Epidemiology & Technology

Blog Archive

CVAT Converting Attribute Annotations to CSV

Recently I started working with Glaucoma Images preparation for AI/CV applications. Computer Vision Annotation Tool (CVAT) was deployed locally and fundus images uploaded into an organizational project within CVAT. Each Image is being annotated as follows Exporting the Attrinbute annotations I thought the best format would be the CVAT for
October 3, 2024

Understanding Cataract Prevalence and Operated variables in RAAB

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There are various ways that cataract can be defined when analysing data from RAAB surveys. Here, I review the RAAB Analysis R scripts to understand how it is being done in the autogenerated tables. Understanding the case_when syntax This syntax is used very commonly for creating new variables based on
August 9, 2024

Using RAAB6/RAAB7 Analysis R scripts on Desktop

The RAAB team has provided the analytic scripts on the GitHub repo. Once you download the scripts, you need some configuration on your desktopn to be able to use them. First is obviously you need to install R package. You also need to install pandoc [from here] Then you need
August 8, 2024

Survival Analysis in Stata

Cheat-sheet DETAILS A Key concept in survival analysis is ANALYSIS TIME. All analyses are performed in terms of time since becoming at risk, called analysis time. Subjects are exposed at t = time = 0 and later fail. Observations with t = time <= 0 are ignored because information before
July 22, 2024

Deviance and Deviance ratio in Logistic models

Once you start using logistic regression and have come beyond the basic model, you will start going into model diagnostics and comparison of model performances across various peculations for a specific outcome. you will then start coming across concepts of deviance and deviance ratios. Let us understand briefly, how to
June 19, 2024

Stata customised tables of Regression results

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Stata added collect and enable suite of commands. I am discovering them now having migrated to Stata 18 from Stata 15. Useful Links Sample Output for etable using Collect suite SAMPLE OUTPUT for Collect
June 17, 2024

LASSO in Stata

Crossvaldiation By default, stata will select model with highest lambda. By default, stata fits up to 100 models with varying lambdas. The model with largest out of sample r-square and minimum CV mean prediction error gets selected by cross-validation LASSO commands SSC Addons based methods Stabdard Lasso estimation commands Lasso
May 24, 2024

Stata and ML resources

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Some links to Stata and ML resources Conference Articles / Presentations / Stata Journal Stata Blog Articles from 2020 Other Resources Seven Steps in developing a prediction model Source: Towards better clinical prediction models: seven steps for development and an ABCD for validation - PMC (nih.gov)
May 20, 2024

Compact Results of Logistic Regression in Stata using ‘estout’ – ‘logisticresults’

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After running a logistic regression in Stata, for inclusion in classical tables, one needs the Odds ratios and 95% confidence intervals. I have developed a small code snippet for getting reasonably compact unstyled results that can be easily copy-pasted in word or excel. This actts as a thin wrapper for
February 20, 2024

Easily get gender wise results of binary outcomes after survey data analysis in Stata

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Problem Statement: You have a survey data and you wish to summarize your prevalence by gender Prerequisites: Stata Code Result You will get the outcome variable name in first column, male total, male %(95% CI), female total, female % (95%CI), total number, total % (95% CI). This can be copied
February 16, 2024