diff --git a/DESCRIPTION b/DESCRIPTION index 119029dcc..18863f7b8 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: metafor -Version: 4.5-3 +Version: 4.5-4 Date: 2023-10-23 Title: Meta-Analysis Package for R Authors@R: person(given = "Wolfgang", family = "Viechtbauer", role = c("aut","cre"), email = "wvb@metafor-project.org", comment = c(ORCID = "0000-0003-3463-4063")) diff --git a/NEWS.md b/NEWS.md index d7e50b508..649f80076 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,7 +1,9 @@ -# metafor 4.5-3 (2023-10-23) +# metafor 4.5-4 (2023-10-23) - a few minor fixes to the dynamic theming of plots based on the foreground and background colors of the plotting device +- slightly improved flexibility for setting package options + # metafor 4.4-0 (2023-09-27) - added `getmfopt()` and `setmfopt()` functions for getting and setting package options and made some of the options more flexible diff --git a/R/AIC.rma.r b/R/AIC.rma.r index 9fa18d7f5..0f9f3343d 100644 --- a/R/AIC.rma.r +++ b/R/AIC.rma.r @@ -1,6 +1,6 @@ AIC.rma <- function(object, ..., k=2, correct=FALSE) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(object), must="rma") diff --git a/R/BIC.rma.r b/R/BIC.rma.r index e1a588469..5fa192e14 100644 --- a/R/BIC.rma.r +++ b/R/BIC.rma.r @@ -1,6 +1,6 @@ BIC.rma <- function(object, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(object), must="rma") diff --git a/R/addpoly.default.r b/R/addpoly.default.r index 6e6e62ae6..50aca6d04 100644 --- a/R/addpoly.default.r +++ b/R/addpoly.default.r @@ -13,7 +13,7 @@ transf, atransf, targs, efac, col, border, lty, fonts, cex, constarea=FALSE, ... ######################################################################### - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() na.act <- getOption("na.action") diff --git a/R/addpoly.predict.rma.r b/R/addpoly.predict.rma.r index 5762f243d..f2304972f 100644 --- a/R/addpoly.predict.rma.r +++ b/R/addpoly.predict.rma.r @@ -4,7 +4,7 @@ transf, atransf, targs, efac, col, border, lty, fonts, cex, constarea=FALSE, ... ######################################################################### - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="predict.rma") diff --git a/R/addpoly.rma.r b/R/addpoly.rma.r index 6b3a56728..087dab28e 100644 --- a/R/addpoly.rma.r +++ b/R/addpoly.rma.r @@ -4,7 +4,7 @@ transf, atransf, targs, efac, col, border, lty, fonts, cex, ...) { ######################################################################### - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="rma") diff --git a/R/aggregate.escalc.r b/R/aggregate.escalc.r index 8d45b47c3..f171a1b7a 100644 --- a/R/aggregate.escalc.r +++ b/R/aggregate.escalc.r @@ -2,7 +2,7 @@ aggregate.escalc <- function(x, cluster, time, obs, V, struct="CS", rho, phi, weighted=TRUE, checkpd=TRUE, fun, na.rm=TRUE, addk=FALSE, subset, select, digits, var.names, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="escalc") diff --git a/R/anova.rma.r b/R/anova.rma.r index c67b0d700..55a3b8214 100644 --- a/R/anova.rma.r +++ b/R/anova.rma.r @@ -1,6 +1,6 @@ anova.rma <- function(object, object2, btt, X, att, Z, rhs, digits, refit=FALSE, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(object), must="rma", notap=c("rma.mh", "rma.peto"), notav="rma.glmm") diff --git a/R/baujat.rma.r b/R/baujat.rma.r index 784929a6e..958a9d4ef 100644 --- a/R/baujat.rma.r +++ b/R/baujat.rma.r @@ -1,6 +1,6 @@ baujat.rma <- function(x, xlim, ylim, xlab, ylab, cex, symbol="ids", grid=TRUE, progbar=FALSE, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="rma", notav=c("rma.glmm", "rma.mv", "robust.rma", "rma.ls", "rma.gen", "rma.uni.selmodel")) diff --git a/R/bldiag.r b/R/bldiag.r index 903369b78..d62870286 100644 --- a/R/bldiag.r +++ b/R/bldiag.r @@ -1,6 +1,6 @@ bldiag <- function(..., order) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() mlist <- list(...) diff --git a/R/blsplit.r b/R/blsplit.r index 74ada4ed1..6955943dc 100644 --- a/R/blsplit.r +++ b/R/blsplit.r @@ -1,6 +1,6 @@ blsplit <- function(x, cluster, fun, args, sort=FALSE) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() if (missing(cluster)) stop(mstyle$stop("Must specify 'cluster' variable.")) diff --git a/R/blup.rma.uni.r b/R/blup.rma.uni.r index 020c107f9..2c89336d5 100644 --- a/R/blup.rma.uni.r +++ b/R/blup.rma.uni.r @@ -1,6 +1,6 @@ blup.rma.uni <- function(x, level, digits, transf, targs, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="rma.uni", notav=c("rma.uni.selmodel", "rma.gen")) diff --git a/R/coef.matreg.r b/R/coef.matreg.r index 4291a67f0..2603291f1 100644 --- a/R/coef.matreg.r +++ b/R/coef.matreg.r @@ -1,6 +1,6 @@ coef.matreg <- function(object, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(object), must="matreg") diff --git a/R/coef.permutest.rma.uni.r b/R/coef.permutest.rma.uni.r index 3842884f2..eb55dd192 100644 --- a/R/coef.permutest.rma.uni.r +++ b/R/coef.permutest.rma.uni.r @@ -1,6 +1,6 @@ coef.permutest.rma.uni <- function(object, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(object), must="permutest.rma.uni") diff --git a/R/coef.rma.r b/R/coef.rma.r index df5296ac4..d7153f55b 100644 --- a/R/coef.rma.r +++ b/R/coef.rma.r @@ -1,6 +1,6 @@ coef.rma <- function(object, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(object), must="rma") diff --git a/R/coef.summary.rma.r b/R/coef.summary.rma.r index e1566dd2f..950044be0 100644 --- a/R/coef.summary.rma.r +++ b/R/coef.summary.rma.r @@ -1,6 +1,6 @@ coef.summary.rma <- function(object, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(object), must="summary.rma") diff --git a/R/confint.rma.glmm.r b/R/confint.rma.glmm.r index e02c60490..1c96cd42e 100644 --- a/R/confint.rma.glmm.r +++ b/R/confint.rma.glmm.r @@ -1,6 +1,6 @@ confint.rma.glmm <- function(object, parm, level, digits, transf, targs, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(object), must="rma.glmm", notav="rma.glmm") diff --git a/R/confint.rma.ls.r b/R/confint.rma.ls.r index 114930633..5b93f817e 100644 --- a/R/confint.rma.ls.r +++ b/R/confint.rma.ls.r @@ -1,6 +1,6 @@ confint.rma.ls <- function(object, parm, level, fixed=FALSE, alpha, digits, transf, targs, verbose=FALSE, control, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(object), must="rma.ls") diff --git a/R/confint.rma.mh.r b/R/confint.rma.mh.r index ecc87bc54..6e45ef9e3 100644 --- a/R/confint.rma.mh.r +++ b/R/confint.rma.mh.r @@ -1,6 +1,6 @@ confint.rma.mh <- function(object, parm, level, digits, transf, targs, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(object), must="rma.mh") diff --git a/R/confint.rma.mv.r b/R/confint.rma.mv.r index b990e9440..69446a3ab 100644 --- a/R/confint.rma.mv.r +++ b/R/confint.rma.mv.r @@ -1,6 +1,6 @@ confint.rma.mv <- function(object, parm, level, fixed=FALSE, sigma2, tau2, rho, gamma2, phi, digits, transf, targs, verbose=FALSE, control, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(object), must="rma.mv") diff --git a/R/confint.rma.peto.r b/R/confint.rma.peto.r index e040474d9..23d0a3b6d 100644 --- a/R/confint.rma.peto.r +++ b/R/confint.rma.peto.r @@ -1,6 +1,6 @@ confint.rma.peto <- function(object, parm, level, digits, transf, targs, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(object), must="rma.peto") diff --git a/R/confint.rma.uni.r b/R/confint.rma.uni.r index d9b80c95b..cd8ac6999 100644 --- a/R/confint.rma.uni.r +++ b/R/confint.rma.uni.r @@ -9,7 +9,7 @@ confint.rma.uni <- function(object, parm, level, fixed=FALSE, random=TRUE, type, digits, transf, targs, verbose=FALSE, control, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(object), must="rma.uni", notav=c("robust.rma", "rma.ls", "rma.gen")) diff --git a/R/confint.rma.uni.selmodel.r b/R/confint.rma.uni.selmodel.r index facdf06f3..0e6b877bf 100644 --- a/R/confint.rma.uni.selmodel.r +++ b/R/confint.rma.uni.selmodel.r @@ -1,6 +1,6 @@ confint.rma.uni.selmodel <- function(object, parm, level, fixed=FALSE, tau2, delta, digits, transf, targs, verbose=FALSE, control, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(object), must="rma.uni.selmodel") diff --git a/R/contrmat.r b/R/contrmat.r index 75e059793..6ae996694 100644 --- a/R/contrmat.r +++ b/R/contrmat.r @@ -1,6 +1,6 @@ contrmat <- function(data, grp1, grp2, last, shorten=FALSE, minlen=2, check=TRUE, append=TRUE) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() if (!is.data.frame(data)) data <- data.frame(data) diff --git a/R/conv.2x2.r b/R/conv.2x2.r index c134935d0..d90a8b172 100644 --- a/R/conv.2x2.r +++ b/R/conv.2x2.r @@ -1,7 +1,7 @@ conv.2x2 <- function(ori, ri, x2i, ni, n1i, n2i, correct=TRUE, data, include, var.names=c("ai","bi","ci","di"), append=TRUE, replace="ifna") { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() if (is.logical(replace)) { if (isTRUE(replace)) { diff --git a/R/conv.delta.r b/R/conv.delta.r index 0b24785fa..7db4b7043 100644 --- a/R/conv.delta.r +++ b/R/conv.delta.r @@ -1,6 +1,6 @@ conv.delta <- function(yi, vi, ni, data, include, transf, var.names, append=TRUE, replace="ifna", ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() if (missing(yi) || missing(vi)) stop(mstyle$stop("Must specify 'yi' and 'vi' arguments.")) diff --git a/R/conv.fivenum.r b/R/conv.fivenum.r index 5d5ef20f1..18ecdc524 100644 --- a/R/conv.fivenum.r +++ b/R/conv.fivenum.r @@ -2,7 +2,7 @@ conv.fivenum <- function(min, q1, median, q3, max, n, data, include, method="default", dist="norm", transf=TRUE, test=TRUE, var.names=c("mean","sd"), append=TRUE, replace="ifna", ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() if (missing(min) && missing(q1) && missing(median) && missing(q3) && missing(max)) stop(mstyle$stop("Must specify at least some of these arguments: 'min', 'q1', 'median', 'q3', 'max'.")) diff --git a/R/conv.wald.r b/R/conv.wald.r index bdd270b7c..c6dda2c4c 100644 --- a/R/conv.wald.r +++ b/R/conv.wald.r @@ -3,7 +3,7 @@ conv.wald <- function(out, ci.lb, ci.ub, zval, pval, n, data, include, # TODO: allow t-distribution based CIs/tests (then also need dfs argument)? - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() if (missing(out) && missing(ci.lb) && missing(ci.ub) && missing(zval) && missing(pval)) stop(mstyle$stop("Must specify at least some of these arguments: 'out', 'ci.lb', 'ci.ub', 'zval', 'pval'.")) diff --git a/R/cooks.distance.rma.mv.r b/R/cooks.distance.rma.mv.r index 058e4404d..e9a8532df 100644 --- a/R/cooks.distance.rma.mv.r +++ b/R/cooks.distance.rma.mv.r @@ -1,6 +1,6 @@ cooks.distance.rma.mv <- function(model, progbar=FALSE, cluster, reestimate=TRUE, parallel="no", ncpus=1, cl, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(model), must="rma.mv") diff --git a/R/cumul.rma.mh.r b/R/cumul.rma.mh.r index ce7584b5f..93f6d37c6 100644 --- a/R/cumul.rma.mh.r +++ b/R/cumul.rma.mh.r @@ -1,6 +1,6 @@ cumul.rma.mh <- function(x, order, digits, transf, targs, progbar=FALSE, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="rma.mh") diff --git a/R/cumul.rma.peto.r b/R/cumul.rma.peto.r index 5a5ae3765..06ef53837 