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MGMS2

Membrane Glycolipid Mass Spectrum Simulator for polymicrobial samples

User

Installation

Production Version

install.packages(c("MALDIquant","MALDIquantForeign"),type="source")
install.packages("MGMS2")
library("MGMS2")

or

R -e 'install.packages("MGMS2")'

Development Version

install.packages(c("MALDIquant","MALDIquantForeign"),type="source")
devtools::install_github("unreno/MGMS2")
library("MGMS2")

or

R -e 'devtools::install_github("unreno/MGMS2")'

Usage

library('MGMS2')

Removal

remove.packages("MGMS2")

Developer

Initial Creation

install.packages(c('devtools','roxygen2'))
library('devtools')
library('roxygen2')
create('MGMS2')

The “create()” function fails with “Error: Directory ‘MGMS2’ does not exist.” after it creates DESCRIPTION and NAMESPACE files and an empty R/ dir. Kinda pointless. Could’ve just used a simple template for this. Is that what its supposed to do?

Creation / Updation / Posting

Create/Edit .R files in R/ folder with properly formated documentation above functions.

Then update NAMESPACE and man/ from within R …

library('devtools')
document()

Or from the bash command line …

R -e 'library(devtools);document()'

Install from the bash command line …

R -e 'library(devtools);document();setwd("..");install("MGMS2",upgrade=FALSE)'

Or from R with some manual checking with sample data …

remove.packages("MGMS2")
library('devtools')
document()

setwd('..')
install('MGMS2',upgrade=FALSE)
library('MGMS2')
lsf.str("package:MGMS2")
"MGMS2" %in% rownames(installed.packages())



spectra.processed.A <- process_monospectra(
    file=system.file("extdata", "listA.txt", package="MGMS2"),
    mass.range=c(1000,2200))
spectra.processed.B <- process_monospectra(
    file=system.file("extdata", "listB.txt", package="MGMS2"),
    mass.range=c(1000,2200))
spectra.processed.C <- process_monospectra(
    file=system.file("extdata", "listC.txt", package="MGMS2"),
    mass.range=c(1000,2200))

spectra.mono.summary.A <- summarize_monospectra(
    processed.obj=spectra.processed.A,
    species='A', directory=tempdir())
spectra.mono.summary.B <- summarize_monospectra(
    processed.obj=spectra.processed.B,
    species='B', directory=tempdir())
spectra.mono.summary.C <- summarize_monospectra(
    processed.obj=spectra.processed.C,
    species='C', directory=tempdir())

mono.info=gather_summary(c(spectra.mono.summary.A, spectra.mono.summary.B, spectra.mono.summary.C))

gather_summary_file(directory=tempdir())

mixture.ratio <- list()
mixture.ratio['A']=1
mixture.ratio['B']=0.5
mixture.ratio['C']=0

sim.template <- create_insilico_mixture_template(mono.info)

insilico.spectrum <- simulate_poly_spectra(sim.template, mixture.ratio)

insilico.spectrums <- simulate_many_poly_spectra(mono.info, mixture.ratio=mixture.ratio, nsim=10 )







remove.packages("MGMS2")

ADD AUTOMATED TESTING

ADD AUTOMATED VERSIONING

Then commit and push to github repo

git commit -m "<LIST UPDATES>" -a
git push

https://cran.r-project.org/

https://xmpalantir.wu.ac.at/cransubmit/

Check for CRAN issues …

R -e 'library(devtools);document();setwd("..");install("MGMS2",upgrade=FALSE)'
VERSION=$( awk '(/^Version/){print $2}' DESCRIPTION )
cd ..
R CMD build MGMS2
R CMD check MGMS2_${VERSION}.tar.gz
R CMD check --as-cran MGMS2_${VERSION}.tar.gz

If all is well, try to submit to CRAN

Packaging References

https://hilaryparker.com/2014/04/29/writing-an-r-package-from-scratch/

https://kbroman.org/pkg_primer/

https://aberdeenstudygroup.github.io/studyGroup/lessons/SG-T4-Rpackages/makingRpackages1_Intro/

http://r-pkgs.had.co.nz

https://r-pkgs.org/release.html

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.
Health stats visible at Monitor.