diff --git a/manuscript.Rnw b/manuscript.Rnw index e114886..802c852 100644 --- a/manuscript.Rnw +++ b/manuscript.Rnw @@ -283,13 +283,6 @@ APIs: \item The \emph{synthetic tree} itself, the `Open Tree'. \end{enumerate} -Additionally, the project provides access to other data, the Graph of Life, that -stores information about the underlying tree alignment graph \citep{Smith2013} -used to synthesize the various sources of information from which the Open Tree -is assembled. Data from this API are not intended for normal users, and its -use will not be demonstrated in this paper, although \texttt{rotl} has functions to -retrieve data it provides. - \texttt{rotl} gives users access to all endpoints provided by version 2 of the OTL APIs, and other versions of the API can be selected by the user as they become available. Phylogenetic trees served by the API can be imported directly into @@ -458,12 +451,12 @@ using the function \texttt{get\_study\_meta}. \label{sec:how-does-rotl-fit} In recent years, R has become an essential part of the toolbox of many -researchers in evolutionary biology and ecology. R greatly facilitates the +researchers in evolutionary biology and ecology. R greatly facilitates the analysis of large datasets, and allows researchers to combine methods in novel ways because many methods for comparative analyses are implemented, and because -it is a relatively easy to use programming language. Additionally, as more data -are made available online and accessible using APIs, several packages have been -developed to interact and download these datasets directly in R, thereby +it is a relatively easy to use programming language. Additionally, as more data +are made available online and accessible using APIs, several packages have been +developed to interact and download these datasets directly in R, thereby enabling direct and reproducible analyses. Notably, the organization rOpenSci (\url{https://ropensci.org}) has fostered a community of researchers who develop tools and methods to facilitate the use of open data as well broaden the