From 0a6744c9d01821eaf5d95347759c7c1c4bcfbda6 Mon Sep 17 00:00:00 2001 From: jessexknight Date: Tue, 9 Nov 2021 19:59:57 -0500 Subject: [PATCH] docs: add effects plot, remove p-values, part of #1 & #2 --- docs/api/app.results.tex | 18 +++++++++++++++++- docs/api/tab/api.tex | 36 +++++++++++++++++++----------------- 2 files changed, 36 insertions(+), 18 deletions(-) diff --git a/docs/api/app.results.tex b/docs/api/app.results.tex index 3706b9e..ee0ba45 100644 --- a/docs/api/app.results.tex +++ b/docs/api/app.results.tex @@ -78,4 +78,20 @@ \subsection{ART Prevention Impact}\label{aa:res:api} \caption{\title} \label{fig:api:\var} \end{figure} -} \ No newline at end of file +} +\begin{figure}[H] + \centering + \includegraphics[width=0.75\linewidth]{effects} + \caption{Effect estimates for factors of heterogeneity on + incidence reduction (\%, IR) and cumulative infections averted (\%, CHI) + from linear multivariate regression with generalized estimating equations.} + \label{fig:effects} + \floatfoot{ + RR: relative risk; + HTC: HIV testing and counselling; + KP: key populations. + priority: modelled ART cascade transitions were faster in KP vs overall due to prioritized programs; + same: cascade transitions were assumed the same in KP as overall. + Factor definitions are given in Appendix~\ref{a:defs}. + } +\end{figure} \ No newline at end of file diff --git a/docs/api/tab/api.tex b/docs/api/tab/api.tex index 5b29a23..8348c13 100644 --- a/docs/api/tab/api.tex +++ b/docs/api/tab/api.tex @@ -1,23 +1,23 @@ -\newcommand{\xtab}[1]{\x{api/inc/#1.xtab} & \x{api/chi/#1.xtab} } -\footnotesize% +\newcommand{\xtab}[1]{\x{api/inc/#1.xtab} & \x{api/chi/#1.xtab} }% +\def\baselinestretch{1.1}\footnotesize% \centerline{% \setlength{\tabcolsep}{.7ex}% -\begin{tabular}{ll rrc rcr rrc rcr} +\begin{tabular}{ll rrc rc rrc rc} \toprule - & & \multicolumn{6}{c}{Incidence Reduction (\%)} - & \multicolumn{6}{c}{Cum. Infections Averted (\%)} \\ - \cmidrule(rl){3-8}\cmidrule(rl){9-14} - Factor & Level & N\tn{a} & Median & (IQR) & Effect\tn{b} & (95\% CI)\tn{b} & p\tn{b} - & N\tn{a} & Median & (IQR) & Effect\tn{b} & (95\% CI)\tn{b} & p\tn{b} \\ + & & \multicolumn{5}{c}{Incidence Reduction (\%)} + & \multicolumn{5}{c}{Cumulative Infections Averted (\%)} \\ + \cmidrule(rl){3-7}\cmidrule(rl){8-12} + Factor & Level & N\tn{a} & Median & (IQR) & Effect\tn{b} & (95\% CI)\tn{b} + & N\tn{a} & Median & (IQR) & Effect\tn{b} & (95\% CI)\tn{b} \\ \midrule -%\begin{tabular}{lll} +%%\begin{tabular}{lll} Time Horizon & 0-10 & \xtab{t.cat.0} \\ (years) & 11-20 & \xtab{t.cat.10} \\ & 21-30 & \xtab{t.cat.20} \\ & 31+ & \xtab{t.cat.30} \\[\tsep] - HIV Prevalence & 0-1 & \xtab{api.prev.cat.Low} \\ + HIV Prevalence & 10+ & \xtab{api.prev.cat.High} \\ (\%) & 1-10 & \xtab{api.prev.cat.Mid} \\ - & 10+ & \xtab{api.prev.cat.High} \\[\tsep] + & 0-1 & \xtab{api.prev.cat.Low} \\[\tsep] HIV Incidence & Increasing & \xtab{api.phase.incr} \\ Trend\tn{c} & Inc-to-stable & \xtab{api.phase.its} \\ & Stable & \xtab{api.phase.stab} \\ @@ -25,13 +25,14 @@ & Decreasing & \xtab{api.phase.decr} \\ \midrule RR Transmission & 0.0-0.039 & \xtab{art.rbeta.cat.0} \\ - on ART & 0.4-0.099 & \xtab{art.rbeta.cat.0.04} \\ + on ART & 0.04-0.099 & \xtab{art.rbeta.cat.0.04} \\ & 0.1+ & \xtab{art.rbeta.cat.0.1} \\[\tsep] - CD4 Threshold for & Mixed & \xtab{art.cd4.*} \\ + CD4 Threshold for & Symptomatic & \xtab{art.cd4.symp} \\ ART Initiation & 200 & \xtab{art.cd4.200} \\ & 350 & \xtab{art.cd4.350} \\ & 500 & \xtab{art.cd4.500} \\ - & Any & \xtab{art.cd4.All} \\[\tsep] + & Any & \xtab{art.cd4.All} \\ + & Mixed & \xtab{art.cd4.*} \\[\tsep] ART Coverage & 0-59 & \xtab{art.cov.cat.0} \\ Target (\%)\tn{c} & 60-84 & \xtab{art.cov.cat.0.6} \\ & 85+ & \xtab{art.cov.cat.0.85} \\ @@ -64,8 +65,9 @@ \floatfoot{ \tnt[a]{N: number of unique scenarios and time horizons; sums across factor levels may be less than 126 and 115 due to missing variables.} - \tnt[b]{Effect estimates and p-values from linear multivariate regression - with generalized estimating equations \cite{Hojsgaard2006}.} + \tnt[b]{Effect estimates from linear multivariate regression + with generalized estimating equations \cite{Hojsgaard2006}; + effects are illustrated in Figure~\ref{fig:effects}.} \tnt[c]{Omitted from regression model due to missing data.} RR: relative risk; HTC: HIV testing and counselling; @@ -73,4 +75,4 @@ priority: modelled ART cascade transitions were faster in KP vs overall due to prioritized programs; same: cascade transitions were assumed the same in KP as overall. Factor definitions are given in Appendix~\ref{a:defs}. -} \ No newline at end of file +}