Publications by M.Morris
Mean Degree Reference Report - Model with HIV
if(params$version == "3"){ pkglib <- "~/R/GHmaster-library" } else { pkglib <- "~/R/GHdev-library" } defaultPaths <- .libPaths() .libPaths(c(pkglib, defaultPaths)) .libPaths() ## [1] "/homes/morrism/R/GHmaster-library" ## [2] "/homes/morrism/R/x86_64-pc-linux-gnu-library/4.0" ## [3] "/usr/lib/R/library" ...
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HIV Prevalence Target Uncertainty
msm.pop.totals_2019 <- WApopdata::msm.pop.totals_2019 PLWH_2019 <- msm.pop.totals_2019$MSM_PLWH_WA pop2019 <- WApopdata::msm_all_age10_race_region_2019 df_2019 <- pop2019 %>% mutate(age.grp10 = ifelse(age.grp10 == "55-65", "55-64", age.grp10)) %>% left_join(PLWH_2019) %>% mutate(prev2019 = UB/num) msm.pop...
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HIV Prevalence Target Uncertainty
library(dplyr) library(tidyr) library(ggplot2) msm.pop.totals_2019 <- WApopdata::msm.pop.totals_2019 PLWH <- msm.pop.totals_2019$MSM_PLWH_WA Introduction We need HIV prevalence targets to calibrate and validate our models. It turns out there is a lot of uncertainty in these target values. HIV prevalence, as a rate, is defined by \[ Prevale...
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Mean Degree Report - caxr
Preliminaries Packages if(params$version == "3"){ pkglib <- "~/R/GHmaster-library" } else { pkglib <- "~/R/GHdev-library" } defaultPaths <- .libPaths() .libPaths(c(pkglib, defaultPaths)) .libPaths() ## [1] "/homes/morrism/R/GHmaster-library" ## [2] "/homes/morrism/R/x86_64-pc-linux-gnu-library/4.0" ## [3] "/usr/lib/R/library"...
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Testing Descriptives
knitr::opts_chunk$set(error = TRUE, message = FALSE, warning = FALSE) library(dplyr) library(tidyr) library(lubridate) library(spatstat) library(ggplot2) library(kableExtra) library(survival) library(survminer) Preliminaries egoDF <- WHAMPData::whampArtnetWA_egodata$main$egos wDF <- WHAMPData::whamp_wide %>% haven::zap_label() %>% ...
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Testing hazard models
knitr::opts_chunk$set(error = TRUE, message = FALSE, warning = FALSE) library(dplyr) library(flexsurv) library(muhaz) library(data.table) library(ggplot2) dat <- readRDS(here::here("Reports","WHAMPsurvey","MM","Testing", "coxdata.RDS")) # remove never testers: never_tested = "T" and age 45+ # 8 men dat <- dat %...
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Prevalent Dx HIV in WA State
Intro The purpose of this analysis is to run simple descriptive plots for Dx HIV+ prevalence (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 persons living with Dx HIV by age group, ra...
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WHAMP Cost statistics
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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ART Dynamics
rm(list = ls()) library(tidyverse) library(Hmisc) library(ggpubr) library(plotly) library(kableExtra) Introduction This report covers the data management and modeling associated with the ART continuum: Input parameters for EpiModel – not constructed here, as the WHAMP data do not support parameter estimation for the ART continuum (see d...
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ZK DAP DOH Parameters and Targets
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) 1 Introduction This report is based mostly on WADOH DAP participation data, which are used to construct parameters and targ...
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