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Harvard Forest Data Archive

HF340

Synthesis of Sarracenia Research in North America 1982-2018

Related Publications

Data

  • hf340-01: scaling sarracenia code and data

Overview

  • Lead: Aaron Ellison, Nicholas Gotelli
  • Investigators:
  • Contact: Aaron Ellison
  • Start date: 1982
  • End date: 2018
  • Status: completed
  • Location: North America
  • Latitude: 30 to 60
  • Longitude: -135 to -50
  • Elevation: 0 to 1000 meter
  • Taxa: Fletcherimyia fletcheri, Habrotrocha rosa, Metriocnemus knabi (pitcher-plant midge), Sarracenia Sarracenia (American pitcher plants), Sarracenia purpurea (northern or purple pitcher plant), Sarraceniopus gibsoni, Wyeomyia smithii (pitcher-plant mosquito)
  • Release date: 2020
  • Revisions:
  • EML file: knb-lter-hfr.340.1
  • DOI: digital object identifier
  • EDI: data package
  • DataONE: data package
  • Related links:
  • Study type: long-term measurement, short-term measurement, historical, modeling
  • Research topic: biodiversity studies; conservation and management; ecological informatics and modelling; historical and retrospective studies; large experiments and permanent plot studies; physiological ecology, population dynamics and species interactions; regional studies
  • LTER core area: populations, organic matter, inorganic nutrients, disturbance
  • Keywords: atmospheric deposition, bacteria, carnivorous plants, competition, demography, food webs, nitrogen, nutrients, predation, rotifers
  • Abstract:

    This archive includes the raw data and code (R scripts) required to reproduce all of the analyses and figures in the book Scaling Sarracenia: Ecology of a Model System by Aaron M. Ellison and Nicholas J. Gotelli. The book is a synthesis of our 25 years of research on the northern (a.k.a. purple) pitcher plant Sarracenia purpurea viewed through the conceptual lens of “scale”: scaling ecological phenomena through levels of biological organization with a model organism, across time and space, and using macroecological relationships.

  • Methods:

    hf340-01-scaling-sarracenia-code-and-data.zip

    This WinZip archive contains all the materials for recreating the figures, models, and analyses in the book. These analyses were conducted in R version 3.6.3. At the time of this writing (26 May 2020), all the scripts execute without error in R 3.6.3 with packages (libraries) corresponding to that version of base R. Although some of the work was initially done through RStudio, this folder is not organized as an R project. However, all paths are relative, and will work correctly if you set the working directory to the \Scripts folder.

    We had to spend a surprising amount of time organizing and assembling these materials, and no matter how much annotation we have provided, we know from experience that it will never be enough for every possible user. Nevertheless, if you are a reasonably proficient R programmer, you should be able to reproduce our analyses without too much trouble.

    There are five folders located here in the root:

    \Scripts - This folder contains the primary set of files (.R) that you should work with for reproducing analyses and figures for each of the chapters. There is a corresponding subfolder for each numbered chapter and appendix in the book that contains the associated scripts (chapters or appendices without scripts do not have an associated folder). Scripts may source other scripts in \Source, or read text (.csv) data files in \Raw_Data or binary R data objects in \Data_Objects.

    \Raw_Data - This folder contains numbered subfolders for corresponding chapters; subfolders contain plain text files (.csv) of raw data or additional subfolders (to facilitate file organization) with .csv data files.

    \Data_Objects - This folder contains .rds files, which are R binary objects that can be opened with the R function readRDS({filename}). These objects are derived from files in \Raw_Data and are used to simplify and speed execution. All of the .rds objects can be recreated by one or more of the scripts in the \Source folder.

    \Source - This folder contains R scripts of helper functions that are used by other scripts and the R scripts used to create the binary .rds files in \Data_Objects

    \SchematicDrawings - These are pdf or powerpoint files (in separate subfolders corresponding to chapters) that do not have code or data associated with them.

    Each script in \Script has a consistent format:

    Script Name - corresponds to the figure or figure it creates, and the necessary analysis to create it.

    #Annotation - is a brief description of what the script is for, who wrote it (AME or NJG), and the date it was created.

    #Load Libraries - This section loads any packages from CRAN that are needed for the script to run. You will need to install these packages before you run the script. As noted above, all scripts were developed and run successfully using R version 3.6.3 and packages optimized for that release.

    #Source Data - calls (source({filename}) to run any file(s) in \Source that are needed for successful execution. Note that the path statement to the sourced script is a relative path assuming that the working directory is \Script (i.e., setwd(..\Script).

    #Read Data - All the read statements for the script are included here. These read statements point to data objects within either \Raw_Data or \Data_Objects. There is also a set of comments that provide the DOI for the publicy-accessible version of the dataset(s) archived by the Environmental Data Initiative (EDI) (https://environmentaldatainitiative.org/). Calls to local data files should always work. Calls to EDI should also work, but there is the possibility that they could be updated or appended in the future (or that the links might no longer work).

    Note that in some cases, the data sets are so small (such as model parameter values or small vectors of data taken from other published papers) that the values are input with assignment statements to create objects on the fly.

    Although many of the scripts do produce corresponding figures, we have commented out the lines of code needed to write the files to disk. Note also that the \Source function GGPlotTheme_SourceFile.R that provides theme settings for our plots loads the Gill Sans Monotype (Gill Sans MT) font.

  • Use:

    This dataset is released to the public under Creative Commons license CC BY (Attribution). Please keep the designated contact person informed of any plans to use the dataset. Consultation or collaboration with the original investigators is strongly encouraged. Publications and data products that make use of the dataset must include proper acknowledgement.

  • Citation:

    Ellison A, Gotelli N. 2020. Synthesis of Sarracenia Research in North America 1982-2018. Harvard Forest Data Archive: HF340.

Detailed Metadata

hf340-01: scaling sarracenia code and data

  • Compression: zip
  • Format: zip
  • Type: zip file