diff --git a/docs/api/app.search.tex b/docs/api/app.search.tex index 65b6deb..2f665cc 100644 --- a/docs/api/app.search.tex +++ b/docs/api/app.search.tex @@ -1,7 +1,7 @@ \section{Search Strategy} \label{a:search} We designed our search strategy with guidance from -an information specialist at our affiliate library. +an information specialist at our affiliate library (KF). % ============================================================================== \subsection{Search Terms} \label{aa:search:terms} @@ -10,6 +10,9 @@ \subsection{Search Terms} \st{.mp} searches the main text fields, including title, abstract, and heading words. We searched MEDLINE and EMBASE via Ovid on 2020 March 20. +Duplicate studies were removed automatically by Ovid and by Covidence; +four additional duplicates with subtly different titles +were later identified and removed manually. \input{tab/search} % ============================================================================== \subsection{Inclusion/Exclusion Criteria} diff --git a/docs/api/methods.tex b/docs/api/methods.tex index 4ff2c18..2eaf8a4 100644 --- a/docs/api/methods.tex +++ b/docs/api/methods.tex @@ -2,20 +2,13 @@ \section{Methods} \label{s:meth} We conducted a scoping review according to the PRISMA extension for scoping reviews (Appendix~\ref{a:prisma}). -First, we developed a conceptual framework to organize -assumptions and representations of risk heterogeneity -in compartmental HIV transmission models. -Then, we designed and implemented the search strategy, -and extracted data relevant to the framework to address our objectives. % ============================================================================== \subsection{Conceptual Framework for Risk Heterogeneity} \label{ss:meth:framework} -We conceptualized ``factors of risk heterogeneity'', meaning -epidemiological stratifications and phenomena which may/not be included in transmission models. -Such factors could include if/how populations, rates, and probabilities -are stratified along various dimensions. -We defined the following 4 domains in which -these factors might influence the transmission impact of ART. +We defined ``factors of risk heterogeneity'' as +epidemiological phenomena and stratifications of populations, rates, or probabilities +which may/not be included in transmission models. +We defined 4 domains in which such factors might influence the transmission impact of ART: \begin{itemize} \item \textbf{Biological Effects:} differential transmission risk within HIV disease course @@ -50,41 +43,21 @@ \subsection{Search} We searched MEDLINE and EMBASE via Ovid using search terms related to Sub-Saharan Africa (SSA), HIV, and transmission modelling (Table~\ref{tab:search}). -Search results were imported into Covidence \cite{Covidence} for screening. -Duplicate studies were removed automatically by Ovid and by Covidence; -four additional duplicates with subtly different titles were later identified and removed manually. -Potentially relevant studies were identified by title and abstract screening, followed -by full-text screening using the inclusion/exclusion criteria below. +Search results were de-duplicated and screened by title and abstract in Covidence \cite{Covidence}, +followed by full-text screening using the criteria below. One reviewer (JK) conducted the search, screening, and data extraction. % ------------------------------------------------------------------------------ \subsubsection{Inclusion/Exclusion Criteria} \label{sss:meth:criteria} -We included peer-reviewed, primarily modelling studies that used non-linear models of sexual HIV transmission +See Table~\ref{tab:criteria} for complete inclusion/exclusion criteria and definitions. +We included peer-reviewed, primary modelling studies that used +non-linear compartmental models of sexual HIV transmission to project the prevention impacts of ART in any setting within SSA. -See Table~\ref{tab:criteria} for complete inclusion/exclusion criteria. -We only included studies published in English anytime before Jan~1, 2020. -We excluded conference publications, and those without primary modelling results and description of the methods, -such as commentaries and reviews. -If a model's details were provided in another peer-reviewed publication, -we extracted data from both publications as required. -\par -Inclusion criteria were as follows: -1) Used a non-linear compartmental model of sexual HIV transmission at the population level. -We defined \emph{non-linear models} as those where -future projected infections are a function of previously projected infections, -and \emph{compartmental models} as those where -system variables represent the numbers of individuals in each state, -rather than unique individuals \cite{Garnett2011}. -Thus, statistical models, models without dynamic transmission, and individual-based models were excluded. -2) The model was parameterized/calibrated to reflect at least one setting within SSA -(see Appendix~\ref{aa:defs:context} for countries). -3) The study simulated at least one scenario with increasing ART coverage, +We included studies published in English anytime before Jan~1, 2020, +that simulated at least one scenario with increasing ART coverage, possibly alongside other interventions. -The included studies formed Dataset~A, -used to complete objectives \ref{rq:1}~and~\ref{rq:2}. -\par -A subset of Dataset~A formed Dataset~B, -used to complete objective~\ref{rq:3}. +The included studies formed Dataset~A, used to complete objectives \ref{rq:1}~and~\ref{rq:2}. +A subset of Dataset~A formed Dataset~B, used to complete objective~\ref{rq:3}. Studies in Dataset~B met three additional criteria: 1) examined scale-up of ART coverage alone (versus combination intervention); 2) examined ART intervention for the whole population (versus ART prioritized to subgroups); and @@ -95,7 +68,7 @@ \subsection{Data Extraction} \label{ss:meth:data} Data extraction used the full text and all available supplementary material. Data were extracted per-study for objectives \ref{rq:1}~and~\ref{rq:2}, and -per-scenario for objective~\ref{rq:3}. +per-scenario for objective~\ref{rq:3}, possibly including multiple time horizons. Detailed variables definitions are given in Appendix~\ref{a:defs}. % ------------------------------------------------------------------------------ \subsubsection{Epidemic Context} diff --git a/docs/api/tab/criteria.tex b/docs/api/tab/criteria.tex index 41fbc99..fad1362 100644 --- a/docs/api/tab/criteria.tex +++ b/docs/api/tab/criteria.tex @@ -45,7 +45,10 @@ rather than unique individuals.} \tnt[4]{SSA was defined based on the countries in the UN regions of East, South, Central, and West Africa, plus South Sudan - (see Table~\ref{tab:search} for full country list).} + (see Table~\ref{tab:search} for full country list). + Studies were included if the model was parameterized/calirated to reflect + at least one context within SSA. + Only model parameters \& outcomes for SSA contexts were extracted.} \tnt[5]{Articles reporting HIV incidence reduction and/or cumulative HIV infections averted among the whole population due to increased coverage or initiation rate of ART for the whole population.}