diff --git a/ChangeLog b/ChangeLog index 1cc4486..a443e6c 100644 --- a/ChangeLog +++ b/ChangeLog @@ -16,4 +16,6 @@ v0.6 - added Azman/Lessler contributions: MCMC estimation functions, ability to v06.3 - minor modifications to address NAMESPACE issues. -v06.4 - merged hackout3 branch to support new distributions \ No newline at end of file +v06.4 - merged hackout3 branch to support new distributions + +v06.5 - minor modifications to fix improper call to `class()` and other new NOTES. \ No newline at end of file diff --git a/DESCRIPTION b/DESCRIPTION index 342ec8f..306cfde 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: coarseDataTools -Version: 0.6-4 -Date: 2019-06-04 +Version: 0.6-5 +Date: 2019-12-05 Title: Analysis of Coarsely Observed Data Authors@R: c(person("Nicholas G.", "Reich", email = "nick@schoolph.umass.edu", role = c("aut", "cre")), person("Justin", "Lessler", email = "jlessler@jhsph.edu", role = "aut"), diff --git a/NAMESPACE b/NAMESPACE index b1da19b..e52e509 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -17,6 +17,7 @@ importFrom(MCMCpack,MCMCmetrop1R) importFrom(grDevices,rgb) importFrom(graphics,lines) importFrom(graphics,plot) +importFrom(methods,is) importFrom(methods,new) importFrom(stats,coef) importFrom(stats,dgamma) diff --git a/R/coarseDataTools-package.R b/R/coarseDataTools-package.R index e61b140..a88c2af 100644 --- a/R/coarseDataTools-package.R +++ b/R/coarseDataTools-package.R @@ -80,6 +80,6 @@ NULL ##' @examples ##' data(nycH1N1) ##' head(nycH1N1) -##' dic.fit(nycH1N1) +##' \dontrun{dic.fit(nycH1N1)} ##' @keywords datasets NULL diff --git a/R/dic.fit.R b/R/dic.fit.R index fa8e101..067fe89 100644 --- a/R/dic.fit.R +++ b/R/dic.fit.R @@ -41,6 +41,7 @@ ##' @param n.boots number of bootstrap resamples (0 means that asymptotic results are desired) ##' @param ... additional options passed to optim ##' @return a cd.fit S4 object. +##' @importFrom methods is ##' @seealso \code{\link{cd.fit}}, \code{\link{dic.fit.mcmc}} ##' @export ##' @examples @@ -77,7 +78,7 @@ dic.fit <- function(dat, ## make sure dat is a matrix dat <- as.matrix(dat[,c("EL", "ER", "SL", "SR", "type")]) - if(class(dat)=="data.frame") stop("dat should be a matrix.") + if(is(dat,"data.frame")) stop("dat should be a matrix.") ## find starting values for DIC analysis using profile likelihoods start.par1 <- optimize(f=pl.par1, interval=par1.int, diff --git a/cran-comments.md b/cran-comments.md index dca2957..b16a56b 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,17 +1,25 @@ -## requested fixes - - fixed NOTES about canonical URLs +## updates in this edition + + - as requested: fixed improper call to `class(dat) == "data.frame"` with a call to `is(dat, "data.frame")` ## R CMD check results -There were no ERRORs or WARNINGs. +> On windows-x86_64-devel (r-devel) + checking sizes of PDF files under 'inst/doc' ... NOTE + Unable to find GhostScript executable to run checks on size reduction -Notes arose from running checks on Rhub: +Unable to figure out whether this is an issue with the server running the checks or something in the package itself that I can/should be changing. -``` +> On fedora-clang-devel (r-devel) + checking CRAN incoming feasibility ...NB: need Internet access to use CRAN incoming checks + NOTE + Maintainer: ‘Nicholas G. Reich ’ + Possibly mis-spelled words in DESCRIPTION: - al (20:34, 21:14, 22:16) Lessler (22:5) + al (20:34, 21:14, 22:16) et (20:31, 21:11, 22:13) -``` -These are expected, as they are abbreviations and last names from citations requested by CRAN maintainers. \ No newline at end of file + +These are expected, as they are abbreviations and last names from citations requested by CRAN maintainers. + diff --git a/man/nycH1N1.Rd b/man/nycH1N1.Rd index 0b051de..6c7585f 100644 --- a/man/nycH1N1.Rd +++ b/man/nycH1N1.Rd @@ -23,6 +23,6 @@ These observations on the incubation period of influenza A come from the investi \examples{ data(nycH1N1) head(nycH1N1) -dic.fit(nycH1N1) +\dontrun{dic.fit(nycH1N1)} } \keyword{datasets}