Sam Abbott seabbs
🏠
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| #' Load the package | |
| library(Thresher) | |
| #' Generate random data | |
| set.seed(3928270) | |
| ranData <- matrix(rnorm(100*12), ncol=12) | |
| colnames(ranData) <- paste("G", 1:12, sep='') | |
| #' Perform dim reduction |
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| #' Adjust test size on a ggplot to make it visible in presentations | |
| #' | |
| #' Change the size of text on a \code{ggplot} so that a plot designed to look good in print is readable when included in a slide in a presentation (or vice verse) | |
| #' @param g A \code{ggplot} graph | |
| #' @param title_size The font size for the title, legend title and axes titles | |
| #' @param text_size The font size for for the axis lables, legend text and facet text | |
| #' @return A \code{ggplot} graph | |
| #' @author Ella Kaye | |
| #' @examples | |
| #' |
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| ## Get packages | |
| if (!require(pacman)) install.packages("pacman"); library(pacman) | |
| p_load_gh("seabbs/getTBinR") | |
| p_load_gh("thomasp85/patchwork") | |
| p_load("tidyverse") | |
| p_load("ggridges") | |
| p_load("viridis") | |
| ## Get data |
seabbs
/ dist_tb_inc_region
Last active
March 7, 2018 13:42
Exploring distributions of TB incidence rates over time by region
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| ## Get required packages, managed via pacman | |
| if (!require(pacman)) install.packages("pacman"); library(pacman) | |
| p_load("getTBinR") | |
| p_load("tidyverse") | |
| p_load("viridis") | |
| p_load("hrbrthemes") | |
| p_load("ggridges") | |
| p_load_gh("thomasp85/patchwork", dependencies = TRUE) | |
seabbs
/ com_tb_inc_mort
Created
February 14, 2018 11:04
Comparison of regional TB incidence and mortality rates
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| # install.packages("getTBinR") | |
| library(getTBinR) | |
| # install.packages("tidyverse") | |
| library(tidyverse) | |
| # install.packages("viridis") | |
| library(viridis) | |
| # install.packages("hrbrthemes") | |
| library(hrbrthemes) | |
| # install.packages("scales") | |
| library(scales) |
seabbs
/ HIV_and_TB
Last active
January 31, 2018 11:33
Exploring HIV and TB incidence in high burden countries
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| # install.packages("getTBinR") | |
| library(getTBinR) | |
| # install.packages("tidyverse") | |
| library(tidyverse) | |
| # install.packages("gridExtra") | |
| library(gridExtra) | |
| # Get the data - WHO data | |
| tb_df <- get_tb_burden() | |
| dict <- get_data_dict() |
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| ## Get the package | |
| install.packages("getTBinR") | |
| ## Run the dashboard - if the dependencies are not installed you will be asked to install them. | |
| getTBinR::run_tb_dashboard() |
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| mapStates = map("state", fill = TRUE, plot = FALSE) | |
| leaflet(data = mapStates) %>% addTiles() %>% | |
| addPolygons(fillColor = topo.colors(10, alpha = NULL), stroke = FALSE) |
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| FLOAT(SCRIPT_REAL("qbinom(0.001, .arg2, .arg1 / .arg2) / .arg2", | |
| WINDOW_SUM(SUM([prob_Accepted]), -[No. of days for rolling average] + 1, 0), | |
| WINDOW_SUM(COUNT([prob_Accepted]), -[No. of days for rolling average] + 1, 0))) |
seabbs
/ explore_case_detection
Created
January 11, 2018 16:16
Explore case detection and incidence rates in the WHO Tuberculosis data
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| # install.packages("getTBinR") | |
| library(getTBinR) | |
| # install.packages("tidyverse") | |
| library(tidyverse) | |
| # install.packages("gridExtra") | |
| library(gridExtra) | |
| # Get the data | |
| tb_burden <- get_tb_burden(download_data = TRUE, save = TRUE) | |
| dict <- get_data_dict(download_data = TRUE, save = TRUE) |