ReplicationFollow the steps below to install the Linguistomics Repository on your computer. Download and install GitHub Desktop•Click here to go to the GitHub Download Page. •Follow the instructions for installing GitHub Desktop on your computer.Clone repoOpen GitHub Desktop and choose "File..Clone Repository..." from the menu bar.Clone a repositoryGitHub.comGitHub EnterpriseURLRepository URL or GitHub username and repositoryhttps://github.com/jhuelsenbeck/LinguistomicsLocal PathDocuments/LinguistomicsChoose...CloneCancelInput names•Type the url of the repository on GitHub. •Type the name of the folder on your computer where you want the repository to be stored. If you change this folder, remember it, because you will need it in a later step. •Click "Clone" and wait for the repo to download.
Download and install Nytril•Click here to go to Nytril.com. •Click "Download" at the top of the page.•Choose your platform and download the installer. •Run and Complete the installationNytril Development EnvironmentWelcome to Nytril SetupSetup will guide you through the installation of Nytril.Click Next to continue.NextCancelRun Nytril Desktop•On a Mac, the Nytril icon will be in your Applications folder•On Windows, the icon will be on the desktop. Nytril Development EnvironmentFileEditViewGitBuildRepoProjectDocumentsDataDeviceHelp
Open Linguistomics Repo•Choose File..Open..Repository...•The Local Folder should be set to the repo download folder from step 2. •Cllck OK.Open RepoLocal FolderDocuments/Linguistomics (from step 2)Repository NameLinguistomicsOKCancel
Open the "Paper" Project•The following dialog box will appear. •Input the text as shown and cllck OK.Open ProjectExisting Main FileNytril/MainNamePapersOKCancelOpen the "Create Data Files" Project•Select "File..Open..Project".•Input the text as shown and cllck OK.Open ProjectExisting Main FileNytril/Create Data FilesNameCreate Data FilesOKCancel
Using the two projectsNow that the installation is complete, you can review the documents inside each project. There are 2 projects in the Linguistomics repo that comprise the two main stages of the experiment. You can see these by clicking on the "Projects" menu. Choosing a project reloads all the source files and documents to the way that they were the last time you viewed that project, so you can switch back and forth between the two, without losing your way. A handy feature of this environment is that by holding down the Ctrl-key and clicking anything in the document, you will be taken to the source of the information in the left-hand pane. Holding down Ctrl-Shift and hovering over an element shows its layout lines. Ctrl-Shift-Click on a diagram to see how the diagram was created in code. The two projects are: •Create Data FilesThis project uses the raw cognate words and segment definitions to build the data files for the MCMC part of the experiment. There are 4 docments in this project: 1DiagnosticsShows the raw data from the data files in a variety of ways in order to allow the researcher to find mistakes in the data. 2Create Experiment FilesA control panel with a button that triggers the creation of the experiment files from the raw cognate data. Use this button when the raw data changes and you want to re-run the whole experiment. 3Configuration FileShows the JSON file that is used to initialize the TongueTwister program. 4Word FileA copy of the raw data for an experiment. •PapersThis contains the result of the completed experiment. 1Paper JOLEShows the finished manuscript. 2SupplementalExtra narrative, equations and figures that did not fit into the main paper. If you have trouble with any of these steps, send an email to Shawn and he will walk you through any trouble spots.