Code for the analysis of "The informativeness of trials in COVID-19: A longitudinal cohort analysis of trials registered on ClinicalTrial.gov"
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The research fairy 89d81c30d5 Remove linear models and exclusion of HI and NM 7 months ago
1_numbat.R Moved intemediary files to a working/ directory 2 years ago
2_feasibility_enrolment.R History retrieval has been made into an R package 1 year ago
3_feasibility_location.R Remove linear models and exclusion of HI and NM 7 months ago
4_quality.R Print out all results 2 years ago
5_progress.R Added remaining steps 2 years ago
6_redundancy.R Added tx/prev to the post hoc analysis 1 year ago
7_duplicates.R Moved drug_names.csv to working/ folder 2 years ago
8_clinicaltrial_dl.R Add comments and improve readability 2 years ago
9_overall_proportion_and_stratified.R stratified updated december 2021 12 months ago
10_irr.R Change filename to redundancy.csv 12 months ago
11_response_to_reviewers.R Look at how many trials per state 1 year ago
12_locations_per_state.R Added a script for enumerating trial sites per state 9 months ago
README.md Updated README 2 years ago
codebook.md Added extraction codebook 2 years ago

README.md

C19InformAnalysis

Code for the analysis of "The informativeness of trials in COVID-19: A longitudinal cohort analysis of trials registered on ClinicalTrial.gov"

To start, also clone the following repositories:

1_numbat.R

Downloads data from Numbat

Output:

  • data/extractions.csv, per-trial extracted data
  • data/arms.csv, per-arm extracted data
  • data/primaryoutcomes.csv, per-outcome extracted data
  • data/locations.csv, per-site extracted data

2_feasibility_enrolment.R

Contains instructions for automatically downloading historical data for clinical trials

Calculates original start dates, original and final primary completion dates, original enrolment and latest actual enrolment

Output:

  • data/historical_versions.csv, per-historical version clinical trial data
  • working/extractions-hist.csv, per-trial data with the above values tabulated from historical data

3_feasibility_location.R

Calculates the total goal enrolment on a per-state basis

Output:

  • output/feasibility_by_state.csv, per-state target enrolments and case counts by 2020-06-30
  • plots/feasibility_by_state.pdf, a linear model for number of trial locations in a state that are in a non-feasible trial vs proportion of cases required to reach enrolment goal
  • plots/feasibility_by_state.png, a linear model for number of trial locations in a state that are in a non-feasible trial vs proportion of cases required to reach enrolment goal

4_quality.R

Calculates measures of trial quality

Output:

  • output/quality.csv, per-trial quality data for phase 2/3 and higher

5_progress.R

Calculates trial progress

6_redundancy.R

Calculates per-trial measures of redundancy

Output:

  • working/potential-dup-trials.csv, a listing of whether a trial is a potential duplicate based on all the pre-specified criteria except the per-arm ones

7_duplicates.R

Provides instructions for de-duplicating drug names from trial arms, combining manual and automatic techniques

Output:

  • working/drug_names.csv, per-arm data with final de-duplicated drug names
  • working/arms_dup_check.csv, a list of arms to check for duplications

8_clinicaltrial_dl.R

Distinguishes single- vs multi-centre trials, identifies lead agency sponsor class and determines whether a trial has a site in the USA.

Output:

  • working/clinicaltrial_dl.csv, per trial data: single- vs multi-centre, lead agency sponsor class, location country