Epidemiological analysis with R

Riga Stradins University Workshop, July 2020

Lecturer: Sergio Uribe, Assoc Prof, PhD Riga Stradins University, July 2020 Required packages pacman::p_load( car, broom, tidyverse, ggfortify, mosaic, huxtable, jtools, latex2exp, pubh, sjlabelled, sjPlot, sjmisc ) theme_set(sjPlot::theme_sjplot2(base_size = 10)) theme_update(legend.position = "top") # options('huxtable.knit_print_df' = FALSE) options('huxtable.knit_print_df_theme' = theme_article) options('huxtable.autoformat_number_format' = list(numeric = "%5.2f")) knitr::opts_chunk$set(collapse = TRUE, comment = NA) Epidemiological Descriptive Analysis Onchocerciasis in Sierra Leone. data(Oncho) Oncho %>% head() idmfareaagegrpsexmfloadlesions 1InfectedSavannah20-39Female1No 2InfectedRainforest40+Male3No 3InfectedSavannah40+Female1No 4Not-infectedRainforest20-39Female0No 5Not-infectedSavannah40+Female0No 6Not-infectedRainforest20-39Female0No A two-by-two contingency table: [Read More]

Regression Modelling for Epidemiology

Riga Stradins University Workshop, July 2020

Lecturer: Sergio Uribe, Assoc Prof, PhD Riga Stradins University, July 2020 pacman::p_load( car, broom, tidyverse, ggfortify, mosaic, huxtable, jtools, latex2exp, pubh, sjlabelled, sjPlot, sjmisc ) theme_set(sjPlot::theme_sjplot2(base_size = 10)) theme_update(legend.position = "top") # options('huxtable.knit_print_df' = FALSE) options('huxtable.knit_print_df_theme' = theme_article) options('huxtable.autoformat_number_format' = list(numeric = "%5.2f")) knitr::opts_chunk$set(collapse = TRUE, comment = NA) Regression data(birthwt, package = "MASS") birthwt <- birthwt %>% mutate(smoke = factor(smoke, labels = c("Non-smoker", "Smoker")), race = factor(race, labels = c("White", "African American", "Other"))) %>% var_labels(bwt = 'Birth weight (g)', smoke = 'Smoking status', race = 'Race') birthwt %>% group_by(race, smoke) %>% summarise( n = n(), Mean = mean(bwt, na. [Read More]