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Working R scripts and relevant .csv files

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These are all the files that currently work, including the output files so you don't have to actually run the R scripts!

AbunData.csv by Jennifer Plaut — last modified 2008-05-29 11:29
This is the cleaned-up WAT013.csv; the format is NOT appropriate for any kind of data analysis, though!
WAT013.csv by Jennifer Plaut — last modified 2008-05-29 11:31
This is the raw data downloaded from the Konza LTER website; the most recent several years of data were given to us by ___________. Prior to inputting these data, the modified Daubenmire scale abundances were converted to percent cover and zeros were inserted for absences. The data on the website also show two sets of data from 1999 control plots 1-15; the data taken on 7/31/99 actually belong in the 2000 dataset (which is missing plots 1-15 control) and have been re-assigned.
WAT013_clean.R by Jennifer Plaut — last modified 2008-05-29 11:33
This R script cleans up WAT013.csv; it standardizes attributes, corrects some species mis-numberings, and gives upper and lower plot mean abundances.
richness.R by Jennifer Plaut — last modified 2008-05-29 11:35
This R script generates .pdf graphs of species richness changes through time.
traits.csv by Jennifer Plaut — last modified 2008-05-29 11:37
The raw traits file.
clean_traits.R by Jennifer Plaut — last modified 2008-06-02 09:37
This R script cleans up traits.csv, standardizing attributes, and outputs clean.traits.csv.
clean.traits.csv by Jennifer Plaut — last modified 2008-06-02 09:43
This is the standardized traits data, to be used for analyses.
species.grid.R by Jennifer Plaut — last modified 2008-05-29 11:52
This R script prompts the user to run mk.grid.R and fill.grid.R, using AbunData.csv to create a species-based abundance table (Full.grid.csv). Index columns are year (1991-2006), treatment (c=control, i=irrigated), elevation (l=lower, u=upper), transect (1 or 2 for each treatment), and plot (1-31, non-continuous). Remember that we have two transects per treatment; T1 is plots 1-15 (1-5 are lower, 10-15 are upper) and T2 is plots 16-31 (16-20 are lower, 27-31 are upper). No T2 data for 1991 and 1992 and we are not dealing with the mid-slope plots.
mk.grid.R by Jennifer Plaut — last modified 2008-05-29 11:53
Generates an empty table for the species-based abundance data.
fill.grid.R by Jennifer Plaut — last modified 2008-05-29 11:54
This R script fills the empty grid from mk.grid.R with data from AbunData.csv. Run these two files in order using the species.grid.R script!
Full.grid.csv by Jennifer Plaut — last modified 2008-05-29 11:55
This is the key species-based abundance table, to be used for analysis. Index columns are year (1991-2006), treatment (c=control, i=irrigated), elevation (l=lower, u=upper), transect (1 or 2 for each treatment), and plot (1-31, non-continuous). Remember that we have two transects per treatment; T1 is plots 1-15 (1-5 are lower, 10-15 are upper) and T2 is plots 16-31 (16-20 are lower, 27-31 are upper). No T2 data for 1991 and 1992 and we are not dealing with the mid-slope plots.
trait.grid.R by Jennifer Plaut — last modified 2008-06-02 11:09
This is code from Dan Bunker which uses Full.grid.csv and clean.traits.csv to generate traits.grid.csv. You will need to download the "reshape" and "Hmisc" packages for R. I haven't fully commented this yet, but it runs fine.
trait.grid.csv by Jennifer Plaut — last modified 2008-06-02 11:10
This is the output from traits.grid.R - abundances summed by trait (for the categorical traits) with the same index columns as Full.grid.csv, the species-based table.
trait.relabun.R by Jennifer Plaut — last modified 2008-06-02 11:12
Uses the raw abundances in trait.grid.csv to calculate the relative abundances for each trait and output trait.relabun.csv. The only thing I can't get it to do is reduce the ridiculous number of significant digits it outputs - anybody got any ideas?
trait.relabun.csv by Jennifer Plaut — last modified 2008-06-02 11:13
This is the relative abundances of each trait on each plot; it's the output of trait.relabun.csv and it's what we should be using for analysis.
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