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Data and analysis of the Schefferville Experiment on Climate Change (& Habitat Fragmentation / Isolation), in the R statistical computing environment.

branch: master

Effect Sizes for aov(): test code & TODO

Added test code to summary_ES(), also confirming that this will not work
(and is unnecessary) for lm, and lme output.
Updated TODO, marking this task as complete.
latest commit 95ca9a1a4f
Jonathan Whiteley authored
CH4-model-fitting Refined figures for thesis
Fauna Refined figures for thesis
Nfix-Cyanobacteria Refined figures for thesis
SECCanova Effect Sizes for summary() of aov, aovlist
_temp Changed references to 'other' patch positions to "intermediate"
data N: updated some of the notes & comments in raw N data
doc minor edits to metadata in /doc/SECC-Naming-Conventions.txt
lib Effect Sizes for aov(): test code & TODO
output Effect Sizes for summary() of aov, aovlist
save Refined figures for thesis
.RData Reset contrast options in `init.R`
.gitignore Added an Icon (Mac-specific): do not track (.gitignore)
ARA.R Updated figures for CH1 scripts for Oecologia (as requested by editor).
Cyanobacteria.R Updated figures for CH1 scripts for Oecologia (as requested by editor).
Decomposition.R Decomposition plots: points over lines
H2O.R Tweaks to large multi-panel FxP graphs (H2O, Patch.dwt)
Moss-Prod-Decomp.R Moss Growth - Productivity: updated graphs
Moss-dwt.R Tweaks to large multi-panel FxP graphs (H2O, Patch.dwt)
Moss-growth.R Moss Growth: Notes regarding borderline significant Fragmentation eff…
Moss_biomass.R Changed references to 'other' patch positions to "intermediate"
N-available-time.R Updated figures (and export settings) to make figure labels bigger in…
N-available.R Changed references to 'other' patch positions to "intermediate"
README README and GNU GPLv3 license
SECC-Data-Template.R SECC Data template update with new factor levels
TODO Effect Sizes for aov(): test code & TODO
_CH1-ARA-cb.R Reset contrast options in `init.R`
_CH2-fauna.R Re-ran Ch2 - Fauna analyses
_CH3-prod-decomp.R H2O graphs for t4 only (24 months), for follow-up chapters (to remind…
_CH4-Synthesis.R CH4: TAN ANOVA - fixed erroneous transformation, re-ran analyses
_Main.R Reset contrast options in `init.R`
do.R Initial commit
README
SECC: The Schefferville Experiment on Climate Change (and Habitat Fragmentation / Isolation)
================================================================

This repository contains data and analysis from my a field experiment set up in Schefferville, Quebec,
as part of Jonathan Whiteley's PhD thesis at McGill University (Montreal, QC, Canada), with Dr. Andrew Gonzalez and Dr. Zoë Lindo.
This repository also contains processing and analysis scripts, written in the [R statistical computing language][R].

    [R]: http://r-project.org

Raw data files in `csv` format are stored in the `/data` directory.  
Scripts to process and load the raw data into a format ready for analysis are in the `/lib` directory, along with most functions used throughout the project.
The processed data and other objects are stored in the `/save` directory for fast loading.  
**More detailed instructions on using the data and files in this repository can be found in files in the `/doc` directory.**

*Scripts can load all data and functions simply by running the code in `/lib/init.R`, or the following line of R code* (after setting the working directory to the root `SECC` directory for the project):

    setwd('./ SECC/')       # replace the path with what works on your system
    source('./lib/init.R')

The code in `/lib/init.R` includes `rm(list=ls())` to clear all memory.  
Therefore, the code above should be one of the first lines in a script (after setting the working directory), without relying on other objects in memory.  
If other objects are required, I suggest saving them to disk (e.g. to `/save`), and load them after running `/lib/init.R`.


The organization of the source code in this project is loosely based on the approach used by the [`ProjectTemplate` package in R](http://www.johnmyleswhite.com/notebook/2010/08/26/projecttemplate/)

    This repository, including data and source code, is Copyright (C) 2011  Jonathan Whiteley

    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.


For questions, or comments, feel free to contact the primary author of this code:

Jonathan Whiteley  
Department of Biology  
McGill University  
1205 Docteur Penfield Ave.  
Montréal, QC    H3A 1B1  

jonathan.whiteley@mail.mcgill.ca  
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