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')
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.
- 1.8.0: New functions
enve.selvector
andenve.prefscore
. - 1.7.1: Improved efficiency of
enve.df2dist
about five-fold. - 1.7.0: Uniformized output for
enve.recplot2.extractWindows
andenve.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
forenve.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
forplot.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.