In arebruvold/targets_test: Demonstration of using neotoma with targets

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neotomaTargets

neotomaTargets is a template for reproducible research using data from the Neotoma database using the targets pipeline.

It includes sample code for downloading data from Neotoma, cleaning the data, analysing the data, and writing a manuscript with R markdown, all in a targets pipeline.

The aim is that you can make a copy of the template and modify it to write your own reproducible manuscripts.

Installation

neotomaTargets is a template repository.

Click on the :green_square: Use this template :green_square: button and follow the instructions to make a copy of this repo into your own account.

neotomaTargets depends on the neotoma and targets packages and some others listed in the DESCRIPTION file. To install these packages, use

devtools::install_deps()

Using neotomaTemplate

To run all the analyses and produce the manuscript, open "make.R" and run tar_make(). This finds the target plan in "_targets.R" (this file must have this name and be in the working directory), which is assembled from sub-plans in "R/*-plan.R" files. If you modify any of the sub-plans and re-run tar_make() only targets which have been outdated will be re-run.

arebruvold/targets_test documentation built on Dec. 19, 2021, 4:37 a.m.