100644 --- a/R/cumul.rma.peto.r +++ b/R/cumul.rma.peto.r @@ -1,6 +1,6 @@ cumul.rma.peto <- function(x, order, digits, transf, targs, progbar=FALSE, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="rma.peto") diff --git a/R/cumul.rma.uni.r b/R/cumul.rma.uni.r index 8594d8b2c..bfb649250 100644 --- a/R/cumul.rma.uni.r +++ b/R/cumul.rma.uni.r @@ -1,6 +1,6 @@ cumul.rma.uni <- function(x, order, digits, transf, targs, progbar=FALSE, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="rma.uni", notav=c("robust.rma", "rma.ls", "rma.gen", "rma.uni.selmodel")) diff --git a/R/deviance.rma.r b/R/deviance.rma.r index 27055ac65..2700de5ae 100644 --- a/R/deviance.rma.r +++ b/R/deviance.rma.r @@ -1,6 +1,6 @@ deviance.rma <- function(object, REML, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(object), must="rma") diff --git a/R/df.residual.rma.r b/R/df.residual.rma.r index bab75a127..499baea7d 100644 --- a/R/df.residual.rma.r +++ b/R/df.residual.rma.r @@ -1,6 +1,6 @@ df.residual.rma <- function(object, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(object), must="rma") diff --git a/R/dfbetas.rma.mv.r b/R/dfbetas.rma.mv.r index 4220b0167..ff30fe5b6 100644 --- a/R/dfbetas.rma.mv.r +++ b/R/dfbetas.rma.mv.r @@ -1,6 +1,6 @@ dfbetas.rma.mv <- function(model, progbar=FALSE, cluster, reestimate=TRUE, parallel="no", ncpus=1, cl, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(model), must="rma.mv", notav="robust.rma") diff --git a/R/dfround.r b/R/dfround.r index 47e1ad2cb..abfae36d4 100644 --- a/R/dfround.r +++ b/R/dfround.r @@ -1,6 +1,6 @@ dfround <- function(x, digits, drop0=TRUE) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() if (inherits(x, "matrix") && length(dim(x)) == 2L) x <- data.frame(x, check.names=FALSE) diff --git a/R/emmprep.r b/R/emmprep.r index b8396a897..cc10995fa 100644 --- a/R/emmprep.r +++ b/R/emmprep.r @@ -1,6 +1,6 @@ emmprep <- function(x, verbose=FALSE, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="rma") diff --git a/R/escalc.r b/R/escalc.r index dec07da60..320265175 100644 --- a/R/escalc.r +++ b/R/escalc.r @@ -3,7 +3,7 @@ data, slab, subset, include, add=1/2, to="only0", drop00=FALSE, vtype="LS", var. ### check argument specifications - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() if (missing(measure) && missing(yi)) stop(mstyle$stop("Must specify an effect size or outcome measure via the 'measure' argument.")) diff --git a/R/fitstats.rma.r b/R/fitstats.rma.r index 445fcdc08..85f8f44b7 100644 --- a/R/fitstats.rma.r +++ b/R/fitstats.rma.r @@ -1,6 +1,6 @@ fitstats.rma <- function(object, ..., REML) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(object), must="rma") diff --git a/R/fitted.rma.r b/R/fitted.rma.r index dc21fd006..a163f0311 100644 --- a/R/fitted.rma.r +++ b/R/fitted.rma.r @@ -1,6 +1,6 @@ fitted.rma <- function(object, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(object), must="rma") diff --git a/R/forest.cumul.rma.r b/R/forest.cumul.rma.r index 6e192a339..a70aaa7fa 100644 --- a/R/forest.cumul.rma.r +++ b/R/forest.cumul.rma.r @@ -8,7 +8,7 @@ lty, fonts, cex, cex.lab, cex.axis, ...) { ######################################################################### - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="cumul.rma") diff --git a/R/forest.default.r b/R/forest.default.r index 559e0ead6..8c0b2828d 100644 --- a/R/forest.default.r +++ b/R/forest.default.r @@ -8,7 +8,7 @@ lty, fonts, cex, cex.lab, cex.axis, ...) { ######################################################################### - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() na.act <- getOption("na.action") diff --git a/R/forest.rma.r b/R/forest.rma.r index 96429e88d..6a8c868b1 100644 --- a/R/forest.rma.r +++ b/R/forest.rma.r @@ -8,7 +8,7 @@ lty, fonts, cex, cex.lab, cex.axis, ...) { ######################################################################### - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="rma", notav=c("rma.ls", "rma.gen")) diff --git a/R/formula.rma.r b/R/formula.rma.r index 31acdf355..afba3edb4 100644 --- a/R/formula.rma.r +++ b/R/formula.rma.r @@ -1,6 +1,6 @@ formula.rma <- function(x, type="mods", ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="rma") diff --git a/R/fsn.r b/R/fsn.r index 6705f4209..7286cb788 100644 --- a/R/fsn.r +++ b/R/fsn.r @@ -3,7 +3,7 @@ fsn <- function(x, vi, sei, subset, data, type, alpha=.05, target, ######################################################################### - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() na.act <- getOption("na.action") diff --git a/R/funnel.default.r b/R/funnel.default.r index 1636a1fd9..3f7f444ff 100644 --- a/R/funnel.default.r +++ b/R/funnel.default.r @@ -6,7 +6,7 @@ label=FALSE, offset=0.4, legend=FALSE, ...) { ######################################################################### - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() na.act <- getOption("na.action") diff --git a/R/funnel.rma.r b/R/funnel.rma.r index ff807f008..4188370e3 100644 --- a/R/funnel.rma.r +++ b/R/funnel.rma.r @@ -6,7 +6,7 @@ label=FALSE, offset=0.4, legend=FALSE, ...) { ######################################################################### - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="rma") diff --git a/R/gosh.rma.r b/R/gosh.rma.r index f3c1ffbbb..551cbafa3 100644 --- a/R/gosh.rma.r +++ b/R/gosh.rma.r @@ -1,6 +1,6 @@ gosh.rma <- function(x, subsets, progbar=TRUE, parallel="no", ncpus=1, cl, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="rma", notav=c("rma.glmm", "rma.mv", "robust.rma", "rma.ls", "rma.gen", "rma.uni.selmodel")) diff --git a/R/hatvalues.rma.mv.r b/R/hatvalues.rma.mv.r index 22f4b0ef1..b8bfc44bc 100644 --- a/R/hatvalues.rma.mv.r +++ b/R/hatvalues.rma.mv.r @@ -1,6 +1,6 @@ hatvalues.rma.mv <- function(model, type="diagonal", ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(model), must="rma.mv") diff --git a/R/hatvalues.rma.uni.r b/R/hatvalues.rma.uni.r index 7399e7c55..3ef243a67 100644 --- a/R/hatvalues.rma.uni.r +++ b/R/hatvalues.rma.uni.r @@ -1,6 +1,6 @@ hatvalues.rma.uni <- function(model, type="diagonal", ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(model), must="rma.uni", notav=c("rma.uni.selmodel", "rma.gen")) diff --git a/R/hc.rma.uni.r b/R/hc.rma.uni.r index 802bd602b..cd347cded 100644 --- a/R/hc.rma.uni.r +++ b/R/hc.rma.uni.r @@ -1,6 +1,6 @@ hc.rma.uni <- function(object, digits, transf, targs, control, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(object), must="rma.uni", notav=c("rma.ls", "rma.gen", "rma.uni.selmodel")) diff --git a/R/influence.rma.uni.r b/R/influence.rma.uni.r index da235178b..3ff591510 100644 --- a/R/influence.rma.uni.r +++ b/R/influence.rma.uni.r @@ -1,6 +1,6 @@ influence.rma.uni <- function(model, digits, progbar=FALSE, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(model), must="rma.uni", notav=c("rma.ls", "rma.gen", "rma.uni.selmodel")) diff --git a/R/labbe.rma.r b/R/labbe.rma.r index f29fe9e52..0e6976ac6 100644 --- a/R/labbe.rma.r +++ b/R/labbe.rma.r @@ -1,7 +1,7 @@ labbe.rma <- function(x, xlim, ylim, xlab, ylab, add=x$add, to=x$to, transf, targs, pch=21, psize, plim=c(0.5,3.5), col, bg, grid=FALSE, lty, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="rma", notav=c("rma.mv", "rma.ls", "rma.gen", "rma.uni.selmodel")) diff --git a/R/leave1out.rma.mh.r b/R/leave1out.rma.mh.r index 00c5960dc..a3d479f36 100644 --- a/R/leave1out.rma.mh.r +++ b/R/leave1out.rma.mh.r @@ -1,6 +1,6 @@ leave1out.rma.mh <- function(x, digits, transf, targs, progbar=FALSE, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="rma.mh") diff --git a/R/leave1out.rma.peto.r b/R/leave1out.rma.peto.r index 0dbcdf4bc..d1f3991f7 100644 --- a/R/leave1out.rma.peto.r +++ b/R/leave1out.rma.peto.r @@ -1,6 +1,6 @@ leave1out.rma.peto <- function(x, digits, transf, targs, progbar=FALSE, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="rma.peto") diff --git a/R/leave1out.rma.uni.r b/R/leave1out.rma.uni.r index 6a2537cc9..7a7cd8ad0 100644 --- a/R/leave1out.rma.uni.r +++ b/R/leave1out.rma.uni.r @@ -1,6 +1,6 @@ leave1out.rma.uni <- function(x, digits, transf, targs, progbar=FALSE, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="rma.uni", notav=c("robust.rma", "rma.ls", "rma.gen", "rma.uni.selmodel")) diff --git a/R/llplot.r b/R/llplot.r index 02e6f5cb6..14ab97128 100644 --- a/R/llplot.r +++ b/R/llplot.r @@ -4,7 +4,7 @@ lty, lwd, col, level=99.99, refline=0, ...) { ######################################################################### - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() ### data setup diff --git a/R/logLik.rma.r b/R/logLik.rma.r index 594612b0d..e3335a52f 100644 --- a/R/logLik.rma.r +++ b/R/logLik.rma.r @@ -1,6 +1,6 @@ logLik.rma <- function(object, REML, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(object), must="rma") diff --git a/R/matreg.r b/R/matreg.r index 23edde8d6..30e9ea7a9 100644 --- a/R/matreg.r +++ b/R/matreg.r @@ -1,6 +1,6 @@ matreg <- function(y, x, R, n, V, cov=FALSE, means, ztor=FALSE, nearpd=FALSE, level=95, digits, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() if (missing(digits)) digits <- 4 diff --git a/R/mfopt.r b/R/mfopt.r index 76f4f8726..12e37ad20 100644 --- a/R/mfopt.r +++ b/R/mfopt.r @@ -1,6 +1,6 @@ setmfopt <- function(...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() mfopts <- getOption("metafor") @@ -12,17 +12,17 @@ setmfopt <- function(...) { newopts <- list(...) for (opt in names(newopts)) { - if (opt == "space" && !is.logical(newopts[[opt]])) + if (opt == "space" && !is.null(newopts[[opt]]) && !is.logical(newopts[[opt]])) stop(mstyle$stop("'space' must be a logical.")) if (opt == "digits" && !is.null(newopts[[opt]]) && !is.vector(newopts[[opt]], mode="numeric")) stop(mstyle$stop("'digits' must be a numeric vector.")) - if (opt == "style" && !is.null(newopts[[opt]]) && !is.list(newopts[[opt]])) + if (opt == "style" && !is.logical(newopts[[opt]]) && !is.null(newopts[[opt]]) && !is.list(newopts[[opt]])) stop(mstyle$stop("'style' must be a list.")) if (opt == "theme" && !is.null(newopts[[opt]]) && !is.element(newopts[[opt]], c("default", "light", "dark", "auto", "custom", "default2", "light2", "dark2", "auto2", "custom2"))) stop(mstyle$stop("'theme' must be either 'default(2)', 'light(2)', 'dark(2)', 'auto(2)', or 'custom(2)'.")) - if (opt == "fg" && !is.character(newopts[[opt]])) + if (opt == "fg" && !is.null(newopts[[opt]]) && !is.character(newopts[[opt]])) stop(mstyle$stop("'fg' must be a character string.")) - if (opt == "bg" && !is.character(newopts[[opt]])) + if (opt == "bg" && !is.null(newopts[[opt]]) && !is.character(newopts[[opt]])) stop(mstyle$stop("'bg' must be a character string.")) mfopts[[opt]] <- newopts[[opt]] } diff --git a/R/misc.func.hidden.escalc.r b/R/misc.func.hidden.escalc.r index ef4675158..92991b54e 100644 --- a/R/misc.func.hidden.escalc.r +++ b/R/misc.func.hidden.escalc.r @@ -26,7 +26,7 @@ .rtet <- function(ai, bi, ci, di, maxcor=.9999) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() if (!requireNamespace("mvtnorm", quietly=TRUE)) stop(mstyle$stop("Please install the 'mvtnorm' package to compute this measure."), call.