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enveomics.R

Installing enveomics.R

To install the latest version of enveomics.R uploaded to CRAN, execute in R:

install.packages('enveomics.R')

To install the current developer version of enveomics.R, execute in R:

install.packages('devtools')
library('devtools')
install_github('lmrodriguezr/enveomics', subdir='enveomics.R')

Using enveomics.R

To load enveomics.R, simply execute:

library(enveomics.R);

And open help messages using any of the following commands:

?enveomics.R
?enve.barplot
?enve.recplot2
?enve.recplot2.compareIdentities
?enve.recplot2.changeCutoff
?enve.recplot2.findPeaks
?enve.recplot2.corePeak
?enve.recplot2.windowDepthThreshold
?enve.recplot2.extractWindows
?enve.recplot2.coordinates
?enve.recplot2.seqdepth
?enve.recplot2.ANIr
?enve.prune.dist
?enve.tribs
?enve.tribs.test
?enve.growthcurve
?enve.col.alpha
?enve.truncate

You can run some examples using these libraries in the enveomics-GUI.

For additional information on recruitment plots, see the Recruitment plots working document.

Changelog

• 1.8.0: New functions enve.selvector and enve.prefscore.
• 1.7.1: Improved efficiency of enve.df2dist about five-fold.
• 1.7.0: Uniformized output for enve.recplot2.extractWindows and enve.recplot2.coordinates to ease automation. Thanks to Tomeu Viver and Roth Conrad for troubleshooting.
• 1.6.0: Speed up in recplot2 with proper structure manipulation (by: Kenji Gerhardt). Also, default value for id.breaks was changed from 300 to 60.
• 1.5.0: Modernized documentation, now in ROxygen2 (by: Tatyana Kiryutina)
• 1.4.4: Removes modeest library as requirement, and replaces mower peak-finder initialization to median (instead of mode).
• 1.4.2: Solved bug #36.
• 1.4.0: New option pos.breaks.tsv for enve.recplot2.
• 1.3.4: Gracefully handles and plots recruitment plots with insufficient data to find peaks.
• 1.3.3: New function enve.recplot2.windowDepthThreshold.
• 1.3.2: New option panel.fun for plot.enve.RecPlot2.
• 1.3.1: New function enve.truncate.
• 1.3: Several bug fixes and new utilities for recruitment plots (recplot2).
• 1.1.0: New function enve.growthcurve and related class enve.GrowthCurve with S3 methods plot and summary.
• 1.0.2: Fine-tuned default parameters in enve.recplot2.findPeaks and solved a minor bug in enve.recplot2 that caused failures in low-coverage datasets when using too many threads.
• 1.0.1: enve.recplot2 now supports pos.breaks=0 to define a bin per subject sequence.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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