/au-r-workshop-data

This repository houses the data used in R workshop (and book): Introduction to R for Natural Resource Scientists

Primary LanguageR

au-r-workshop-data

This repository houses the data for the R workshop and book: Introduction to R for Natural Resource Scientists. The book is located at the URL: https://bstaton1.github.io/au-r-workshop/.

To acquire the data for this book, you should:

  1. click the green Clone or download button at the top right of this page,
  2. click Download ZIP,
  3. and unzip the contents of this folder into the location on your computer: C:/Users/YOU/Documents/R-Book/Data

Where YOU is replaced with something specific to your computer. The full file path does not need to be the same as above, but it is recommended to at least maintain the /R-Book/Data portion. Make sure you place this somewhere easy to find on your computer.

Data Sets

The contents of each data file is described below, listed in alphabetical order.

asl.csv

Description

Contains the ages, sexes, and lengths of approximately 50,000 Chinook salmon (Oncorhynchus tshawytscha) sampled over 50 years (1996-2015).

Source: simulated by author

Variables:

  • year: the year the individual fish were sampled
  • sex: the sex of the sampled fish
  • age: the age of the sampled fish
  • length: the length of the sampled fish, in mm, mid-eye to fork of tail length

Found in Chapter(s): 5

creel.csv

Description

Contains the number of hours fished by 300 anglers separated by the fishery sector each angler participated in.

Source: simulated by author

Variables:

  • fishery: the fishery sector the angler participated in: "Harvest", "Non.Tournament", "Tournament"
  • hours: the number of reported hours the angler fished in the year of interest.

Found in Chapter(s): 2

daily_catch.csv

Description

Contains the daily harvest of pink salmon (Oncorhynchus gorbuscha) in a commercial fishery. Records span the same 50 days in each of 50 consecutive odd-numbered years (1917-2015).

Source: simulated by author

Variables:

  • doy: the day of the year the observation corresponds to.
  • y_*: 50 columns which separate the year each observation corresponds to.

Found in Chapter(s): 5

daily_escape.csv

Description

Contains the daily escapement counts of pink salmon (Oncorhynchus gorbuscha) made at a counting tower. Records span the same 50 days in each of 50 consecutive odd-numbered years (1917-2015).

Source: simulated by author

Variables:

  • doy: the day of the year the observation corresponds to.
  • y_*: 50 columns which separate the year each observation corresponds to.

Found in Chapter(s): 5

feeding.csv

Description

Contains the results of an experiment where the investigator manipulated the density of a prey item and observed how many were consumed by a predator in a given time interval. The experiment was replicated 50 times at randomly-generated prey densities.

Source: simulated by author

Variables:

  • prey: the density of the prey item
  • cons*: the number of prey consumed by the predator

Found in Chapter(s): 4

growth.csv

Description

Contains 100 samples taken randomly from a fish population. The length (total length; mm) and age (years) are recorded.

Source: simulated by author

Variables:

  • age: the age of the fish in years
  • length: the total length of the fish in mm.

Found in Chapter(s): 3,4

ponds.csv

Description

Contains data from a hypothetical pond experiment. Nutrients were experimentally added to 5 replicated mesocosms within two different ponds. The ponds had 5 replicate mesocosms for the control group (no nutrients added) per pond as well.

There is an error in this data set you should fix using a spreadsheet program before reading it into R (this was intentional).

Source: simulated by author

Variables:

  • pond: identifier for the pond: S.28 or S.30
  • treatment: identifier for the treatment type: Add or Control
  • replicate: the id for the replicate within each pond/treatment combination
  • chl.a: measurements of average chlorophyll a present in each mesocosm
  • daph, bosm, cope, and chao: measurements of average density of four zooplankton taxa in each mesocosm

Found in Chapter(s): 1,4

sockeye.csv

Description

Contains records of various biological variables measured for both hatchery and wild fish in paired years from the Redfish Lake sockeye salmon (Oncorhynchus nerka) in Idaho.

Source: Kline and Flag (2004)

Variables:

  • year: the year the observation corresponds to
  • type: the type of fish the observation corresponds to
  • weight: the average weight (grams) of fish
  • fecund: the average number of eggs carried by females
  • egg_size: the diameter of the average egg (mm)
  • survival: the average percent survival of all eggs laid to the eyed-egg stage

Found in Chapter(s): 2,3,4

streams.csv

Description

Contains information on 20 streams in the Southeastern United States.

Source: simulated by the author

Variables:

  • state: the state the stream is located in
  • stream_width: the width of the stream
  • flow: the flow rate of the stream (volume/sec)

Found in Chapter(s): 1

Chapter 6 Data

There is a separate folder in this directory devoted to Chapter 6. Some of these files are shapefiles (.shp), and are stored in folders that contain other associated files. This file structure is standard for geospatial data.

bear.csv

Description

Contains (among many other things) the dates, locations, and IDs of brown bears (Ursus arctos) tracked via telemetry around Slovenia.

Source:

Kaczensky, P., F. Knauer, M. Jonozovic, and M. Blazic. 1999. "Slovenian Brown Bear 1993-1999 Telemetry Data Set." https://www.movebank.org/panel_embedded_movebank_webapp?destination=panel_embedded_movebank_webapp.

Variables:

  • Too many to list here. Take a look at the file, the important variables are fairly self-explanatory.

Found in Chapter(s): 6

caves

Description

Contains the locations of ecologically important caves in Slovenia.

Source:

Republic of Slovenia, Environmental Agency of the. 2018. "Ecologically Important Areas (Caves)." http://gis.arso.gov.si/geoserver/ows?SERVICE=WFS&REQUEST=GetFeature&VERSION=1.1.0&TYPENAME=arso:EPO_JAME&PROPERTYNAME=SHAPE,ID_STEV,IME&OUTPUTFORMAT=SHAPE-ZIP&format_options=charset:UTF-8.

Variables:

  • latitude and longitude (points) of the caves in Slovenia.

Found in Chapter(s): 6

railways

Description

Contains the track of railways in Slovenia.

Source:

MapCruzin. 2018. "Slovenia Railways [Computer File]." http://www.mapcruzin.com/download-shapefile/slovenia-railways-shape.zip.

Variables:

  • latitude and longitude (polylines) of the railways in Slovenia.

Found in Chapter(s): 6

SVN_adm

Description

Contains three shapefiles, only two are used:

  • SVN_adm0.shp: contains the political boundary of Slovenia
  • SVN_adm1.shp: contains the political boundaries of the states of Slovenia.

Source:

Boundaries, Global Administrative. 2018. "Slovenia Geopackage [Computer File]." https://biogeo.ucdavis.edu/data/gadm3.6/gpkg/gadm36_SVN_gpkg.zip

Variables:

  • the latitude and longitude (polygons) of the political boundaries.

Found in Chapters(s): 6

points_to_line.R

A user-defined function that takes a set of points and turns them into polylines. Optionally, the data can be passed arguments to sort the points in a track or to group them as separate lines via an ID variable.

Source:

Walker, Kyle. 2015. "Convert Xy Coordinates to Lines in R." Rpubs. https://rpubs.com/walkerke/points_to_line.