=FALSE) @@ -169,7 +169,7 @@ .Fcalc <- function(a, b, g, x) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() if (!requireNamespace("gsl", quietly=TRUE)) stop(mstyle$stop("Please install the 'gsl' package to use measure='UCOR'."), call.=FALSE) diff --git a/R/misc.func.hidden.funnel.r b/R/misc.func.hidden.funnel.r index 4d408ac80..e71f4742e 100644 --- a/R/misc.func.hidden.funnel.r +++ b/R/misc.func.hidden.funnel.r @@ -2,7 +2,7 @@ .funnel.legend <- function(legend, level, shade, back, yaxis, trimfill, pch, col, bg, pch.fill, pch.vec, col.vec, bg.vec, colci) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() lopts <- list(x = "topright", y = NULL, diff --git a/R/misc.func.hidden.glmm.r b/R/misc.func.hidden.glmm.r index cd55af495..d8eaf9d8c 100644 --- a/R/misc.func.hidden.glmm.r +++ b/R/misc.func.hidden.glmm.r @@ -6,7 +6,7 @@ .dnoncenhypergeom <- function (x=NA_real_, n1, n2, m1, psi) { ### x=ai, n1=ai+bi, n2=ci+di, m1=ai+ci, psi=ORi - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() mode.compute <- function(n1, n2, m1, psi, ll, uu) { a <- psi - 1 @@ -67,7 +67,7 @@ .dnchgi <- function(logOR, ai, bi, ci, di, mu.i, tau2, random, dnchgcalc, dnchgprec) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() k <- length(logOR) dnchgi <- rep(NA_real_, k) @@ -110,7 +110,7 @@ .dnchg <- function(parms, ai, bi, ci, di, X.fit, random, verbose=FALSE, digits, dnchgcalc, dnchgprec, intCtrl) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() p <- ncol(X.fit) k <- length(ai) diff --git a/R/misc.func.hidden.mv.r b/R/misc.func.hidden.mv.r index 64eff9352..c475c5391 100644 --- a/R/misc.func.hidden.mv.r +++ b/R/misc.func.hidden.mv.r @@ -37,7 +37,7 @@ return(vcvals) if (length(ids) != length(vcvals)) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() stop(mstyle$stop(paste0("Length of 'vccon$", vcname, "' (", length(ids), ") does not match length of ", vcname, " (", length(vcvals), ").")), call.=FALSE) } @@ -56,7 +56,7 @@ .process.G.aftersub <- function(mf.g, struct, formula, tau2, rho, isG, k, sparse, verbose) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() if (verbose > 1) message(mstyle$message(paste0("Processing '", paste0(formula, collapse=""), "' term (#1) ..."))) @@ -254,7 +254,7 @@ .process.G.afterrmna <- function(mf.g, g.nlevels, g.levels, g.values, struct, formula, tau2, rho, Z.G1, Z.G2, isG, sparse, distspec, verbose) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() if (verbose > 1) message(mstyle$message(paste0("Processing '", paste0(formula, collapse=""), "' term (#2) ..."))) @@ -865,7 +865,7 @@ sparse, cholesky, nearpd, vctransf, vccov, vccon, verbose, digits, REMLf, dofit=FALSE, hessian=FALSE) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() ### only NA values in sigma2.val, tau2.val, rho.val, gamma2.val, phi.val should be estimated; otherwise, replace with fixed values @@ -1355,7 +1355,7 @@ .ddf.calc <- function(dfs, X, k, p, mf.s=NULL, mf.g=NULL, mf.h=NULL, beta=TRUE) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() if (beta) { diff --git a/R/misc.func.hidden.profile.r b/R/misc.func.hidden.profile.r index 042ffd2cc..fd78f502d 100644 --- a/R/misc.func.hidden.profile.r +++ b/R/misc.func.hidden.profile.r @@ -4,7 +4,7 @@ parallel=FALSE, profile=FALSE, confint=FALSE, subset=FALSE, objective, model=0L, verbose=FALSE, outlist=NULL) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() if (parallel == "snow") library(metafor) @@ -97,7 +97,7 @@ parallel=FALSE, profile=FALSE, confint=FALSE, subset=FALSE, objective, verbose=FALSE) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() if (parallel == "snow") library(metafor) @@ -217,7 +217,7 @@ parallel=FALSE, profile=FALSE, confint=FALSE, subset=FALSE, objective, verbose=FALSE) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() if (parallel == "snow") library(metafor) @@ -285,7 +285,7 @@ parallel=FALSE, profile=FALSE, confint=FALSE, subset=FALSE, objective, verbose=FALSE) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() if (parallel == "snow") library(metafor) diff --git a/R/misc.func.hidden.r b/R/misc.func.hidden.r index b70df7476..4c6915c46 100644 --- a/R/misc.func.hidden.r +++ b/R/misc.func.hidden.r @@ -4,7 +4,7 @@ .set.btt <- function(btt, p, int.incl, Xnames, fixed=FALSE) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() if (missing(btt) || is.null(btt)) { @@ -228,12 +228,12 @@ .level <- function(level, allow.vector=FALSE) { if (!allow.vector && length(level) != 1L) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() stop(mstyle$stop("Argument 'level' must specify a single value."), call.=FALSE) } if (!is.numeric(level)) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() stop(mstyle$stop("The 'level' argument must be numeric."), call.=FALSE) } @@ -334,7 +334,7 @@ .print.time <- function(x) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() hours <- floor(x/60/60) minutes <- floor(x/60) - hours*60 @@ -381,7 +381,7 @@ ddd[okargs[i]] <- NULL if (length(ddd) > 0L) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() warning(mstyle$warning(paste0("Extra argument", ifelse(length(ddd) > 1L, "s ", " "), "(", paste0("'", names(ddd), "'", collapse=", "), ") disregarded.")), call.=FALSE) } @@ -391,7 +391,7 @@ .getx <- function(x, mf, data, enclos=sys.frame(sys.parent(n=2)), checknull=TRUE, checknumeric=FALSE, default) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() mf.getx <- match.call() dname <- deparse1(mf.getx[[match("data", names(mf.getx))]]) @@ -477,7 +477,7 @@ .chkclass <- function(class, must, notap, notav, type="Method") { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() obj <- as.character(match.call()[2]) obj <- substr(obj, 7, nchar(obj)-1) @@ -533,7 +533,7 @@ ok <- TRUE if (!ok) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() warning(mstyle$warning(paste0("The 'vi' argument is for specifying the sampling variances,\nbut '", x, "' sounds like this variable may contain standard\nerrors (maybe use 'sei=", x, "' instead?).")), call.=FALSE) try(assign("runvicheck", FALSE, envir=.metafor), silent=TRUE) } @@ -1114,9 +1114,22 @@ ### stuff related to colored/styled output -.get.mstyle <- function(withcrayon) { +.get.mstyle <- function() { - if (withcrayon) { + crayonloaded <- "crayon" %in% .packages() + + styleopt <- getmfopt("style") + + if (is.logical(styleopt)) { + + if (isTRUE(styleopt)) { + styleopt <- NULL + } else { + crayonloaded <- FALSE + } + } + + if (crayonloaded) { if (exists(".mstyle")) { .mstyle <- get(".mstyle") @@ -1124,8 +1137,6 @@ .mstyle <- list() } - styleopt <- getmfopt("style") - if (!is.null(styleopt)) .mstyle <- styleopt @@ -1408,7 +1419,7 @@ if (is.null(x)) # if x is NULL, return x (i.e., NULL) return(x) - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() argname <- deparse(substitute(x)) @@ -1456,7 +1467,7 @@ if (is.null(x) || is.null(subset)) # if x or subset is NULL, return x return(x) - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() xname <- deparse(substitute(x)) @@ -1498,7 +1509,7 @@ .chkopt <- function(optimizer, optcontrol) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() ### set NLOPT_LN_BOBYQA as the default algorithm for nloptr optimizer ### and by default use a relative convergence criterion of 1e-8 on the function value @@ -1670,7 +1681,7 @@ .chkconv <- function(optimizer, opt.res, optcontrol, fun, verbose) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() if (optimizer == "optimParallel::optimParallel" && verbose) { tmp <- capture.output(print(opt.res$loginfo)) diff --git a/R/misc.func.hidden.selmodel.r b/R/misc.func.hidden.selmodel.r index c2a741925..9db7c917d 100644 --- a/R/misc.func.hidden.selmodel.r +++ b/R/misc.func.hidden.selmodel.r @@ -50,7 +50,7 @@ wi.fun, steps, pgrp, alternative, pval.min, intCtrl, verbose, digits, dofit=FALSE) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() beta <- par[1:pX] tau2 <- par[pX+1] @@ -113,7 +113,7 @@ wi.fun, steps, pgrp, alternative, pval.min, intCtrl, verbose, digits, dofit=FALSE) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() beta <- par[1:pX] tau2 <- par[pX+1] @@ -211,7 +211,7 @@ wi.fun, steps, pgrp, alternative, pval.min, intCtrl, verbose, digits, dofit=FALSE) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() beta <- par[1:pX] tau2 <- par[pX+1] diff --git a/R/misc.func.hidden.uni.r b/R/misc.func.hidden.uni.r index cab04ce2a..7efdc67e3 100644 --- a/R/misc.func.hidden.uni.r +++ b/R/misc.func.hidden.uni.r @@ -22,7 +22,7 @@ .QE.func <- function(tau2val, Y, vi, X, k, objective, verbose=FALSE, digits=4) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() if (any(tau2val + vi < 0)) stop(mstyle$stop("Some marginal variances are negative."), call.=FALSE) @@ -45,7 +45,7 @@ .GENQ.func <- function(tau2val, P, vi, Q, level, k, p, getlower, verbose=FALSE, digits=4) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() S <- diag(sqrt(vi + tau2val), nrow=k, ncol=k) lambda <- Re(eigen(S %*% P %*% S, symmetric=TRUE, only.values=TRUE)$values) @@ -123,7 +123,7 @@ .permci <- function(val, obj, j, exact, iter, progbar, level, digits, control) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() ### fit model with shifted outcome args <- list(yi=obj$yi - c(val*obj$X[,j]), vi=obj$vi, weights=obj$weights, mods=obj$X, intercept=FALSE, method=obj$method, weighted=obj$weighted, @@ -175,7 +175,7 @@ REMLf, link, mZ, alpha.min, alpha.max, alpha.transf, tau2.min, tau2.max, optbeta) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() if (optbeta) { beta <- par[seq_len(pX)] diff --git a/R/model.matrix.rma.r b/R/model.matrix.rma.r index 4469b8992..920ad7cb6 100644 --- a/R/model.matrix.rma.r +++ b/R/model.matrix.rma.r @@ -1,6 +1,6 @@ model.matrix.rma <- function(object, asdf=FALSE, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(object), must="rma") diff --git a/R/nobs.rma.r b/R/nobs.rma.r index 6b6cc9e66..c1b1de157 100644 --- a/R/nobs.rma.r +++ b/R/nobs.rma.r @@ -1,6 +1,6 @@ nobs.rma <- function(object, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(object), must="rma") diff --git a/R/permutest.rma.ls.r b/R/permutest.rma.ls.r index 9bbe3ec08..d70beb3f4 100644 --- a/R/permutest.rma.ls.r +++ b/R/permutest.rma.ls.r @@ -1,6 +1,6 @@ permutest.rma.ls <- function(x, exact=FALSE, iter=1000, progbar=TRUE, digits, control, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="rma.ls") diff --git a/R/permutest.rma.uni.r b/R/permutest.rma.uni.r index 99d879c84..517eefdb9 100644 --- a/R/permutest.rma.uni.r +++ b/R/permutest.rma.uni.r @@ -1,6 +1,6 @@ permutest.rma.uni <- function(x, exact=FALSE, iter=1000, permci=FALSE, progbar=TRUE, digits, control, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="rma.uni", notav=c("robust.rma", "rma.ls", "rma.gen", "rma.uni.selmodel")) diff --git a/R/plot.cumul.rma.r b/R/plot.cumul.rma.r index