Luís Alves de Sousa's repositories
Conference_2020
This repository holds the content for the NHS-R Community conference, November 2020. Plenary session and lightning talk material will be shared in the relevant folders, and workshop details are below
COVID-Deaths-Averted-analysis
Analysis calculating the number of deaths averted from COVID-19 vaccination programs in WHO European Region
dados-SICOeVM
Mini-projeto "Dados da SICO-eVM (plataforma de vigilância da mortalidade" no âmbito do repositório de dados sobre a COVID-19 em Portugal
further-changepoints-course
File for the course Further Changepoint Analysis Techniques
nhs_pathways_monitoring
Real-time monitoring of potential COVID-19 cases reported through NHS pathways data
OmicronSeverity
Source code to accompany Lancet Paper, Nyberg, Ferguson et al, March 2022
Prediction_performance_survival
Code repository for the manuscript: 'Assessing performance in prediction models with survival outcomes: practical guidance' (manuscript in preparation)
Repeated_Measurements
Shiny App for Repeated Measurements Course
stat_rethinking_2022
Statistical Rethinking course winter 2022
.doom.d
My doom emacs private layer.
BayesLearnCourse
Bayesian Statistics I at Stockholm University
covid19-hospital-activity
Short-term forecasts of Trust-level COVID-19 hospital admissions in England.
covid19.sgene.utla.rt
Local area reproduction numbers and S-gene target failure.
date
A date and time library based on the C++11/14/17 <chrono> header
epinowcast
Nowcast right censored epidemiological count data
geocompr
Open source book: Geocomputation with R
hit-analysis
Analysis of herd immunity threshold for SARS-CoV-2
HOQCutil
HOQC utilities
idbrms
Population-level infectious disease modelling as an extension of brms.
inc2prev
Estimate incidence from ONS prevalence estimates
reinfections
SARS-CoV-2 reinfection trends in South Africa: analysis of routine surveillance data (Pulliam et al. 2021)
schedule
EpiForecasts server job scheduling (CRON, docker, and bash)
ValidationCompRisks
Code repository for the manuscript 'Validation of the performance of competing risks prediction models: a guide through modern methods' (in preparation)