Publications by M.Morris
PrEP Dynamics
rm(list = ls()) library(tidyr) library(stringr) library(skimr) library(dplyr) library(broom) library(Hmisc) library(ggplot2) library(ggpubr) library(plotly) library(gridExtra) library(nnet) library(kableExtra) library(survey) # Define a couple of functions for model comparison tables # for formulas get_formula <- function(prefi...
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Income and Insurance Report
rm(list = ls()) library(tidyr) library(stringr) library(skimr) library(dplyr) library(pander) library(broom) library(reshape2) library(ggplot2) library(ggpubr) library(plotly) library(gridExtra) library(nnet) library(kableExtra) # Define a couple of functions for model comparison tables # for formulas get_formula <- function(pr...
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WHAMP STI
rm(list = ls()) library(dplyr) library(ggplot2) library(ggpubr) library(plotly) library(kableExtra) library(expss) Introduction This report provides descriptive statistics on the annual incidence of bacterial STIs reported in the WHAMP survey. The analysis is based on three variables BSTIA (GC), BSTIB (CT), and BSTIC (syphilis). Note that...
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New Dx HIV in WA State MSM
Intro The purpose of this analysis is to run simple descriptive plots for new Dx HIV+ (count) trends by age, race and region, to make sure there are no anomalies in the data, and to get a sense of what these trends look like. The data were provided by Steven Erly at WADOH, as aggregated counts of new Dx HIV by age group, race and region. The expo...
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Targets: DOH Dx Prevalence and Incidence
rm(list = ls()) library(dplyr) library(ggplot2) #library(ggpubr) library(plotly) library(kableExtra) # This executes the script for building everything -- may not need to rebuild ## the data come from the WApopdata repository runmode = "script" # to control whether target summaries are built if(runmode == "script") { source(here::he...
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WHAMP partner distributions
rm(list = ls()) library(dplyr) library(ggplot2) library(ggpubr) library(plotly) library(kableExtra) Back to Outline Introduction This report presents descriptive statistics for the sexual partnerships used to drive the dynamic sexual network model. The data used here come from the WHAMP Survey supplemented by the ARTnet WA cases (927 and ...
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WHAMP Report Shell
Introduction This report presents the findings from the Washington HIV/AIDS Modeling for Prevention project (WHAMP). The goal of the project was to develop epidemiological modeling tools for projecting the next 10 years of the HIV epidemic among MSM in Washington State, track the costs of the state’s two major treatment and prevention programs,...
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DOH DAP
rm(list = ls()) library(dplyr) library(data.table) library(readxl) library(tidyverse) library(knitr) library(kableExtra) library(reshape2) library(ggplot2) library(plotly) library(gt) library(tiff) library(grid) # some plotting utility functions layout_3x5 <- function( gg, x = -0.15, y = -0.06, x_legend=1.05, y_legend=0.95,...
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STERGM fits
knitr::opts_chunk$set(error = TRUE, message = FALSE, warning=F) Data: whamp Package Versions: 3 Model: hiv_caxr_ Preliminaries Packages startKnitTime <- Sys.time() ## To update # if (params$version == 3) { # source(here("install_master_pkgs.R")) # } else { # source(here("install_dev_pkgs.R")) # } defaultPaths <- .libPaths() if(pa...
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HIV Tx parameters (DRW)
Care cascade {#carecasacde)} In this section, we use Washington State HIV surveillance data1 in combination with estimates of the intertest interval from the WHPP survey, the average time from seroconversion to onset of AIDS-associated symptoms2, and the average time from treatment initiation to viral suppression3 from the literature. The table ...
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