d2caa846d..c68def1c6 100644 --- a/R/plot.cumul.rma.r +++ b/R/plot.cumul.rma.r @@ -3,7 +3,7 @@ digits, cols, grid=TRUE, pch=19, cex=1, lwd=2, ...) { ######################################################################### - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="cumul.rma") diff --git a/R/plot.gosh.rma.r b/R/plot.gosh.rma.r index 10c03c1dc..9c7fd8747 100644 --- a/R/plot.gosh.rma.r +++ b/R/plot.gosh.rma.r @@ -1,7 +1,7 @@ plot.gosh.rma <- function(x, het="I2", pch=16, cex, out, col, alpha, border, xlim, ylim, xhist=TRUE, yhist=TRUE, hh=0.3, breaks, adjust, lwd, labels, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="gosh.rma") diff --git a/R/plot.infl.rma.uni.r b/R/plot.infl.rma.uni.r index 1cee7fd15..deaaf3deb 100644 --- a/R/plot.infl.rma.uni.r +++ b/R/plot.infl.rma.uni.r @@ -1,7 +1,7 @@ plot.infl.rma.uni <- function(x, plotinf=TRUE, plotdfbs=FALSE, dfbsnew=FALSE, logcov=TRUE, layout, slab.style=1, las=0, pch=21, bg, bg.infl, col.na, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="infl.rma.uni") diff --git a/R/plot.permutest.rma.uni.r b/R/plot.permutest.rma.uni.r index a3affb200..56b5cfcab 100644 --- a/R/plot.permutest.rma.uni.r +++ b/R/plot.permutest.rma.uni.r @@ -4,7 +4,7 @@ plot.permutest.rma.uni <- function(x, beta, alpha, QM=FALSE, QS=FALSE, ######################################################################### - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="permutest.rma.uni") diff --git a/R/plot.profile.rma.r b/R/plot.profile.rma.r index d00eab9ab..c24d7a05b 100644 --- a/R/plot.profile.rma.r +++ b/R/plot.profile.rma.r @@ -2,7 +2,7 @@ plot.profile.rma <- function(x, xlim, ylim, pch=19, xlab, ylab, main, refline=TR ######################################################################### - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="profile.rma") diff --git a/R/plot.rma.glmm.r b/R/plot.rma.glmm.r index 03fc5cd21..64a35e294 100644 --- a/R/plot.rma.glmm.r +++ b/R/plot.rma.glmm.r @@ -2,7 +2,7 @@ plot.rma.glmm <- function(x, qqplot=FALSE, ...) { ######################################################################### - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="rma.glmm", notav="rma.glmm") diff --git a/R/plot.rma.mh.r b/R/plot.rma.mh.r index 2bf1c8307..c91f97c33 100644 --- a/R/plot.rma.mh.r +++ b/R/plot.rma.mh.r @@ -2,7 +2,7 @@ plot.rma.mh <- function(x, qqplot=FALSE, ...) { ######################################################################### - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="rma.mh") diff --git a/R/plot.rma.peto.r b/R/plot.rma.peto.r index 55df707dc..18bf7f2e0 100644 --- a/R/plot.rma.peto.r +++ b/R/plot.rma.peto.r @@ -2,7 +2,7 @@ plot.rma.peto <- function(x, qqplot=FALSE, ...) { ######################################################################### - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="rma.peto") diff --git a/R/plot.rma.uni.r b/R/plot.rma.uni.r index dda56d505..4f96d2333 100644 --- a/R/plot.rma.uni.r +++ b/R/plot.rma.uni.r @@ -2,7 +2,7 @@ plot.rma.uni <- function(x, qqplot=FALSE, ...) { ######################################################################### - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="rma.uni", notav=c("robust.rma", "rma.ls", "rma.gen", "rma.uni.selmodel")) diff --git a/R/plot.rma.uni.selmodel.r b/R/plot.rma.uni.selmodel.r index 5397525ea..3372c2e33 100644 --- a/R/plot.rma.uni.selmodel.r +++ b/R/plot.rma.uni.selmodel.r @@ -4,7 +4,7 @@ plot.rma.uni.selmodel <- function(x, xlim, ylim, n=1000, prec="max", scale=FALSE ######################################################################### - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="rma.uni.selmodel") diff --git a/R/plot.vif.rma.r b/R/plot.vif.rma.r index bf25dd429..4c46a9c88 100644 --- a/R/plot.vif.rma.r +++ b/R/plot.vif.rma.r @@ -4,7 +4,7 @@ plot.vif.rma <- function(x, ######################################################################### - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="vif.rma") diff --git a/R/predict.rma.ls.r b/R/predict.rma.ls.r index 1b1dd4c70..3037a13a8 100644 --- a/R/predict.rma.ls.r +++ b/R/predict.rma.ls.r @@ -3,7 +3,7 @@ level, digits, transf, targs, vcov=FALSE, ...) { ######################################################################### - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(object), must="rma.ls") diff --git a/R/predict.rma.r b/R/predict.rma.r index 4bf9d54ee..75187cfb9 100644 --- a/R/predict.rma.r +++ b/R/predict.rma.r @@ -3,7 +3,7 @@ level, digits, transf, targs, vcov=FALSE, ...) { ######################################################################### - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(object), must="rma", notav="rma.ls") diff --git a/R/print.anova.rma.r b/R/print.anova.rma.r index cfafef9cc..80249a563 100644 --- a/R/print.anova.rma.r +++ b/R/print.anova.rma.r @@ -1,6 +1,6 @@ print.anova.rma <- function(x, digits=x$digits, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="anova.rma") diff --git a/R/print.confint.rma.r b/R/print.confint.rma.r index 50e863c20..004ebffe5 100644 --- a/R/print.confint.rma.r +++ b/R/print.confint.rma.r @@ -1,6 +1,6 @@ print.confint.rma <- function(x, digits=x$digits, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="confint.rma") diff --git a/R/print.escalc.r b/R/print.escalc.r index 4f4c572e7..f58632a5d 100644 --- a/R/print.escalc.r +++ b/R/print.escalc.r @@ -1,6 +1,6 @@ print.escalc <- function(x, digits=attr(x,"digits"), ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="escalc") diff --git a/R/print.fsn.r b/R/print.fsn.r index 57485f427..8d8433ab8 100644 --- a/R/print.fsn.r +++ b/R/print.fsn.r @@ -1,6 +1,6 @@ print.fsn <- function(x, digits=x$digits, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="fsn") diff --git a/R/print.gosh.rma.r b/R/print.gosh.rma.r index fc8a2afa0..041f11da6 100644 --- a/R/print.gosh.rma.r +++ b/R/print.gosh.rma.r @@ -1,6 +1,6 @@ print.gosh.rma <- function(x, digits=x$digits, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="gosh.rma") diff --git a/R/print.hc.rma.uni.r b/R/print.hc.rma.uni.r index dd9a41f60..1923896c5 100644 --- a/R/print.hc.rma.uni.r +++ b/R/print.hc.rma.uni.r @@ -1,6 +1,6 @@ print.hc.rma.uni <- function(x, digits=x$digits, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="hc.rma.uni") diff --git a/R/print.infl.rma.uni.r b/R/print.infl.rma.uni.r index f28241d8c..d893b0a08 100644 --- a/R/print.infl.rma.uni.r +++ b/R/print.infl.rma.uni.r @@ -1,6 +1,6 @@ print.infl.rma.uni <- function(x, digits=x$digits, infonly=FALSE, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="infl.rma.uni") diff --git a/R/print.list.anova.rma.r b/R/print.list.anova.rma.r index bcc875e6d..7969ea7c6 100644 --- a/R/print.list.anova.rma.r +++ b/R/print.list.anova.rma.r @@ -1,6 +1,6 @@ print.list.anova.rma <- function(x, digits=x[[1]]$digits, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="list.anova.rma") diff --git a/R/print.list.confint.rma.r b/R/print.list.confint.rma.r index 2f2bf2dbb..d2af0e6d8 100644 --- a/R/print.list.confint.rma.r +++ b/R/print.list.confint.rma.r @@ -1,6 +1,6 @@ print.list.confint.rma <- function(x, digits=x$digits, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="list.confint.rma") diff --git a/R/print.list.rma.r b/R/print.list.rma.r index 93e75cb28..aed9a4000 100644 --- a/R/print.list.rma.r +++ b/R/print.list.rma.r @@ -1,6 +1,6 @@ print.list.rma <- function(x, digits=x$digits, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="list.rma") diff --git a/R/print.matreg.r b/R/print.matreg.r index 9fbc3e30f..42c24f627 100644 --- a/R/print.matreg.r +++ b/R/print.matreg.r @@ -1,6 +1,6 @@ print.matreg <- function(x, digits=x$digits, signif.stars=getOption("show.signif.stars"), signif.legend=signif.stars, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="matreg") diff --git a/R/print.permutest.rma.uni.r b/R/print.permutest.rma.uni.r index 104994c9a..0aff0a71c 100644 --- a/R/print.permutest.rma.uni.r +++ b/R/print.permutest.rma.uni.r @@ -1,6 +1,6 @@ print.permutest.rma.uni <- function(x, digits=x$digits, signif.stars=getOption("show.signif.stars"), signif.legend=signif.stars, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="permutest.rma.uni") diff --git a/R/print.profile.rma.r b/R/print.profile.rma.r index b9d67db03..4e3bf4640 100644 --- a/R/print.profile.rma.r +++ b/R/print.profile.rma.r @@ -2,7 +2,7 @@ print.profile.rma <- function(x, ...) { ######################################################################### - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="profile.rma") diff --git a/R/print.ranktest.r b/R/print.ranktest.r index faeb5878f..e62e03d3d 100644 --- a/R/print.ranktest.r +++ b/R/print.ranktest.r @@ -1,6 +1,6 @@ print.ranktest <- function(x, digits=x$digits, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="ranktest") diff --git a/R/print.regtest.r b/R/print.regtest.r index 299c90127..f9ab09da4 100644 --- a/R/print.regtest.r +++ b/R/print.regtest.r @@ -1,6 +1,6 @@ print.regtest <- function(x, digits=x$digits, ret.fit=x$ret.fit, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="regtest") diff --git a/R/print.rma.glmm.r b/R/print.rma.glmm.r index e7cb76e74..bc9b01154 100644 --- a/R/print.rma.glmm.r +++ b/R/print.rma.glmm.r @@ -1,6 +1,6 @@ print.rma.glmm <- function(x, digits, showfit=FALSE, signif.stars=getOption("show.signif.stars"), signif.legend=signif.stars, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="rma.glmm") diff --git a/R/print.rma.mh.r b/R/print.rma.mh.r index 612850f32..f19339018 100644 --- a/R/print.rma.mh.r +++ b/R/print.rma.mh.r @@ -1,6 +1,6 @@ print.rma.mh <- function(x, digits, showfit=FALSE, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="rma.mh") diff --git a/R/print.rma.mv.r b/R/print.rma.mv.r index bf9c1af9f..cfe6a1561 100644 --- a/R/print.rma.mv.r +++ b/R/print.rma.mv.r @@ -1,6 +1,6 @@ print.rma.mv <- function(x, digits, showfit=FALSE, signif.stars=getOption("show.signif.stars"), signif.legend=signif.stars, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="rma.mv") diff --git a/R/print.rma.peto.r b/R/print.rma.peto.r index ddc4b6cb5..67a36b719 100644 --- a/R/print.rma.peto.r +++ b/R/print.rma.peto.r @@ -1,6 +1,6 @@ print.rma.peto <- function(x, digits, showfit=FALSE, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="rma.peto") diff --git a/R/print.rma.uni.r b/R/print.rma.uni.r index ca2d51d61..54ad20034 100644 --- a/R/print.rma.uni.r +++ b/R/print.rma.uni.r @@ -1,6 +1,6 @@ print.rma.uni <- function(x, digits, showfit=FALSE, signif.stars=getOption("show.signif.stars"), signif.legend=signif.stars, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="rma.uni") diff --git a/R/print.summary.matreg.r b/R/print.summary.matreg.r index fa5863e3e..76787964f 100644 --- a/R/print.summary.matreg.r +++ b/R/print.summary.matreg.r @@ -1,6 +1,6 @@ print.summary.matreg <- function(x, digits=x$digits, signif.stars=getOption("show.signif.stars"), signif.legend=signif.stars, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="summary.matreg") diff --git a/R/print.summary.rma.r b/R/print.summary.rma.r index f52385b5c..1d7a4dece 100644 --- a/R/print.summary.rma.r +++ b/R/print.summary.rma.r @@ -1,6 +1,6 @@ print.summary.rma <- function(x, digits=x$digits, showfit=TRUE, signif.stars=getOption("show.signif.stars"), signif.legend=signif.stars, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="summary.rma") diff --git a/R/print.tes.r b/R/print.tes.r index bc65de45c..ba0c06ed3 100644 --- a/R/print.tes.r +++ b/R/print.tes.r @@ -1,6 +1,6 @@ print.tes <- function(x, digits=x$digits, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="tes") diff --git a/R/print.vif.rma.r b/R/print.vif.rma.r index b004af4d1..a27196884 100644 --- a/R/print.vif.rma.r +++ b/R/print.vif.rma.r @@ -1,6 +1,6 @@ print.vif.rma <- function(x, digits=x$digits, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="vif.rma") diff --git a/R/profile.rma.ls.r b/R/profile.rma.ls.r index 287c619dc..008e47b3d 100644 --- a/R/profile.rma.ls.r +++ b/R/profile.rma.ls.r @@ -1,7 +1,7 @@ profile.rma.ls <- function(fitted, alpha, xlim, ylim, steps=20, lltol=1e-03, progbar=TRUE, parallel="no", ncpus=1, cl, plot=TRUE, pch=19, refline=TRUE, cline=FALSE, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(fitted), must="rma.ls") diff --git a/R/profile.rma.mv.r b/R/profile.rma.mv.r index 24c7c75f2..387a3d9c7 100644 --- a/R/profile.rma.mv.r +++ b/R/profile.rma.mv.r @@ -1,7 +1,7 @@ profile.rma.mv <- function(fitted, sigma2, tau2, rho, gamma2, phi, xlim, ylim, steps=20, lltol=1e-03, progbar=TRUE, parallel="no", ncpus=1, cl, plot=TRUE, pch=19, refline=TRUE, cline=FALSE, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(fitted), must="rma.mv") diff --git a/R/profile.rma.uni.r b/R/profile.rma.uni.r index 47b754587..58986e1be 100644 --- a/R/profile.rma.uni.r +++ b/R/profile.rma.uni.r @@ -1,7 +1,7 @@ profile.rma.uni <- function(fitted, xlim, ylim, steps=20, lltol=1e-03, progbar=TRUE, parallel="no", ncpus=1, cl, plot=TRUE, pch=19, refline=TRUE, cline=FALSE, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(fitted), must="rma.uni", notav=c("rma.gen", "rma.uni.selmodel")) diff --git a/R/profile.rma.uni.selmodel.r b/R/profile.rma.uni.selmodel.r index a810c5277..31382dd2e 100644 --- a/R/profile.rma.uni.selmodel.r +++ b/R/profile.rma.uni.selmodel.r @@ -1,7 +1,7 @@ profile.rma.uni.selmodel <- function(fitted, tau2, delta, xlim, ylim, steps=20, lltol=1e-03, progbar=TRUE, parallel="no", ncpus=1, cl, plot=TRUE, pch=19, refline=TRUE, cline=FALSE, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(fitted), must="rma.uni.selmodel") diff --git a/R/qqnorm.rma.glmm.r b/R/qqnorm.rma.glmm.r index a06d3c57c..e3781c7a3 100644 --- a/R/qqnorm.rma.glmm.r +++ b/R/qqnorm.rma.glmm.r @@ -1,6 +1,6 @@ qqnorm.rma.glmm <- function(y, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(y), must="rma.glmm", notav="rma.glmm") diff --git a/R/qqnorm.rma.mh.r b/R/qqnorm.rma.mh.r index ae7453236..f9612aa5f 100644 --- a/R/qqnorm.rma.mh.r +++ b/R/qqnorm.rma.mh.r @@ -1,6 +1,6 @@ qqnorm.rma.mh <- function(y, type="rstandard", pch=21, col, bg, label=FALSE, offset=0.3, pos=13, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(y), must="rma.mh") diff --git a/R/qqnorm.rma.mv.r b/R/qqnorm.rma.mv.r index 3c266c8e2..234ceed62 100644 --- a/R/qqnorm.rma.mv.r +++ b/R/qqnorm.rma.mv.r @@ -1,6 +1,6 @@ qqnorm.rma.mv <- function(y, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(y), must="rma.mv", notav="rma.mv") diff --git a/R/qqnorm.rma.peto.r b/R/qqnorm.rma.peto.r index 4926da963..bf4f31a35 100644 --- a/R/qqnorm.rma.peto.r +++ b/R/qqnorm.rma.peto.r @@ -1,6 +1,6 @@ qqnorm.rma.peto <- function(y, type="rstandard", pch=21, col, bg, label=FALSE, offset=0.3, pos=13, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(y), must="rma.peto") diff --git a/R/qqnorm.rma.uni.r b/R/qqnorm.rma.uni.r index 32844256d..923b055c0 100644 --- a/R/qqnorm.rma.uni.r +++ b/R/qqnorm.rma.uni.r @@ -2,7 +2,7 @@ qqnorm.rma.uni <- function(y, type="rstandard", pch=21, col, bg, envelope=TRUE, level=y$level, bonferroni=FALSE, reps=1000, smooth=TRUE, bass=0, label=FALSE, offset=0.3, pos=13, lty, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(y), must="rma.uni", notav=c("rma.gen", "rma.uni.selmodel")) diff --git a/R/radial.rma.r b/R/radial.rma.r index 236dde4ac..e6db443b5 100644 --- a/R/radial.rma.r +++ b/R/radial.rma.r @@ -4,7 +4,7 @@ transf, targs, pch=21, col, bg, back, arc.res=100, cex, cex.lab, cex.axis, ...) ######################################################################### - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="rma", notav=c("robust.rma", "rma.mv", "rma.ls", "rma.gen", "rma.uni.selmodel")) diff --git a/R/ranef.rma.mv.r b/R/ranef.rma.mv.r index 88a7aaf3a..74ce6cd7e 100644 --- a/R/ranef.rma.mv.r +++ b/R/ranef.rma.mv.r @@ -1,6 +1,6 @@ ranef.rma.mv <- function(object, level, digits, transf, targs, verbose=FALSE, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(object), must="rma.mv") diff --git a/R/ranef.rma.uni.r b/R/ranef.rma.uni.r index 3a4bce648..f6afcde69 100644 --- a/R/ranef.rma.uni.r +++ b/R/ranef.rma.uni.r @@ -1,6 +1,6 @@ ranef.rma.uni <- function(object, level, digits, transf, targs, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(object), must="rma.uni", notav=c("rma.gen", "rma.uni.selmodel")) diff --git a/R/ranktest.r b/R/ranktest.r index 3b57a9066..e3acbea8b 100644 --- a/R/ranktest.r +++ b/R/ranktest.r @@ -2,7 +2,7 @@ ranktest <- function(x, vi, sei, subset, data, digits, ...) { ######################################################################### - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() na.act <- getOption("na.action") diff --git a/R/rcalc.r b/R/rcalc.r index 2515f2b04..58196eb7b 100644 --- a/R/rcalc.r +++ b/R/rcalc.r @@ -1,6 +1,6 @@ rcalc <- function(x, ni, data, rtoz=FALSE, nfun="min", sparse=FALSE, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() if (!(inherits(x, "formula") || inherits(x, "matrix") || inherits(x, "list"))) stop(mstyle$stop("Argument 'x' must be either a formula, a matrix, or a list of matrices.")) diff --git a/R/regplot.rma.r b/R/regplot.rma.r index ff9146207..cf837562b 100644 --- a/R/regplot.rma.r +++ b/R/regplot.rma.r @@ -7,7 +7,7 @@ lcol, lwd, lty, legend=FALSE, xvals, ...) { ######################################################################### - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="rma", notav=c("rma.mh","rma.peto")) diff --git a/R/regtest.r b/R/regtest.r index 67f4bfd9b..c1070c8d2 100644 --- a/R/regtest.r +++ b/R/regtest.r @@ -2,7 +2,7 @@ regtest <- function(x, vi, sei, ni, subset, data, model="rma", predictor="sei", ######################################################################### - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() na.act <- getOption("na.action") diff --git a/R/replmiss.r b/R/replmiss.r index fce9ff780..fd889b377 100644 --- a/R/replmiss.r +++ b/R/replmiss.r @@ -1,6 +1,6 @@ replmiss <- function(x, y, data) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() ### check if data argument has been specified diff --git a/R/reporter.rma.uni.r b/R/reporter.rma.uni.r index eab805cbf..642fdf70f 100644 --- a/R/reporter.rma.uni.r +++ b/R/reporter.rma.uni.r @@ -1,6 +1,6 @@ reporter.rma.uni <- function(x, dir, filename, format="html_document", open=TRUE, digits, forest, funnel, footnotes=FALSE, verbose=TRUE, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="rma.uni", notav=c("robust.rma", "rma.ls", "rma.gen", "rma.uni.selmodel")) diff --git a/R/residuals.rma.r b/R/residuals.rma.r index 47e24ef07..68a801660 100644 --- a/R/residuals.rma.r +++ b/R/residuals.rma.r @@ -1,6 +1,6 @@ residuals.rma <- function(object, type="response", ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(object), must="rma") diff --git a/R/rma.glmm.r b/R/rma.glmm.r index 0cd035c50..efb5c549e 100644 --- a/R/rma.glmm.r +++ b/R/rma.glmm.r @@ -9,7 +9,7 @@ test="z", level=95, btt, nAGQ=7, verbose=FALSE, digits, control, ...) { ###### setup - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() ### check argument specifications ### (arguments "to" and "vtype" are checked inside escalc function) diff --git a/R/rma.mh.r b/R/rma.mh.r index 8c344d6ca..cb9fdae32 100644 --- a/R/rma.mh.r +++ b/R/rma.mh.r @@ -7,7 +7,7 @@ correct=TRUE, level=95, verbose=FALSE, digits, ...) { ###### setup - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() ### check argument specifications diff --git a/R/rma.mv.r b/R/rma.mv.r index 324465265..0c1a62bde 100644 --- a/R/rma.mv.r +++ b/R/rma.mv.r @@ -38,7 +38,7 @@ cvvc=FALSE, sparse=FALSE, verbose=FALSE, digits, control, ...) { ### check argument specifications - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() if (!is.element(method, c("FE","EE","CE","ML","REML"))) stop(mstyle$stop("Unknown 'method' specified.")) diff --git a/R/rma.peto.r b/R/rma.peto.r index c7235eeef..c7073ad0e 100644 --- a/R/rma.peto.r +++ b/R/rma.peto.r @@ -7,7 +7,7 @@ level=95, verbose=FALSE, digits, ...) { ###### setup - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() ### check argument specifications diff --git a/R/rma.uni.r b/R/rma.uni.r index 26bd73bd6..9cf8675a7 100644 --- a/R/rma.uni.r +++ b/R/rma.uni.r @@ -9,7 +9,7 @@ test="z", level=95, btt, att, tau2, verbose=FALSE, digits, control, ...) { ###### setup - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() ### check argument specifications ### (arguments "to" and "vtype" are checked inside escalc function) diff --git a/R/robust.rma.mv.r b/R/robust.rma.mv.r index 06a828e94..ca59e285d 100644 --- a/R/robust.rma.mv.r +++ b/R/robust.rma.mv.r @@ -1,6 +1,6 @@ robust.rma.mv <- function(x, cluster, adjust=TRUE, clubSandwich=FALSE, digits, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="rma.mv") diff --git a/R/robust.rma.uni.r b/R/robust.rma.uni.r index 037a354c6..cabbb5a8e 100644 --- a/R/robust.rma.uni.r +++ b/R/robust.rma.uni.r @@ -1,6 +1,6 @@ robust.rma.uni <- function(x, cluster, adjust=TRUE, clubSandwich=FALSE, digits, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="rma.uni", notav=c("rma.ls", "rma.gen", "rma.uni.selmodel")) diff --git a/R/rstandard.rma.mh.r b/R/rstandard.rma.mh.r index c2a729a3e..e6f9f3534 100644 --- a/R/rstandard.rma.mh.r +++ b/R/rstandard.rma.mh.r @@ -1,6 +1,6 @@ rstandard.rma.mh <- function(model, digits, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(model), must="rma.mh") diff --git a/R/rstandard.rma.mv.r b/R/rstandard.rma.mv.r index 9bcccf2f0..caf6bd23f 100644 --- a/R/rstandard.rma.mv.r +++ b/R/rstandard.rma.mv.r @@ -1,6 +1,6 @@ rstandard.rma.mv <- function(model, digits, cluster, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(model), must="rma.mv", notav="robust.rma") diff --git a/R/rstandard.rma.peto.r b/R/rstandard.rma.peto.r index 6987b0c6d..8fcd665d4 100644 --- a/R/rstandard.rma.peto.r +++ b/R/rstandard.rma.peto.r @@ -1,6 +1,6 @@ rstandard.rma.peto <- function(model, digits, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(model), must="rma.peto") diff --git a/R/rstandard.rma.uni.r b/R/rstandard.rma.uni.r index b63d4cf7f..c6e942e89 100644 --- a/R/rstandard.rma.uni.r +++ b/R/rstandard.rma.uni.r @@ -1,6 +1,6 @@ rstandard.rma.uni <- function(model, digits, type="marginal", ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(model), must="rma.uni", notav=c("robust.rma", "rma.gen", "rma.uni.selmodel")) diff --git a/R/rstudent.rma.mh.r b/R/rstudent.rma.mh.r index 5bd74c240..4f8618ba2 100644 --- a/R/rstudent.rma.mh.r +++ b/R/rstudent.rma.mh.r @@ -1,6 +1,6 @@ rstudent.rma.mh <- function(model, digits, progbar=FALSE, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(model), must="rma.mh") diff --git a/R/rstudent.rma.mv.r b/R/rstudent.rma.mv.r index 911bfd19e..c5a7ec9df 100644 --- a/R/rstudent.rma.mv.r +++ b/R/rstudent.rma.mv.r @@ -1,6 +1,6 @@ rstudent.rma.mv <- function(model, digits, progbar=FALSE, cluster, reestimate=TRUE, parallel="no", ncpus=1, cl, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(model), must="rma.mv", notav="robust.rma") diff --git a/R/rstudent.rma.peto.r b/R/rstudent.rma.peto.r index 3d825d2fa..810dd993d 100644 --- a/R/rstudent.rma.peto.r +++ b/R/rstudent.rma.peto.r @@ -1,6 +1,6 @@ rstudent.rma.peto <- function(model, digits, progbar=FALSE, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(model), must="rma.peto") diff --git a/R/selmodel.rma.uni.r b/R/selmodel.rma.uni.r index 0be945248..1208aed4d 100644 --- a/R/selmodel.rma.uni.r +++ b/R/selmodel.rma.uni.r @@ -3,7 +3,7 @@ selmodel.rma.uni <- function(x, type, alternative="greater", prec, delta, steps, # TODO: add a H0 argument? since p-value may not be based on H0: theta_i = 0 # TODO: argument for which deltas to include in LRT (a delta may also not be constrained under H0, so it should not be included in the LRT then) - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="rma.uni", notav=c("rma.ls", "rma.gen", "robust.rma")) diff --git a/R/simulate.rma.r b/R/simulate.rma.r index c3fc04c47..94b232825 100644 --- a/R/simulate.rma.r +++ b/R/simulate.rma.r @@ -1,6 +1,6 @@ simulate.rma <- function(object, nsim=1, seed=NULL, olim, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(object), must="rma", notav=c("rma.gen", "rma.glmm", "rma.mh", "rma.peto", "rma.uni.selmodel")) diff --git a/R/summary.escalc.r b/R/summary.escalc.r index 0a2cfa1bc..a100e0729 100644 --- a/R/summary.escalc.r +++ b/R/summary.escalc.r @@ -1,7 +1,7 @@ summary.escalc <- function(object, out.names=c("sei","zi","pval","ci.lb","ci.ub"), var.names, H0=0, append=TRUE, replace=TRUE, level=95, olim, digits, transf, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(object), must="escalc") diff --git a/R/summary.matreg.r b/R/summary.matreg.r index a590c944f..490fe3927 100644 --- a/R/summary.matreg.r +++ b/R/summary.matreg.r @@ -1,6 +1,6 @@ summary.matreg <- function(object, digits, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(object), must="matreg") diff --git a/R/summary.rma.r b/R/summary.rma.r index e0eb8755b..4a7a6dbde 100644 --- a/R/summary.rma.r +++ b/R/summary.rma.r @@ -1,6 +1,6 @@ summary.rma <- function(object, digits, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(object), must="rma") diff --git a/R/tes.r b/R/tes.r index 1f8a725ee..ba07c4db1 100644 --- a/R/tes.r +++ b/R/tes.r @@ -7,7 +7,7 @@ tes <- function(x, vi, sei, subset, data, ######################################################################### - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() na.act <- getOption("na.action") diff --git a/R/to.long.r b/R/to.long.r index 4fc3e5e18..27f265814 100644 --- a/R/to.long.r +++ b/R/to.long.r @@ -1,7 +1,7 @@ to.long <- function(measure, ai, bi, ci, di, n1i, n2i, x1i, x2i, t1i, t2i, m1i, m2i, sd1i, sd2i, xi, mi, ri, ti, sdi, ni, data, slab, subset, add=1/2, to="none", drop00=FALSE, vlong=FALSE, append=TRUE, var.names) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() ### check argument specifications diff --git a/R/to.table.r b/R/to.table.r index dea304739..a4aa1e930 100644 --- a/R/to.table.r +++ b/R/to.table.r @@ -1,7 +1,7 @@ to.table <- function(measure, ai, bi, ci, di, n1i, n2i, x1i, x2i, t1i, t2i, m1i, m2i, sd1i, sd2i, xi, mi, ri, ti, sdi, ni, data, slab, subset, add=1/2, to="none", drop00=FALSE, rows, cols) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() ### check argument specifications diff --git a/R/to.wide.r b/R/to.wide.r index 2c80f1e2a..eef9f0bd5 100644 --- a/R/to.wide.r +++ b/R/to.wide.r @@ -1,7 +1,7 @@ to.wide <- function(data, study, grp, ref, grpvars, postfix=c(".1",".2"), addid=TRUE, addcomp=TRUE, adddesign=TRUE, minlen=2, var.names=c("id","comp","design")) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() if (!is.data.frame(data)) data <- data.frame(data) diff --git a/R/trimfill.rma.uni.r b/R/trimfill.rma.uni.r index 09ca37b67..3aa93519b 100644 --- a/R/trimfill.rma.uni.r +++ b/R/trimfill.rma.uni.r @@ -2,7 +2,7 @@ trimfill.rma.uni <- function(x, side, estimator="L0", maxiter=100, verbose=FALSE ######################################################################### - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="rma.uni", notav=c("robust.rma", "rma.ls", "rma.gen", "rma.uni.selmodel")) diff --git a/R/update.rma.r b/R/update.rma.r index 5b183697a..a89e48502 100644 --- a/R/update.rma.r +++ b/R/update.rma.r @@ -2,7 +2,7 @@ update.rma <- function(object, formula., ..., evaluate=TRUE) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(object), must="rma", notav="robust.rma") diff --git a/R/vcalc.r b/R/vcalc.r index 688fc5c11..4ee16a582 100644 --- a/R/vcalc.r +++ b/R/vcalc.r @@ -1,7 +1,7 @@ vcalc <- function(vi, cluster, subgroup, obs, type, time1, time2, grp1, grp2, w1, w2, data, rho, phi, rvars, checkpd=TRUE, nearpd=FALSE, sparse=FALSE, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() ############################################################################ diff --git a/R/vcov.matreg.r b/R/vcov.matreg.r index e93841d44..7285bab08 100644 --- a/R/vcov.matreg.r +++ b/R/vcov.matreg.r @@ -1,6 +1,6 @@ vcov.matreg <- function(object, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(object), must="matreg") diff --git a/R/vcov.rma.r b/R/vcov.rma.r index 56aceea4b..1fbc88403 100644 --- a/R/vcov.rma.r +++ b/R/vcov.rma.r @@ -1,6 +1,6 @@ vcov.rma <- function(object, type="fixed", ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(object), must="rma") diff --git a/R/vec2mat.r b/R/vec2mat.r index 4c6c12660..ed441e588 100644 --- a/R/vec2mat.r +++ b/R/vec2mat.r @@ -1,6 +1,6 @@ vec2mat <- function(x, diag=FALSE, corr=!diag, dimnames) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() p <- length(x) diff --git a/R/vif.rma.r b/R/vif.rma.r index 6639ac574..7e3028f90 100644 --- a/R/vif.rma.r +++ b/R/vif.rma.r @@ -3,7 +3,7 @@ vif.rma <- function(x, btt, att, table=FALSE, reestimate=FALSE, sim=FALSE, progb ######################################################################### - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(x), must="rma") diff --git a/R/weights.rma.glmm.r b/R/weights.rma.glmm.r index 30b57de64..7458c1f2c 100644 --- a/R/weights.rma.glmm.r +++ b/R/weights.rma.glmm.r @@ -1,6 +1,6 @@ weights.rma.glmm <- function(object, ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(object), must="rma.glmm", notav="rma.glmm") diff --git a/R/weights.rma.mh.r b/R/weights.rma.mh.r index e3afaf17c..e16a85a07 100644 --- a/R/weights.rma.mh.r +++ b/R/weights.rma.mh.r @@ -1,6 +1,6 @@ weights.rma.mh <- function(object, type="diagonal", ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(object), must="rma.mh") diff --git a/R/weights.rma.mv.r b/R/weights.rma.mv.r index 540ea9b93..b20b93a10 100644 --- a/R/weights.rma.mv.r +++ b/R/weights.rma.mv.r @@ -1,6 +1,6 @@ weights.rma.mv <- function(object, type="diagonal", ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(object), must="rma.mv") diff --git a/R/weights.rma.peto.r b/R/weights.rma.peto.r index 1ee36a3c9..e5899d463 100644 --- a/R/weights.rma.peto.r +++ b/R/weights.rma.peto.r @@ -1,6 +1,6 @@ weights.rma.peto <- function(object, type="diagonal", ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(object), must="rma.peto") diff --git a/R/weights.rma.uni.r b/R/weights.rma.uni.r index d0d4038d5..8997d5fdb 100644 --- a/R/weights.rma.uni.r +++ b/R/weights.rma.uni.r @@ -1,6 +1,6 @@ weights.rma.uni <- function(object, type="diagonal", ...) { - mstyle <- .get.mstyle("crayon" %in% .packages()) + mstyle <- .get.mstyle() .chkclass(class(object), must="rma.uni", notav=c("rma.gen", "rma.uni.selmodel")) diff --git a/R/zzz.r b/R/zzz.r index a246ebbf8..0493c926b 100644 --- a/R/zzz.r +++ b/R/zzz.r @@ -1,6 +1,6 @@ .onAttach <- function(libname, pkgname) { - ver <- "4.5-3" + ver <- "4.5-4" loadmsg <- paste0("\nLoading the 'metafor' package (version ", ver, "). For an\nintroduction to the package please type: help(metafor)\n") diff --git a/README.md b/README.md index 662b1c35a..af91c6e93 100644 --- a/README.md +++ b/README.md @@ -5,7 +5,7 @@ metafor: A Meta-Analysis Package for R [![R build status](https://github.com/wviechtb/metafor/workflows/R-CMD-check/badge.svg)](https://github.com/wviechtb/metafor/actions) [![Code Coverage](https://codecov.io/gh/wviechtb/metafor/branch/master/graph/badge.svg)](https://app.codecov.io/gh/wviechtb/metafor) [![CRAN Version](https://www.r-pkg.org/badges/version/metafor)](https://cran.r-project.org/package=metafor) -[![devel Version](https://img.shields.io/badge/devel-4.5--3-brightgreen.svg)](https://www.metafor-project.org/doku.php/installation#development_version) +[![devel Version](https://img.shields.io/badge/devel-4.5--4-brightgreen.svg)](https://www.metafor-project.org/doku.php/installation#development_version) [![Monthly Downloads](https://cranlogs.r-pkg.org/badges/metafor)](https://cranlogs.r-pkg.org/badges/metafor) [![Total Downloads](https://cranlogs.r-pkg.org/badges/grand-total/metafor)](https://cranlogs.r-pkg.org/badges/grand-total/metafor) diff --git a/docs/404.html b/docs/404.html index f18c4c353..20169908e 100644 --- a/docs/404.html +++ b/docs/404.html @@ -54,7 +54,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/ISSUE_TEMPLATE.html b/docs/ISSUE_TEMPLATE.html index 391ee15f3..0ec7f4f7c 100644 --- a/docs/ISSUE_TEMPLATE.html +++ b/docs/ISSUE_TEMPLATE.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/articles/index.html b/docs/articles/index.html index 1dee2a4e2..310c16d2f 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/articles/pkgdown/diagram.html b/docs/articles/pkgdown/diagram.html index 414c2c73c..aad2d4d51 100644 --- a/docs/articles/pkgdown/diagram.html +++ b/docs/articles/pkgdown/diagram.html @@ -55,7 +55,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/authors.html b/docs/authors.html index 29eee7c39..ab71c2aec 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/index.html b/docs/index.html index 6472453ca..888228903 100644 --- a/docs/index.html +++ b/docs/index.html @@ -55,7 +55,7 @@ metafor - 4.5-3 + 4.5-4 @@ -127,7 +127,7 @@

