renv", quietly = TRUE)) {
  install.packages("renv")
}
# Initialize renv for the project:
renv::init(bare = TRUE, settings = list(use.cache = FALSE))

# Install required packages:
renv::install("BiocManager")
BiocManager::install("IRanges")

# renv::update()
renv::install(c("tidyverse", "ggthemes", "systemfonts",  "styler", "readxl", "writexl", "DBI", "dbplyr", "knitr", "pandoc", "janitor", "data.table", "duckdb" ,"powerjoin", "collapse", "tidyfast", "datapasta", "fst", "dtplyr", "bit64", "zoo", "fuzzyjoin", "arrow", "hrbrthemes", "here", "table1", "rvest", "tidymodels", "pscl", "survminer"))

# Save the project's package state:
renv::snapshot()

2. Update config/config.json

Follow the instructions in the config/README.md file for detailed configuration steps.

3. Run code

Detailed instructions on the code workflow are provided in the code directory