PathoStat New package submission

[mani2012]

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[bioc-issue-bot]

Hi @mani2012

Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: PathoStat
Type: Package
Title: PathoStat Statistical Microbiome Analysis Package
Version: 0.99.0
Date: 2016-09-25
Author: Solaiappan Manimaran <manimaran_1975@hotmail.com>, 
    Matthew Bendall <bendall@gwmail.gwu.edu>, 
    Sandro Valenzuela Diaz <sandrolvalenzuelad@gmail.com>, 
    Eduardo Castro <castronallar@gmail.com>, 
    Tyler Faits <tfaits@gmail.com>, 
    W. Evan Johnson <wej@bu.edu>
Maintainer: Solaiappan Manimaran <manimaran_1975@hotmail.com>
Description: The purpose of this package is to perform Statistical 
    Microbiome Analysis on metagenomics results from sequencing data samples. 
    In particular, it supports analyses on the PathoScope generated report 
    files. PathoStat provides various functionalities including Relative 
    Abundance charts, Diversity estimates and plots, tests of Differential 
    Abundance, Time Series visualization, and Core OTU analysis. 
URL: https://github.com/mani2012/PathoStat
BugReports: https://github.com/mani2012/PathoStat/issues
License: GPL (>= 2)
Depends: R (>= 3.3.1)
Imports:
    MCMCpack,
    limma,
    corpcor,
    rmarkdown,
    knitr,
    pander,
    matrixStats,
    reshape2,
    scales,
    ggplot2,
    rentrez,
    BatchQC,
    DT,
    gtools,
    tidyr,
    plyr,
    dplyr,
    ape,
    phyloseq,
    shiny,
    grDevices,
    stats,
    methods,
    XML,
    graphics,
    utils,
    alluvial
Collate:
    'pathoStat.R'
    'utils.R'
    'taxonomy.R'
    'confRegion.R'
    'allClasses.R'
    'coreOTUModule.R'
Suggests: testthat
biocViews: Microbiome, Metagenomics, GraphAndNetwork, Microarray, 
    PrincipalComponent, Sequencing, Software, Visualization, RNASeq
SystemRequirements: pandoc (http://pandoc.org/installing.html) for generating
    reports from markdown files.
VignetteBuilder: knitr
RoxygenNote: 5.0.1

[bioc-issue-bot]

Your package has been approved for building. Your package is now submitted to our queue.

IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your repository will NOT trigger a new build.

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/PathoStat_buildreport_20160926070942.html

[mtmorgan]

DESCRIPTION

• Looks good!

vignettes

• Once in Bioconductor, biocLite('PathoStats') installs dependencies, so these do not need to be enumerated at PathoStatIntro.Rmd:41
• consider naming chunks {r setup, options...} to help debug when errors occur.
• Provide a more comprehensive vignette that describes in greater detail the inputs and outputs of the main package functions, so that someone reading the vignette gains a comprehensive understanding of what the package does, how the package can be used for analysis of their own data, and how the package works with other Bioconductor packages.

R

• The following comments are about specific lines of code, but there are many examples of similar issues throughout.
• no need to require(phyloseq) in allClasses.R or other packages (e.g., library(gtools) in confRegion.R), provided the NAMESPACE file is formulated properly.
• avoid 1:n (e.g., cnofRegion.R:6) in favor of seq_len() or seq_along() (avoids issues when n == 0).

• vectorize, rather than iterate, e.g., (there are important issues like this throughout the code)

  for (i in 1:3)  {
      if (x[i] <= 0)  {
          x[i] = delta
      }
  }

  is x[x[i] < 0] = delta

• simplify

  check <- FALSE
  if (chi < chisqval) {
    check <- TRUE
  }
  return (check)

  as simply returning chi < chisqval

• if a loop involves a part that can be vectorized and a part that cannot, separate these. Use the 'apply' family rather than iteration where possible; it simplifies memory management. For instance, confRegion.R:95

  for (i in 1:n) {
    me <- confinterval(A[,i], size)
    p1up <- p1up + A[,i][1]+me[1]
    p1low <- p1low + A[,i][1]-me[1]
    p2up <- p2up + A[,i][2]+me[2]
    p2low <- p2low + A[,i][2]-me[2]
  }

  might be (untested!)

  me <- apply(A, 2, confinterval, size)
  p1up <- sum(A[1,] + me[,1])
  ...

