Software

Links to other epidemiological software can be found on the Useful Links page.

FreeCalc

FreeCalc is an epidemiological probability calculator designed to assist with the planning and analysis of surveys to demonstrate freedom from disease, or surveys to detect disease. FreeCalc has two modules, Sample Size calculation and Analysis of Results. Commonly used approaches to demonstrating freedom from disease have either

At the heart of FreeCalc is a new probability formula which adjusts for imperfect tests, and for population size, providing an exact result.

Sample Size

This module accepts as input

Using an iterative procedure, it calculates the number of animals that must be tested in order to provide evidence, at the specified level of confidence, that disease is not present. It also reports the Cutpoint Number of Reactors, or the maximum number of test-positive results that can be observed and still conclude the population is free from disease (ie. false positives).

Analysis of results

The analysis module accepts as input

It then calculates the exact probability of observing such a result under the null hypothesis (that disease is present) and under the alternative hypothesis (that the population is free from disease). It provides an interpretation of what conclusions can be drawn from these figures.

In addition to the exact probability formula, two other formula may be used:

FreeCalc runs on Windows 95 and later operating systems. The calculations performed are extremely complex, and for large sample sizes, may be quite slow. A fast processor (or a little patience) will help.

FreeCalc is Shareware, which means that you are free to download, use, copy and distribute the program as you wish, at no charge. The only requirements are that:

The current windows version is 2. Users are requested to email comments and bug reports to the author: Angus Cameron

To install FreeCalc, you need to download the compressed zip file below. Create a new directory for the program (eg. C:\Program Files\FreeCalc), copy the file to this directory and decompress it. You can download a free evaluation version of WinZip for decompressing Zip files here.

You may wish to create a backup of the installation files on floppy disk. Copy the decompressed files onto a floppy disk. The program can be restored from this disk at a later date.

When the files are decompressed, the program is ready to run. You can create a shortcut or menu entry for the program if you wish.

References

Cameron, AR and Baldock, FC (1998) A new probability formula for surveys to substantiate freedom from disease. Prev Vet Med 34(1):1-17

Cameron, AR and Baldock, FC (1998) Two-stage sampling in surveys to substantiate freedom from disease. Prev Vet Med 34(1):19-30

Download

Survey Toolbox

Survey Toolbox is a suite of software programs which are designed to make planning, conducting and analysing statistically valid, efficient and practical animal health surveys easier. These programs were written for veterinarians in developing countries, but many have uses for anybody involved in planning surveys.

Contents

Random Sampling from a sampling frame Enables simple random sampling or probability proportional to size sampling, with or without replacement from a sampling frame. The frame may be in dBASE or Pardox formats.
Random selection of animals in a village Assists with the construction of a sampling frame and random selection of individual animals from a population made up of many small groups.
Random Geographic Coordinate Sampling Tools to assist with a sampling technique that allows a true random sample to be drawn without the need for a sampling frame.
Two-stage prevalence survey design and analysis This program calculates sample sizes for, and analyses results from, two stage prevalence surveys using one of three sampling strategies: Probability proportional to size sampling at the first stage (when a good sampling frame with herd size data is available), Simple random sampling (when no herd size data is available) or Random geographic coordinate sampling (when no sampling frame is available).
True Prevalence Prevalence estimates from a survey can be misleading due to imperfect diagnostic tests used. This program converts the apparent prevalence from a survey to the true prevalence, taking false positive and false negative results into account.
Comparison of two prevalences The aim of prevalence surveys is usually to detect change. This program compares two prevalence estimates and their variance estimates, to determine if any difference is likely to be real or simply due to chance.
Survival Analysis Sample size This program calculates the sample size required when using survival analysis to compare the disease experience of two groups.
Survival Analysis This program performs simple survival analysis of data with censored observations. It produces Kaplan-Meier survival curves, summary statistics, and compares two survival curves using the log rank test and the hazard ratio. Although it may be applied to any type of survival data, it is specifically designed to analyse the results of retrospective disease outbreak surveys
Capture Recapture This program estimates the size of a population based on observations from two independent data sources. It may be used to calculate disease incidence based on a combination of diseases reports or laboratory submissions, and a structured disease survey.
FreeCalc - Freedom from Disease The FreeCalc program is used to help plan and analyse surveys to detect disease, or demonstrate freedom from disease. It contains a sample size calculator, as well as an analysis module. The program may be used for herd level surveys or large area (state, province, national) surveys.