metafor: A Meta-Analysis Package for R

-

License: GPL (>=2) R build status Code Coverage CRAN Version devel Version Monthly Downloads Total Downloads

+

License: GPL (>=2) R build status Code Coverage CRAN Version devel Version Monthly Downloads Total Downloads

Description

diff --git a/docs/news/index.html b/docs/news/index.html index c99839cb0..3d237d1f3 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4
@@ -96,8 +96,10 @@

Changelog

-

metafor 4.5-3 (2023-10-23)

-
+

metafor 4.5-4 (2023-10-23)

+

metafor 4.4-0 (2023-09-27)2023-09-27

diff --git a/docs/reference/addpoly.html b/docs/reference/addpoly.html index b0bbe31a6..995ca14bb 100644 --- a/docs/reference/addpoly.html +++ b/docs/reference/addpoly.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/addpoly.predict.rma.html b/docs/reference/addpoly.predict.rma.html index 92d3bb0c4..285702d9d 100644 --- a/docs/reference/addpoly.predict.rma.html +++ b/docs/reference/addpoly.predict.rma.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/addpoly.rma.html b/docs/reference/addpoly.rma.html index 37fafc2f6..8627fe461 100644 --- a/docs/reference/addpoly.rma.html +++ b/docs/reference/addpoly.rma.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/aggregate.escalc.html b/docs/reference/aggregate.escalc.html index 0e3b677a0..884210a6f 100644 --- a/docs/reference/aggregate.escalc.html +++ b/docs/reference/aggregate.escalc.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/anova.rma.html b/docs/reference/anova.rma.html index df63de5a5..f841355bb 100644 --- a/docs/reference/anova.rma.html +++ b/docs/reference/anova.rma.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/baujat.html b/docs/reference/baujat.html index 0fd0091a9..0937fc34c 100644 --- a/docs/reference/baujat.html +++ b/docs/reference/baujat.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/bldiag.html b/docs/reference/bldiag.html index 762d6f791..2af44d3ae 100644 --- a/docs/reference/bldiag.html +++ b/docs/reference/bldiag.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/blsplit.html b/docs/reference/blsplit.html index c6b938551..1b85716be 100644 --- a/docs/reference/blsplit.html +++ b/docs/reference/blsplit.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/blup.html b/docs/reference/blup.html index 76643fcac..60c521f75 100644 --- a/docs/reference/blup.html +++ b/docs/reference/blup.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/coef.permutest.rma.uni.html b/docs/reference/coef.permutest.rma.uni.html index 358361865..d1e9dd9c7 100644 --- a/docs/reference/coef.permutest.rma.uni.html +++ b/docs/reference/coef.permutest.rma.uni.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/coef.rma.html b/docs/reference/coef.rma.html index 36a5dd9b6..0c5a11134 100644 --- a/docs/reference/coef.rma.html +++ b/docs/reference/coef.rma.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/confint.rma.html b/docs/reference/confint.rma.html index 5aae28b59..0b821fd30 100644 --- a/docs/reference/confint.rma.html +++ b/docs/reference/confint.rma.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/contrmat.html b/docs/reference/contrmat.html index f040bac8d..5834af801 100644 --- a/docs/reference/contrmat.html +++ b/docs/reference/contrmat.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/conv.2x2.html b/docs/reference/conv.2x2.html index f6a6978a1..19eb6f7ab 100644 --- a/docs/reference/conv.2x2.html +++ b/docs/reference/conv.2x2.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/conv.delta.html b/docs/reference/conv.delta.html index 95121d5a5..69dbd0341 100644 --- a/docs/reference/conv.delta.html +++ b/docs/reference/conv.delta.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/conv.fivenum.html b/docs/reference/conv.fivenum.html index b7a0749e5..863374662 100644 --- a/docs/reference/conv.fivenum.html +++ b/docs/reference/conv.fivenum.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/conv.wald.html b/docs/reference/conv.wald.html index af048529a..3ce9f3be3 100644 --- a/docs/reference/conv.wald.html +++ b/docs/reference/conv.wald.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/cumul.html b/docs/reference/cumul.html index 095597075..31a9dfd54 100644 --- a/docs/reference/cumul.html +++ b/docs/reference/cumul.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/dfround.html b/docs/reference/dfround.html index e0167cbde..a87831e2d 100644 --- a/docs/reference/dfround.html +++ b/docs/reference/dfround.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/emmprep.html b/docs/reference/emmprep.html index fddf658f2..c8a6da844 100644 --- a/docs/reference/emmprep.html +++ b/docs/reference/emmprep.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/escalc.html b/docs/reference/escalc.html index 457a1e799..59d6a01e6 100644 --- a/docs/reference/escalc.html +++ b/docs/reference/escalc.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/fitstats.html b/docs/reference/fitstats.html index 53ad9f139..d545530a3 100644 --- a/docs/reference/fitstats.html +++ b/docs/reference/fitstats.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/fitted.rma.html b/docs/reference/fitted.rma.html index 771e3900a..b5051038e 100644 --- a/docs/reference/fitted.rma.html +++ b/docs/reference/fitted.rma.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/forest.cumul.rma.html b/docs/reference/forest.cumul.rma.html index 342d4f371..00dc69753 100644 --- a/docs/reference/forest.cumul.rma.html +++ b/docs/reference/forest.cumul.rma.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/forest.default.html b/docs/reference/forest.default.html index 15b570488..2ce08a3b4 100644 --- a/docs/reference/forest.default.html +++ b/docs/reference/forest.default.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/forest.html b/docs/reference/forest.html index d86a43b01..a200c558e 100644 --- a/docs/reference/forest.html +++ b/docs/reference/forest.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/forest.rma.html b/docs/reference/forest.rma.html index 1bb73cec2..86bee2768 100644 --- a/docs/reference/forest.rma.html +++ b/docs/reference/forest.rma.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/formatters.html b/docs/reference/formatters.html index 51d3300e1..1ccf5b1c6 100644 --- a/docs/reference/formatters.html +++ b/docs/reference/formatters.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/formula.rma.html b/docs/reference/formula.rma.html index a37aa1c54..f6b59a5af 100644 --- a/docs/reference/formula.rma.html +++ b/docs/reference/formula.rma.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 @@ -149,13 +149,13 @@

Examples

res <- rma(yi, vi, mods = ~ ablat + alloc, data=dat) formula(res, type="mods") #> ~ablat + alloc -#> <environment: 0x555dbe9c21f8> +#> <environment: 0x55b8d01115a0> ### specify moderators via 'yi' argument res <- rma(yi ~ ablat + alloc, vi, data=dat) formula(res, type="yi") #> yi ~ ablat + alloc -#> <environment: 0x555dbe4e2b70> +#> <environment: 0x55b8cd31a658> diff --git a/docs/reference/fsn.html b/docs/reference/fsn.html index 3af99c5de..8931177d1 100644 --- a/docs/reference/fsn.html +++ b/docs/reference/fsn.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/funnel.html b/docs/reference/funnel.html index 70fe3abe3..3befd8ad9 100644 --- a/docs/reference/funnel.html +++ b/docs/reference/funnel.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/gosh.html b/docs/reference/gosh.html index ea6424cc4..053468355 100644 --- a/docs/reference/gosh.html +++ b/docs/reference/gosh.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/hc.html b/docs/reference/hc.html index 745f06166..591ca14b2 100644 --- a/docs/reference/hc.html +++ b/docs/reference/hc.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/index.html b/docs/reference/index.html index d4f4f63af..49a8b332d 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/influence.rma.mv.html b/docs/reference/influence.rma.mv.html index df7ecb2d6..59ba0ded2 100644 --- a/docs/reference/influence.rma.mv.html +++ b/docs/reference/influence.rma.mv.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/influence.rma.uni.html b/docs/reference/influence.rma.uni.html index c2aa89407..bfe33be57 100644 --- a/docs/reference/influence.rma.uni.html +++ b/docs/reference/influence.rma.uni.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/labbe.html b/docs/reference/labbe.html index 0ad56b1f3..e0df25937 100644 --- a/docs/reference/labbe.html +++ b/docs/reference/labbe.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/leave1out.html b/docs/reference/leave1out.html index 54b2c546b..0be65f4ae 100644 --- a/docs/reference/leave1out.html +++ b/docs/reference/leave1out.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/llplot.html b/docs/reference/llplot.html index c387d8e7f..a28ce4f7c 100644 --- a/docs/reference/llplot.html +++ b/docs/reference/llplot.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/matreg.html b/docs/reference/matreg.html index fa2f07c0b..ec900ded7 100644 --- a/docs/reference/matreg.html +++ b/docs/reference/matreg.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/metafor-package.html b/docs/reference/metafor-package.html index 6bc49ec03..71ecf77aa 100644 --- a/docs/reference/metafor-package.html +++ b/docs/reference/metafor-package.html @@ -31,7 +31,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/metafor.news.html b/docs/reference/metafor.news.html index c89f793f3..4abf1d396 100644 --- a/docs/reference/metafor.news.html +++ b/docs/reference/metafor.news.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 @@ -121,11 +121,13 @@

References

Examples

# \dontrun{
 metafor.news()
-#>                  Changes in version 4.5-3 (2023-10-23)                  
+#>                  Changes in version 4.5-4 (2023-10-23)                  
 #> 
 #>   - a few minor fixes to the dynamic theming of plots based on the
 #>     foreground and background colors of the plotting device
 #> 
+#>   - slightly improved flexibility for setting package options
+#> 
 #>                  Changes in version 4.4-0 (2023-09-27)                  
 #> 
 #>   - added getmfopt() and setmfopt() functions for getting and setting
diff --git a/docs/reference/methods.anova.rma.html b/docs/reference/methods.anova.rma.html
index 124c9ce4a..688c16121 100644
--- a/docs/reference/methods.anova.rma.html
+++ b/docs/reference/methods.anova.rma.html
@@ -29,7 +29,7 @@
       
       
         metafor
-        4.5-3
+        4.5-4
diff --git a/docs/reference/methods.confint.rma.html b/docs/reference/methods.confint.rma.html index 8073b68a9..b7d96e1aa 100644 --- a/docs/reference/methods.confint.rma.html +++ b/docs/reference/methods.confint.rma.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/methods.escalc.html b/docs/reference/methods.escalc.html index 1e3ae0ddb..80c2e363c 100644 --- a/docs/reference/methods.escalc.html +++ b/docs/reference/methods.escalc.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/methods.list.rma.html b/docs/reference/methods.list.rma.html index 371b401cd..2d2adf362 100644 --- a/docs/reference/methods.list.rma.html +++ b/docs/reference/methods.list.rma.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/methods.matreg.html b/docs/reference/methods.matreg.html index 8cc0f79d7..21eb7604b 100644 --- a/docs/reference/methods.matreg.html +++ b/docs/reference/methods.matreg.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/methods.vif.rma.html b/docs/reference/methods.vif.rma.html index e92eb6dbe..a4ab1e2ad 100644 --- a/docs/reference/methods.vif.rma.html +++ b/docs/reference/methods.vif.rma.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/mfopt.html b/docs/reference/mfopt.html index b07bb3e45..006197242 100644 --- a/docs/reference/mfopt.html +++ b/docs/reference/mfopt.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 @@ -134,7 +134,7 @@

Details

a named vector to specify how various aspects of the output should be rounded (unset by default). See here for details.

style
-

a list whose elements specify the styles for various parts of the output when the crayon package is loaded and a terminal is used that support ‘ANSI’ color/highlight codes (unset by default). See here for details.

+

a list whose elements specify the styles for various parts of the output when the crayon package is loaded and a terminal is used that supports ‘ANSI’ color/highlight codes (unset by default). See here for details. Can also be a logical and set to FALSE to switch off output styling when the crayon package is loaded.

theme

character string to specify how plots created by the package should be themed. The default is "default", which means that the default foreground and background colors of plotting devices are used. Alternative options are "light" and "dark", which forces plots to be drawn with a light or dark background, respectively. See here for further details. RStudio users can also set this to "auto", in which case plotting colors are chosen depending on the RStudio theme used (for some themes, using "auto2" might be aesthetically more pleasing). One can also use setmfopt(theme="custom", fg=<color>, bg=<color>) to set the foreground and background colors to custom choices (depending on the colors chosen, using "custom2" might be aesthetically more pleasing).

diff --git a/docs/reference/misc-models.html b/docs/reference/misc-models.html index 85d02c68e..2e649ca6f 100644 --- a/docs/reference/misc-models.html +++ b/docs/reference/misc-models.html @@ -31,7 +31,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/misc-options.html b/docs/reference/misc-options.html index ffd78735e..811139c85 100644 --- a/docs/reference/misc-options.html +++ b/docs/reference/misc-options.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 @@ -206,6 +206,7 @@

Styled Output with the crayon Pac

For example, using the color scheme above (for a light colored background), the output should look like this:

Note that support for 256 different colors and text formatting (such as underlined and bold text) differs across terminals.