• coreOTUModule.R:32 avoid highly nested evaluations that make code difficult to parse and debug, e.g.,

  coremat <- data.frame(do.call(rbind, lapply(prev, function(p){
    sapply(det, function(d) sum(rowSums(otu_table(pstat) >= d) >= p))
  })))

  It looks like in this code chunk otu_table(pstat) is being called repeatedly; this expression should be 'hoisted' from the body

  otu_pstat = otu_table(pstat)

  it then seems that rowSums(otu_pstat >= d) is calculated for each p, so again hoist outside the inner loop

  otu_d <- sapply(det, function(d) rowSums(otu_pstat >= d))

  the lapply() seems like it'll always return a single scalar, so

  det <- sapply(prev, function(p) sum(otu_d > p))

  and the original chunk of code is

  otu_pstat = otu_table(pstat)
  otu_d <- sapply(det, function(d) rowSums(otu_pstat >= d))
  det <- sapply(prev, function(p) sum(otu_d > p))
  data.frame(det=det, prev=prev)

  this is both easier to understand and faster. In particular the original formulation scaled as the product of the length of det and prev, whereas the updated formulation scales as the sum of these lengths.

  A further improvement would use vapply() rather than sapply().

  Please review all of your code for similar issues.

• consider indenting code at coreOTUModule.R:55 to improve readability
• utils.R:46 this 'copy-and-append' strategy (also line 56, for instance) has very poor memory cahracteristics; use lapply() (and unlist()?) to avoid the need to explicity grow memory.

man

• Aim for all man pages to have runnable examples, e.g., coreOTUModule.Rd, coreOTUModuleUI.Rd
• clearly mark documented functions that are not exported, e.g,. findTaxonLevelData, as 'INTERNAL'.

[bioc-issue-bot]

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

[bioc-issue-bot]

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

[bioc-issue-bot]

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

[bioc-issue-bot]

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

[bioc-issue-bot]

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

e25f193 Fixing based on inputs from Bioconductor review by...

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/PathoStat_buildreport_20161003202552.html

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

9c85c6d Adding automatically suggested PatternLogic to bio...

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/PathoStat_buildreport_20161003205445.html

[mani2012]

Hi Martin, Thank you so much for your review and comments, which were very helpful. We have updated our PathoStat package based on your review and suggestions.

We have followed all your suggestions for updating the R code, and we have addressed all those issues. The only NOTE on 'Adding runnable examples for coreOTUModule.Rd', we would like to mention that we have added example codes for how this coreOTUmodule can be included in another shiny app, but this function is not to be called directly by the user of our PathoStat package (we have used the dontrun directive for this purpose) ; it will only be useful for calling this function from another shiny app with the shiny server input.

For the vignette, we are working on creating another more comprehensive vignette. We shall shortly add the detailed vignette to the package. Could you please review our PathoStat package again to make sure that there are no other issues?

Thanks, Mani

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

0d70def Calculating the confidence interval boundary marke...

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/PathoStat_buildreport_20161005214749.html

[mtmorgan]

Thank you for your changes so far. I think the only remaining issue is the vignette.

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

81234b2 Checking the confidence region on the jittered poi...

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/PathoStat_buildreport_20161007123256.html

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

66c16d6 Fixing Warning in log(p/(1 - p)) : NaNs produced

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/PathoStat_buildreport_20161007150443.html

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

4c2a078 Adding detailed PathoStat User Manual and PathoSta...

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "WARNINGS". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/PathoStat_buildreport_20161011021951.html

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

be9540d Fixing some BiocCheck WARNINGS and NOTES

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/PathoStat_buildreport_20161011024837.html

[mani2012]

Hi Martin,

Thanks again for your review. We have now added a detailed PathoStat User Manual and PathoStat Advanced Usage vignettes to our package.

We look forward to having our package added to the BioConductor release.

Thanks, Mani

[mtmorgan]

Thanks for your work on this package, it looks great, and I am happy to accept it to Bioconductor. It will be added to the Bioconductor svn repository and nightly builds. You will receive additional information in the next several days.