Cristian Correa and Andrew P. Hendry. 2012. Invasive salmonids and lake order interact in the decline of puye grande Galaxias platei in western Patagonia lakes. Ecological Applications 22:828–842.

Supplement

R source code and data.
Ecological Archives A022-045-S1.

Copyright

Authors
File list (downloads)
Description

Author(s)

Cristián Correa
Redpath Museum & Dept of Biology
McGill University
859 Sherbrooke Street West
Montreal, Quebec H3A 2K6, Canada
E-mail: cristian.correa@mail.mcgill.ca
cristiancorrea@gmail.com

Andrew Hendry
Redpath Museum & Dept of Biology
McGill University
859 Sherbrooke Street West
Montreal, Quebec H3A 2K6, Canada

File list

Galaxias_eclipsed_by_aliens-RCode.R (md5: fc6e794b5c6fc3d6aeddf0a0e9e2f7cd)

Galaxias_eclipsed_by_aliens-Data.csv (md5: 9686361dbb5fe4416852e983afa7b334)

Description

The R source code “Galaxias_eclipsed_by_aliens-RCode.R” is used to manipulate and analyze the data contained in the “Galaxias_eclipsed_by_aliens-Data.csv” file. Specifically, the code imports the data; conducts principal component analyses on fish catch-per-unit effort (CPUE) data and calculates the fish’s indices of abundance; compares environmental variables between invaded and uninvaded lakes; fits all models in the model set (Table 1, main article); rank the fitted models and produces an AICc table; and examines the properties of the top-ten models (those ranked superior to the naïve model). A similar analysis is also conducted using CPUE data in stead of indices of abundance. Throughout the data manipulation and analysis, the code produces multiple tables and plots that help visualizing and interpreting the results. 

The data file contains the following variables as specified in the paper (see also the Appendices):

Column title	Checksum	Definition
Name	NA	Lake's name.
Area.ha	10747.13	Lake area (ha)
ShD	45.18	Shoreline development index.
Altitude.m	11957.00	Altitude (m).
Order	40.00	Lake order (Strahler stream order at lake outlet).
Depth_max.m	962.00	Maximum depth (m).
Spec_Cond.uS	1470.95	Specific conductivity (μS).
Secci.m	180.00	Secchi disk readings (m).
Defor.perc	1192.31	Percentage of deforested area within a lake basin (Appendix B).
platei_traps	-20.67	Catch-per-unit-effort (CPUE) of G. platei using traps. Transformed mean number of fish per trap [y' = ln(y + 0.1)].
platei_elec	14.84	CPUE of G. platei using elecrofishing. The catch-per-transect was divided by the total discharge time (min), and the resulting values were averaged across transects and then transformed [z' = ln(z + 1)].
mykiss_elec	0.99	CPUE of O. mykiss using elecrofishing. Details as in platei_elec.
trutta_elec	2.95	CPUE of S. trutta using elecrofishing. Details as in platei_elec.
trout_elec	3.77	CPUE of trout (species pooled) using elecrofishing. Details as in platei_elec.
platei_gillnet	18.21	CPUE of G. platei using gillnets. The average overnight catch-per-net was calculated and transformed for analysis [x' = ln(x + 1)].
mykiss_gillnet	11.34	CPUE of O. mykiss using gillnets. Details as in platei_gillnet.
trutta_gillnet	22.66	CPUE of S. trutta using gillnets. Details as in platei_gillnet.
trout_gillnet	31.39	CPUE of trout (species pooled) using gillnets. Details as in platei_gillnet.