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ltertools - Tools Developed by the Long Term Ecological Research Community

R-CMD-check GitHub issues GitHub pull requests

The goal of ltertools is to centralize the R functions created by members of the Long Term Ecological Research (LTER) community. Many of these functions likely have broad relevance that expands beyond the context of their creation and this package is an attempt to share those tools and limit the amount of “re-inventing the wheel” that we each do in our own silos.

The conceptual theme of functions in ltertools is necessarily broad given the scope of the community we aim to serve. That said, the identity of this package will likely become more clear as we accrue contributed functions. In the meantime, please do not hesitate to add or request a function for fear that it doesn’t “fit” this package. That may eventually become a concern but at this stage we are aiming to house all extant functions regardless of their relatedness to one another.

Installation

You can install the development version of ltertools from GitHub with:

# install.packages("devtools")
devtools::install_github("lter/ltertools")

Function Overview

As functions are added to the package they will be briefly summarized below and attributed to their author(s)

Reproducibility

  • make_json – creates a JSON containing name/value pairs from a named vector. If desired, can also add the created JSON’s filename to the .gitignore (if one exists in the working directory)

Harmonization

  • begin_key – creates the first two columns of a ‘column key’ and–if the optional guess_tidy argument is set to TRUE–“guesses” at what the tidy names ‘should be’

  • harmonize – performs column key-based harmonization. We strongly recommend using the begin_key to start the creation of a column key to make sure the formatting requirements of this function are met

Data Wrangling

  • read – Reads in all files of specified types in a particular folder and stores them as elements in a list. List element names are the respective file names. Currently supports CSV, TXT, XLS, and XLSX file formats

  • solar_day_info – Identify sunrise, sunset, solar noon, and day length for all dates within a user-specified range at particular coordinates. Function concept contributed by Miguel C. Leon

  • cv – Calculate coefficient of variation (CV) from a vector of numbers

  • convert_temp – Convert temperature values from one set of units to another

LTER Information

  • site_timeline – Create a timeline of sites that meet user-specified site code and/or habitat criteria. Uses built in lter_sites data object that includes much useful site information

Contributing

See CONTRIBUTING.md for specifics but at a glance:

  • To contribute one of your functions in exchange for authorship credit: open a GitHub issue

  • To suggest minor fixes or point out bugs: open a GitHub issue

  • To implement major / structural changes: fork the repository, add your content to the dev folder, and open a pull request when you are finished

ltertools will maintain a consistent “feel” and style of functions but we (the maintainers) are happy to perform these edits on your behalf. If you’d like to take care of this yourself (completely optional!) you are welcome to do so. Please see CONTRIBUTING.md for a specific style guide.

Synonymous Function Procedure

If you would like to contribute a function that is similar to a function that already exists in ltertools please do not hesitate! In the event that this happens, the following steps will be followed:

  1. The functions will be combined to preserve the earlier function’s elements while expanding to include the maximum number of novel features (i.e., arguments / options)

    • The older function’s name will be retained to avoid unnecessary deprecation flags

  2. Both function authors will be credited in the combined function’s description and in this README (see above)