CRAN Package Check Results for Package bayescount

Last updated on 2014-04-17 10:47:45.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.9.9-1 1.35 25.02 26.37 NOTE
r-devel-linux-x86_64-debian-gcc 0.9.9-1 1.54 25.43 26.97 NOTE
r-devel-linux-x86_64-fedora-clang 0.9.9-1 51.55 NOTE
r-devel-linux-x86_64-fedora-gcc 0.9.9-1 49.63 NOTE
r-devel-macosx-x86_64-clang 0.9.9-1 48.38 NOTE
r-devel-macosx-x86_64-gcc 0.9.9-1 NOTE
r-devel-windows-ix86+x86_64 0.9.9-1 6.00 37.00 43.00 NOTE
r-patched-linux-x86_64 0.9.9-1 1.57 25.78 27.36 NOTE
r-patched-solaris-sparc 0.9.9-1 303.50 NOTE
r-patched-solaris-x86 0.9.9-1 63.90 NOTE
r-release-linux-ix86 0.9.9-1 4.00 44.00 48.00 NOTE
r-release-linux-x86_64 0.9.9-1 1.46 25.23 26.69 NOTE
r-release-macosx-x86_64 0.9.9-1 NOTE
r-release-windows-ix86+x86_64 0.9.9-1 6.00 42.00 48.00 NOTE
r-oldrel-windows-ix86+x86_64 0.9.9-1 7.00 41.00 48.00 NOTE

Check Details

Version: 0.9.9-1
Check: dependencies in R code
Result: NOTE
    'library' or 'require' calls to packages already attached by Depends:
     ‘coda’ ‘lattice’ ‘runjags’
     Please remove these calls from your code.
    Packages in Depends field not imported from:
     ‘coda’ ‘lattice’ ‘runjags’
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
    See the information on DESCRIPTION files in the chapter ‘Creating R
    packages’ of the ‘Writing R Extensions’ manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-macosx-x86_64-clang, r-devel-macosx-x86_64-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-sparc, r-patched-solaris-x86, r-release-linux-ix86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.9.9-1
Check: R code for possible problems
Result: NOTE
    Found the following assignments to the global environment:
    File ‘bayescount/R/bayescount.R’:
     assign(paste(runname, ".", model, ".results", sep = ""), results,
     pos = ".GlobalEnv")
    File ‘bayescount/R/likelihood.R’:
     assign("gresults", results, pos = .GlobalEnv)
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-macosx-x86_64-clang, r-patched-linux-x86_64, r-release-linux-ix86, r-release-linux-x86_64

Version: 0.9.9-1
Check: Rd line widths
Result: NOTE
    Rd file 'bayescount.Rd':
     \examples lines wider than 100 characters:
     # run the function with all values as default, and 'name' and 'data' (from a local .csv file) to be input by the user when prompted:
     # analyse data using zero-inflated gamma Poisson and zero-inflated lognormal Poisson models in 5 text .csv files named 'mydata/data.*nu ... [TRUNCATED]
     bayescount(name=paste("Data ", i, sep=""), data=paste("mydata/data.", i, ".csv", sep=""), model=c("ZIGP", "ZILP"), setnames=TRU ... [TRUNCATED]
     # analyse local data (2 datasets with 20 animals each with 10 repeat samples) using a zero-inflated lognormal Poisson model:
     # Missing data is permissible but means the likelihood cannot be calculated - a warning will be printed:
     bayescount(name="analysis", data=data, model = "ZILP", setnames=c("Simulated group A", "Simulated group B"), likelihood=TRUE)
    
    Rd file 'bayescount.single.Rd':
     \examples lines wider than 100 characters:
     # use a zero-inflated lognormal Poisson model to analyse some count data, and suppressing JAGS output:
    
    Rd file 'likelihood.Rd':
     \examples lines wider than 100 characters:
     # calculate the likelihood of obtaining a set of count data from a zero-inflated Poisson distribution with set mean and zero-inflation ... [TRUNCATED]
     # now calculate the likelihood for the same data using an MCMC object to provide the values for mean and zero-inflation
     zis <- (1-c(values[,'prob'][[1]], values[,'prob'][[2]]))*100 # The function outputs the prevalence of disease when raw.ouput is TRUE, ... [TRUNCATED]
    
    Rd file 'maximise.likelihood.Rd':
     \usage lines wider than 90 characters:
     maximise.likelihood(data=stop("Data must be specified"), model=stop("Please specify a distribution"), mean=NA, variance=NA,
    
    Rd file 'run.model.Rd':
     \examples lines wider than 100 characters:
     # Return the model specification and starting values for a lognormal Poisson, then run the model using run.jags:
     run.jags(model=modelstring, inits=initial.values, check.conv=TRUE, data=datastring, monitor=monitors)
    
    These lines will be truncated in the PDF manual.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 0.9.9-1
Check: dependencies in R code
Result: NOTE
    'library' or 'require' calls to packages already attached by Depends:
     'coda' 'lattice' 'runjags'
     Please remove these calls from your code.
    See the information on DESCRIPTION files in the chapter 'Creating R
    packages' of the 'Writing R Extensions' manual.
Flavor: r-release-macosx-x86_64