GALAXY at CTSU: information about overviews

Contents List

• Introduction
• General reference files
• Overview directories
• General files in each overview directory (e.g. BC:BRIEF.DAT)
• Files for trial centre/group no. x in overview directory (e.g. BC:LBC123.DAT)
• Subdirectories (e.g. BC$AK:)
• Notes
• Programs
• Database interface

Introduction

Each user is given a private subdirectory and is 'put' there when identifying themself after login. A 'visitor' can use ZW:, the 'scratch' directory. A focused set of instructions for an impatient overview user is in JG$DK:EMMA.DAT. One day in the not very distant future someone hopes to make time to write a proper manual: it could be quite large.

Data for each overview are constructed in a uniform way. A set of 'universal' software is available for processing and analysis. Once the user has become familiar with the system, it is not necessary to perform craniotomies when moving from one subject to another. Further overviews can be incorporated without limit. Brief information about files and software follows.

General reference files

Overview directories

General files in each overview directory (e.g. BC:BRIEF.DAT)

Files for trial centre/group no. x in overview directory (e.g. BC:LBC123.DAT)

Subdirectories (e.g. BC$AK:)

Notes

Each trial (or trial stratum, if the trial is not monolithic) from a given centre or group is given a serial number formed as 100 x (trial centre/group) + (2-digit number), e.g. 12301, 12302.

Each treatment arm of each trial or stratum is given a serial number formed as 100 x (trial/stratum number) + (2-digit number), e.g. 1230101, 1230102.

The serial numbers are 'permanent' and are attached to each standard format ('pink form' style) patient record. Trials are also given year mnemonics, e.g. 84J (the 'J'th trial listed as beginning in 1984). Where a trial is divided into strata the stratum numbers are appended, e.g. 84J1, 84J2. The year mnemonics are subject to change as new information is received.

Programs

To find out what parameters to give a program, type a question mark after its name - e.g. to find out what parameters to give BLACKBOX, type BLACKBOX ?. If a 'blank' is needed in the sequence, use a dot - e.g. to give GAZEBO a first and third parameter only type GAZEBO firstparameter . thirdparameter.

Please don't alter the database without warning Jon Godwin (hold a séance if dead). Briefly:

1. Data conditioning - every data set received has idiosyncrasies ranging from the lack of a trial/stratum identifier at the beginning of each patient record to the need for complete conversion from some alien format or even just tabular results.
1. Universal program which calls an ad hoc subroutine for each data set received to convert it into 'pink form' style format:
TRAUMA
If updating information has previously been received, there will also be a 'difference mask' (Section 3).
2. CTSU diktats about the interpretation of death causes etc vary continually. They can be applied uniformly, in a removable way, to the 'pink form' style format file(s). Universal program to apply diktats of the moment:
DIKTAT (HD only at present)
2. Data testing - having converted into 'pink form' style format using TRAUMA, there are four main components to the testing process. The results are usually returned to trialists for checking:
1. Universal program to check for logical errors in the data (e.g. missing items, meaningless codes and impossible dates):
STARE
2. Universal program to tabulate a breakdown of variables and check for imbalances between groups and prognostic categories:
INQUIST
3. Universal program to list patients with lapsed follow-up, uncertain cause of death and certain other questions requiring special attention:
LBASIC
4. Universal program to create cumulative curves of patients randomised, proportion still alive on-study and raw life-table curves:
LIFE
3. Revision - when corrected or updated information is received, a 'difference' is formed (in 'pink form' style format) against the previous version and is used to create a new one. This makes it possible to audit and possibly remove changes which sometimes prove deleterious:
1. Universal program to compare two data sets and form a 'difference mask':
DIFFFE
2. Universal program to update a data set using a 'difference mask':
UPDATE
3. Difference mask amalgamator:
LAYBIT
4. Analysis - having built the necessary data sets, having formed a list of comparisons for a particular scientific question and created a steering file, the final step is to create and present the 'overview':
1. Universal program to calculate annual (O - E) and V etc for a particular overview:
BLACKBOX
2. Universal supplementary program to form subtracted annual (O - E) and V etc for certain endpoints of a particular overview:
POSTER
3. Universal program to create 'forest' plots:
GAZEBO
4. Universal program to create life-table curves:
ABSEIL
5. Universal program to generate histograms of prognostic variables for overview patients:
HISTER
5. In addition, there is a project management system to keep track of centre/group and trial/stratum information, data status and checks, steering files, personnel, addresses, correspondence, bibliography, the diary of events and action items.
1. Universal program to view the status of the whole project:
OVERLOOK
2. Universal project program to produce detailed summary of a particular centre/group and its personnel, trials/strata, data checks, flags, steering files, bibliography, diary etc:
RUGRAT
3. Universal program to review the full names, prognostic and treatment allocation details etc for one or more trials/strata:
WORLDE
4. Universal program to review the year code, brief name and linked trials/strata for a particular trial/stratum:
SERBIA
5. Universal program to check the data flags for a particular trial/stratum:
WRECKE
6. 'Abbreviated trial list' generator (creates file YLIST from files LIST and SERIAL):
TERSE
7. Cosmeticiser for overview trial list prior to laser printing or export to IBM system:
CUTTER
8. 'RGBRIEF' generator (creates file RGBRIEF from files BRIEF and SERIAL):
RGBRIEF
9. Universal program to list steering file details:
TITLES
10. Universal program to list centre/group and trial/stratum details:
TLIST
11. Universal program to summarise data and check EXTRAS file:
WCHECK (BC only at present)
12. Universal program to generate version of data file(s) with ICD code text appended to records, if required:
ICDADD
13. Universal program to list year codes, serial numbers and brief names for a particular steering file:
GROWLE
14. Universal program to check for entries missing from the BRIEF and SERIAL files:
SBCHECK
15. Universal program to check for various anomalies in LIST file:
LCHECK
16. Universal program to build TOTAL and summarise overview details:
TOTALS
17. Universal program to build web-ready version of LIST file:
ARACHNE
18. 'Labyrinth-friendly' overview trial list generator:
JLIST (BC only at present)
6. Finally, there are various useful 'interactive' miscellanea:
1. Laser printing for documents:
BURGER (and variants ABURGER ... HBURGER for different printers)
2. Logrank evaluator:
FOREST
3. Heterogeneity evaluator:
HETERO
4. ICD code evaluator:
ICD
5. Laser printing for graphics:
LASER (and variants ALASER ... HLASER for different printers)
6. Evaluator for various distribution functions:
NAGBAG
7. Odds ratio and significance evaluator:
ZOE

Database interface

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[End of document, updated to 13 MAY 2005]