diff --git a/DESCRIPTION b/DESCRIPTION index 5b9c4c1..a50b7e2 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: mcradds Type: Package Title: Processing and Analyzing of Diagnostics Trials -Version: 1.1.0 +Version: 1.1.1 Authors@R: c( person("Kai", "Gu", , "gukai1212@163.com", role = c("aut", "cre", "cph")) ) @@ -47,7 +47,7 @@ Suggests: Config/testthat/edition: 3 VignetteBuilder: knitr Roxygen: list(markdown = TRUE) -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.1 Collate: 'pkg_class.R' 'pkg_methods.R' diff --git a/NEWS.md b/NEWS.md index bdeb29d..bbbf109 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,7 @@ +# mcradds 1.1.1 + +* Fix the `autoplot` test error due to ggplot dependence update. + # mcradds 1.1.0 ### Enhancements diff --git a/R/autoplot.R b/R/autoplot.R index 970f04d..97fb611 100644 --- a/R/autoplot.R +++ b/R/autoplot.R @@ -459,7 +459,8 @@ setMethod( p + theme_light() + theme( - legend.position = c(0.02, 0.98), + legend.position = c("inside"), + legend.position.inside = c(0.02, 0.98), legend.justification = c("left", "top"), legend.background = element_rect(fill = "transparent"), legend.title = if (!legend.title) element_blank(), diff --git a/R/correlation.R b/R/correlation.R index 95c27c8..1bf2406 100644 --- a/R/correlation.R +++ b/R/correlation.R @@ -89,7 +89,7 @@ pearsonTest <- function(x, y, #' interval(`lowerci` and `upperci`), Z statistic (`Z`) and p-value (`pval`) #' @export #' -#' @seealso [cor.test()] [boot()] to see the detailed arguments. +#' @seealso [cor.test()] [boot::boot()] to see the detailed arguments. #' @references NCSS correlation document #' #' @examples diff --git a/cran-comments.md b/cran-comments.md index 9423a48..35ca225 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,18 +1,7 @@ ## Resubmission -This is a resubmission. In this version I have: - -I have refreshed the `mcr` relevant functions as they were unavailable in last -version, and added a set of new features in current version. +This is a resubmission, only few issues were updated. ## R CMD check results -0 errors | 0 warnings | 1 note - - -## revdepcheck results - -We checked 0 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. - - * We saw 0 new problems - * We failed to check 0 packages +0 errors | 0 warnings | 0 note diff --git a/man/VCAinference.Rd b/man/VCAinference.Rd index 9807ce0..439d70c 100644 --- a/man/VCAinference.Rd +++ b/man/VCAinference.Rd @@ -10,7 +10,7 @@ VCAinference(...) \item{...}{ Arguments passed on to \code{\link[VCA:VCAinference]{VCA::VCAinference}} \describe{ - \item{\code{obj}}{(object) of class 'VCA' or, alternatively, a list of 'VCA' objects, where all other argument can be + \item{\code{obj}}{(object) of class 'VCA' or, alternatively, a list of 'VCA' objects, where all other arguments can be specified as vectors, where the i-th vector element applies to the i-th element of 'obj' (see examples)} \item{\code{alpha}}{(numeric) value specifying the significance level for \eqn{100*(1-alpha)}\% confidence intervals.} \item{\code{total.claim}}{(numeric) value specifying the claim-value for the Chi-Squared test for the total variance (SD or CV, see \code{claim.type}).} @@ -21,10 +21,9 @@ specified as vectors, where the i-th vector element applies to the i-th element "CV" = claim-values specified in terms of coefficient(s) of variation (CV) and are specified as percentages.\cr If set to "SD" or "CV", claim-values will be converted to variances before applying the Chi-Squared test (see examples).} - \item{\code{VarVC}}{(logical) TRUE = if element "Matrices" exists (see \code{\link[VCA]{anovaVCA}}), the covariance -matrix of the estimated VCs will be computed (see \code{\link[VCA]{vcovVC}}, which is used in CIs for + \item{\code{VarVC}}{(logical) TRUE = the covariance matrix of the estimated VCs will be computed (see \code{\link[VCA]{vcovVC}}), where diagonal + elements correspond to the variances of the individual VCs. This matrix is required for estimation of CIs for intermediate VCs if 'method.ci="sas"'. -Note, this might take very long for larger datasets, since there are many matrix operations involved. FALSE (Default) = computing covariance matrix of VCs is omitted, as well as CIs for intermediate VCs.} \item{\code{excludeNeg}}{(logical) TRUE = confidence intervals of negative variance estimates will not be reported. \cr FALSE = confidence intervals for all VCs will be reported including those with negative VCs.\cr diff --git a/man/spearmanTest.Rd b/man/spearmanTest.Rd index ecff653..6103064 100644 --- a/man/spearmanTest.Rd +++ b/man/spearmanTest.Rd @@ -58,5 +58,5 @@ spearmanTest(x, y, h0 = 0.5, alternative = "greater") NCSS correlation document } \seealso{ -\code{\link[=cor.test]{cor.test()}} \code{\link[=boot]{boot()}} to see the detailed arguments. +\code{\link[=cor.test]{cor.test()}} \code{\link[boot:boot]{boot::boot()}} to see the detailed arguments. } diff --git a/mcradds.Rproj b/mcradds.Rproj index bf86390..2e6156f 100644 --- a/mcradds.Rproj +++ b/mcradds.Rproj @@ -17,6 +17,6 @@ StripTrailingWhitespace: Yes BuildType: Package PackageUseDevtools: Yes -PackagePath: C:/Users/TJ0695/Documents/mcradds +PackagePath: C:/Users/TH0528/Documents/mcradds PackageInstallArgs: --no-multiarch --with-keep.source PackageRoxygenize: rd,namespace diff --git a/tests/testthat/_snaps/autoplot/autoplot-basummary-with-relative-diff.svg b/tests/testthat/_snaps/autoplot/autoplot-basummary-with-relative-diff.svg index 235740a..46c7e34 100644 --- a/tests/testthat/_snaps/autoplot/autoplot-basummary-with-relative-diff.svg +++ b/tests/testthat/_snaps/autoplot/autoplot-basummary-with-relative-diff.svg @@ -18,7 +18,7 @@ - + diff --git a/tests/testthat/_snaps/autoplot/autoplot-mcresult-with-default-arguments.svg b/tests/testthat/_snaps/autoplot/autoplot-mcresult-with-default-arguments.svg index 74af939..595a302 100644 --- a/tests/testthat/_snaps/autoplot/autoplot-mcresult-with-default-arguments.svg +++ b/tests/testthat/_snaps/autoplot/autoplot-mcresult-with-default-arguments.svg @@ -217,13 +217,11 @@ Method1 Method2 -Deming RegressionFit (n=120) +Deming RegressionFit (n=120) - - Identity Y = 1.01 * X + 4.34 diff --git a/tests/testthat/_snaps/autoplot/autoplot-mcresult-with-multiple-arguments.svg b/tests/testthat/_snaps/autoplot/autoplot-mcresult-with-multiple-arguments.svg index d7a17d8..a17ae65 100644 --- a/tests/testthat/_snaps/autoplot/autoplot-mcresult-with-multiple-arguments.svg +++ b/tests/testthat/_snaps/autoplot/autoplot-mcresult-with-multiple-arguments.svg @@ -216,14 +216,12 @@ 1400 Method1 Method2 - - - - - - - -Identity -Y = 1.031 * X + 3.189 + + + + + +Identity +Y = 1.031 * X + 3.189