Acknowledgements

Initial development of the Survey Toolbox took place as part of a research project funded by the Australian Centre for International Agricultural Research (ACIAR), who also provided specific funding for the preparation of the accompanying Surveillance Manual.

Other collaborating organisations without whom this work would not have been possible include:

Particular thanks go to Dr Chris Baldock (AusVet Animal Health Services), Dr Pramod Sharma (University of Queensland), Dr John Copland (ACIAR), Dr Pornchai Chamnanpood (Thai DLD), and Drs Singkham Phonvisay and Siseng Khounsy (Lao DLF).

Requirements

Survey Toolbox runs on Windows 95 and later operating systems. The full installation requires about 4 Mb of free disk space. In addition to the programs described above, there is a separate program for Random Geographic Coordinate Sampling (RGCS), that requires ArcView version 3 or later. Users without this program may use the stand-alone RGCS module in Survey Toolbox.

Version 1.04

The current release of Survey Toolbox is Version 1.04. This is a minor upgrade to the previous version 1.03.

Downloading Survey Toolbox

Survey toolbox is Shareware, which means that you are free to download, use, copy and distribute the program as you wish, at no charge. The only requirements are that:

The current version is 1.04. This is a fully functional and tested version, but may still have some quirks. This version corrects a problem with the installation process which resulted in some required files not being accessible, particularly when using the Random Animal program. The help system of some of the programs is either rudimentary or completely missing. Users are requested to email comments and bug reports to the author: Angus Cameron

To install Survey Toolbox, you need to download each of the five compressed zip files below. Copy the files to a temporary directory (eg C:\temp or C:\windows\temp), and decompress them. You can download a free evaluation version of WinZip for decompressing Zip files here.

You may wish to create a backup of the installation files on floppy disk. Copy the decompressed files from each of the five downloaded files onto a separate 1.44 Mb floppy disk. The program can be installed from these disks at a later date.

When the files are decompressed, run Setup.exe (either from Windows Explorer, or using the Start Menu, and choosing Settings | Control Panel | Add/Remove Programs | Install, and then browsing to the Setup.exe file in your temp directory.

The installation and use of the programs is described in the the Surveillance Manual

Download as six separate files (each fits on one floppy disk)

Download as a single large file (about 7 megabytes)

QCEL Laboratory Quality Control Toolkit

QCEL (Quality Control for ELISAs) is an internal laboratory quality control toolkit for ELISAs and other types of laboratory tests. The program uses the Shewart-Cusum technique to track the results of QC samples, allowing early identification of problems that may lead to unreliable results. The program is available free of charge.

Requirements

The program is written for MS-DOS, and will run under Windows 3.1 and later versions (including Windows 95) in a DOS window. The program occupies very little disk space, requiring only about 240 kb. It will run with only 520 kb RAM.

License and Support

The program is distributed free of charge as Shareware, which means that you are free to download, use, copy and distribute the program as you wish, at no charge. The only requirements are that:

The authors are busy with other things, and it is unlikely that the program will be further developed or supported. However, if you have specific questions or comments, you may email Angus Cameron. A reply is not guaranteed.

The authors do not accept any responsibility for loss or damage caused by the program. (We have tested it thoroughly on our systems, and it works well, but we need to put this bit in).

Acknowledgements

QCEL was written by Angus Cameron and Stuart Blacksell. The authors would like to acknowledge the following organisations for their support:

Downloading and Installing QCEL

To download QCEL, click on the link below. The file is a compressed zip file. Create a new directory on your hard disk, (eg C:\QCEL) and copy the file into it. To extract the files, use a decompression program (such as PKUNZIP or WinZip). Once the files have been extracted, you can delete the installation file, or move it to a floppy disk for backup.

When installed, there will be eight files:

To start the program, change to the program's directory that you set up during installation (eg C:\QCEL) and type QCEL at the DOS prompt. For Windows users, you can set up a shortcut to the program on your desktop.