In arebruvold/targets_test: Demonstration of using neotoma with targets

Text based on plos sample manuscript, see https://journals.plos.org/ploscompbiol/s/latex

knitr::opts_chunk$set(echo = FALSE, include = TRUE, warning = TRUE, message = TRUE, error = TRUE)

#packages only loaded in this file
library("english")

#set default theme
theme_set(theme_bw())

# load required targets
tar_load(count_summary)

Introduction

The template for this manuscript was made with

rmarkdown::draft("manuscript", template = "plos", package = "rticles")

This also generated the csl and eps files and a sample bib file. I have changed the output in the YAML to use bookdown to allow cross-referencing to figures. The bibliography section in the YAML is given the dynamically updated bibliography file. The rticles package has templates for many journals.

Methods

Norwegian pollen data were downloaded from Neotoma and processed with the experimental package neotoma2tibble before pollen counts sums were calculated.

The target that downloads the pollen data uses dynamic branching. This means that if the list of required sites is updated, only the new sites need to be downloaded.

In a real project, use the renv package for dependency management.

All analyses were done in R v. r getRversion() [@R] and used neotoma v. r packageVersion("neotoma") [@neotoma] to extract pollen data from the Neotoma database, and tidyverse v. r packageVersion("tidyverse") [@tidyverse] for data manipulation. Packages targets v. r packageVersion("targets") [@targets], and rmarkdown v. r packageVersion("rmarkdown") [@rmarkdown1] were used to ensure reproducibility.

Results

r Words(length(tar_read(pollen_sites))) Norwegian pollen sites were downloaded from Neotoma (Fig. \@ref(fig:site-map)).

tar_read(site_map)

Count sums ranged between r count_summary$mn and r count_summary$mx (Fig. \@ref(fig:count-plot)).

tar_read(count_plot)

References {#references .unnumbered}

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