+

To switch off output styling when the crayon package is loaded, use setmfopt(style=FALSE).

diff --git a/docs/reference/misc-recs.html b/docs/reference/misc-recs.html index 7818d90c2..2a43f9bf1 100644 --- a/docs/reference/misc-recs.html +++ b/docs/reference/misc-recs.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/model.matrix.rma.html b/docs/reference/model.matrix.rma.html index f02999fd3..95b1723e8 100644 --- a/docs/reference/model.matrix.rma.html +++ b/docs/reference/model.matrix.rma.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/permutest.html b/docs/reference/permutest.html index 22412d872..0608aafec 100644 --- a/docs/reference/permutest.html +++ b/docs/reference/permutest.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/plot.cumul.rma.html b/docs/reference/plot.cumul.rma.html index 365b1ab07..cdd289a2a 100644 --- a/docs/reference/plot.cumul.rma.html +++ b/docs/reference/plot.cumul.rma.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/plot.gosh.rma.html b/docs/reference/plot.gosh.rma.html index e7dfd84bd..89bb0287f 100644 --- a/docs/reference/plot.gosh.rma.html +++ b/docs/reference/plot.gosh.rma.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/plot.infl.rma.uni.html b/docs/reference/plot.infl.rma.uni.html index f6470871a..73e29e291 100644 --- a/docs/reference/plot.infl.rma.uni.html +++ b/docs/reference/plot.infl.rma.uni.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/plot.permutest.rma.uni.html b/docs/reference/plot.permutest.rma.uni.html index 12da06035..8951b1f57 100644 --- a/docs/reference/plot.permutest.rma.uni.html +++ b/docs/reference/plot.permutest.rma.uni.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/plot.rma.html b/docs/reference/plot.rma.html index 04b145e5c..994c6ecea 100644 --- a/docs/reference/plot.rma.html +++ b/docs/reference/plot.rma.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/plot.rma.uni.selmodel.html b/docs/reference/plot.rma.uni.selmodel.html index d6c28e8be..7f9223295 100644 --- a/docs/reference/plot.rma.uni.selmodel.html +++ b/docs/reference/plot.rma.uni.selmodel.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/plot.vif.rma.html b/docs/reference/plot.vif.rma.html index 4107cdb31..394c9be16 100644 --- a/docs/reference/plot.vif.rma.html +++ b/docs/reference/plot.vif.rma.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/predict.rma.html b/docs/reference/predict.rma.html index d95b426bc..02dde8ee5 100644 --- a/docs/reference/predict.rma.html +++ b/docs/reference/predict.rma.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/print.anova.rma.html b/docs/reference/print.anova.rma.html index 9f9b242db..2860da03b 100644 --- a/docs/reference/print.anova.rma.html +++ b/docs/reference/print.anova.rma.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/print.confint.rma.html b/docs/reference/print.confint.rma.html index 7682f779c..d54a1f96b 100644 --- a/docs/reference/print.confint.rma.html +++ b/docs/reference/print.confint.rma.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/print.escalc.html b/docs/reference/print.escalc.html index 1bc238dca..aec6c5d1d 100644 --- a/docs/reference/print.escalc.html +++ b/docs/reference/print.escalc.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/print.fsn.html b/docs/reference/print.fsn.html index 702db9a3f..c84d20edd 100644 --- a/docs/reference/print.fsn.html +++ b/docs/reference/print.fsn.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/print.gosh.rma.html b/docs/reference/print.gosh.rma.html index 4e38493c3..7e125b9ac 100644 --- a/docs/reference/print.gosh.rma.html +++ b/docs/reference/print.gosh.rma.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/print.hc.rma.uni.html b/docs/reference/print.hc.rma.uni.html index 43b892c86..88df59f0b 100644 --- a/docs/reference/print.hc.rma.uni.html +++ b/docs/reference/print.hc.rma.uni.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/print.list.rma.html b/docs/reference/print.list.rma.html index 0617b9704..fea9a57f3 100644 --- a/docs/reference/print.list.rma.html +++ b/docs/reference/print.list.rma.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/print.matreg.html b/docs/reference/print.matreg.html index ae6829442..f88c290a7 100644 --- a/docs/reference/print.matreg.html +++ b/docs/reference/print.matreg.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/print.permutest.rma.uni.html b/docs/reference/print.permutest.rma.uni.html index 92aee58a1..558f9b4f8 100644 --- a/docs/reference/print.permutest.rma.uni.html +++ b/docs/reference/print.permutest.rma.uni.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/print.ranktest.rma.html b/docs/reference/print.ranktest.rma.html index 38b384110..622a2f27c 100644 --- a/docs/reference/print.ranktest.rma.html +++ b/docs/reference/print.ranktest.rma.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/print.regtest.rma.html b/docs/reference/print.regtest.rma.html index a0438bc94..28403f83c 100644 --- a/docs/reference/print.regtest.rma.html +++ b/docs/reference/print.regtest.rma.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/print.rma.html b/docs/reference/print.rma.html index 7177d460d..d132b6fd5 100644 --- a/docs/reference/print.rma.html +++ b/docs/reference/print.rma.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/profile.rma.html b/docs/reference/profile.rma.html index e27777bde..83b3f5750 100644 --- a/docs/reference/profile.rma.html +++ b/docs/reference/profile.rma.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/qqnorm.rma.html b/docs/reference/qqnorm.rma.html index b43b75eec..f5906bafd 100644 --- a/docs/reference/qqnorm.rma.html +++ b/docs/reference/qqnorm.rma.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/radial.html b/docs/reference/radial.html index 2f3827523..b372bd17e 100644 --- a/docs/reference/radial.html +++ b/docs/reference/radial.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/ranef.html b/docs/reference/ranef.html index 0317ad655..2ed909db0 100644 --- a/docs/reference/ranef.html +++ b/docs/reference/ranef.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/ranktest.html b/docs/reference/ranktest.html index ea5d16c62..fb08abefc 100644 --- a/docs/reference/ranktest.html +++ b/docs/reference/ranktest.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/rcalc.html b/docs/reference/rcalc.html index 38c635d22..5bcee7a34 100644 --- a/docs/reference/rcalc.html +++ b/docs/reference/rcalc.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/regplot.html b/docs/reference/regplot.html index 41860b6fa..94c0c8d36 100644 --- a/docs/reference/regplot.html +++ b/docs/reference/regplot.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/regtest.html b/docs/reference/regtest.html index 70b204d26..fc7c9817c 100644 --- a/docs/reference/regtest.html +++ b/docs/reference/regtest.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/replmiss.html b/docs/reference/replmiss.html index 138cdc3f8..e6841dd66 100644 --- a/docs/reference/replmiss.html +++ b/docs/reference/replmiss.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/reporter.html b/docs/reference/reporter.html index 38c0891c0..df7b62377 100644 --- a/docs/reference/reporter.html +++ b/docs/reference/reporter.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 @@ -191,12 +191,12 @@

Examples

### generate report reporter(res) #> -#> Directory for generating the report is: /tmp/Rtmp6w4ftg +#> Directory for generating the report is: /tmp/RtmpXJYkNB #> Copying references.bib and apa.csl to report directory ... #> Saving model object to report_res.rdata ... #> Creating report_res.rmd file ... #> Rendering report_res.rmd file ... -#> Generated /tmp/Rtmp6w4ftg/report_res.html ... +#> Generated /tmp/RtmpXJYkNB/report_res.html ... #> Opening report ... diff --git a/docs/reference/residuals.rma.html b/docs/reference/residuals.rma.html index 1d064d216..433d62e37 100644 --- a/docs/reference/residuals.rma.html +++ b/docs/reference/residuals.rma.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/rma.glmm.html b/docs/reference/rma.glmm.html index 96f30e52a..b8142bb1f 100644 --- a/docs/reference/rma.glmm.html +++ b/docs/reference/rma.glmm.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/rma.mh.html b/docs/reference/rma.mh.html index a752c0ddf..c40f0f152 100644 --- a/docs/reference/rma.mh.html +++ b/docs/reference/rma.mh.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/rma.mv.html b/docs/reference/rma.mv.html index aced1975e..8f9794866 100644 --- a/docs/reference/rma.mv.html +++ b/docs/reference/rma.mv.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/rma.peto.html b/docs/reference/rma.peto.html index 6fac41495..d3f108fed 100644 --- a/docs/reference/rma.peto.html +++ b/docs/reference/rma.peto.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/rma.uni.html b/docs/reference/rma.uni.html index 368449e5e..b54cc3ea2 100644 --- a/docs/reference/rma.uni.html +++ b/docs/reference/rma.uni.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/robust.html b/docs/reference/robust.html index 993d582f2..fadcb190f 100644 --- a/docs/reference/robust.html +++ b/docs/reference/robust.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/selmodel.html b/docs/reference/selmodel.html index b57de3211..3ecd2ec11 100644 --- a/docs/reference/selmodel.html +++ b/docs/reference/selmodel.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/simulate.rma.html b/docs/reference/simulate.rma.html index 3dbc5bc99..f997f66e2 100644 --- a/docs/reference/simulate.rma.html +++ b/docs/reference/simulate.rma.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/tes.html b/docs/reference/tes.html index 26dd3d501..25b217c1e 100644 --- a/docs/reference/tes.html +++ b/docs/reference/tes.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/to.long.html b/docs/reference/to.long.html index ab106b2dc..fc56323e6 100644 --- a/docs/reference/to.long.html +++ b/docs/reference/to.long.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/to.table.html b/docs/reference/to.table.html index 575f2af80..e479fa725 100644 --- a/docs/reference/to.table.html +++ b/docs/reference/to.table.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/to.wide.html b/docs/reference/to.wide.html index 37a69d920..3a694a55d 100644 --- a/docs/reference/to.wide.html +++ b/docs/reference/to.wide.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/transf.html b/docs/reference/transf.html index e3b7ccb7c..c154020cd 100644 --- a/docs/reference/transf.html +++ b/docs/reference/transf.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/trimfill.html b/docs/reference/trimfill.html index 3be4a6a4e..6a6589535 100644 --- a/docs/reference/trimfill.html +++ b/docs/reference/trimfill.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/update.rma.html b/docs/reference/update.rma.html index 6515adc4d..9a3a381d1 100644 --- a/docs/reference/update.rma.html +++ b/docs/reference/update.rma.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/vcalc.html b/docs/reference/vcalc.html index c10a22628..b2b94722e 100644 --- a/docs/reference/vcalc.html +++ b/docs/reference/vcalc.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/vcov.rma.html b/docs/reference/vcov.rma.html index 0903e9887..6e5cea75c 100644 --- a/docs/reference/vcov.rma.html +++ b/docs/reference/vcov.rma.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/vec2mat.html b/docs/reference/vec2mat.html index b4c4c2e03..c7307845e 100644 --- a/docs/reference/vec2mat.html +++ b/docs/reference/vec2mat.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/vif.html b/docs/reference/vif.html index 66cef29b9..1bb905544 100644 --- a/docs/reference/vif.html +++ b/docs/reference/vif.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/docs/reference/weights.rma.html b/docs/reference/weights.rma.html index 00b8b9a5d..c7eb4c536 100644 --- a/docs/reference/weights.rma.html +++ b/docs/reference/weights.rma.html @@ -29,7 +29,7 @@ metafor - 4.5-3 + 4.5-4 diff --git a/man/mfopt.Rd b/man/mfopt.Rd index bec6f545f..0f90c8461 100644 --- a/man/mfopt.Rd +++ b/man/mfopt.Rd @@ -25,7 +25,7 @@ setmfopt(...) \item{\code{silent}}{logical to specify whether a startup message should be issued when loading the package (the default is \code{FALSE}). Obviously, this option must be set before loading the package (e.g., with \code{options(metafor=list(silent=TRUE))}). Note that messages about required packages that are automatically loaded are not suppressed by this. To fully suppress all startup messages, load the package with \code{\link{suppressPackageStartupMessages}}.} \item{\code{space}}{logical to specify whether an empty line should be added before and after the output (the default is \code{TRUE}). See \link[=misc-options]{here} for details.} \item{\code{digits}}{a named vector to specify how various aspects of the output should be rounded (unset by default). See \link[=misc-options]{here} for details.} - \item{\code{style}}{a list whose elements specify the styles for various parts of the output when the \href{https://cran.r-project.org/package=crayon}{crayon} package is loaded and a terminal is used that support \sQuote{ANSI} color/highlight codes (unset by default). See \link[=misc-options]{here} for details.} + \item{\code{style}}{a list whose elements specify the styles for various parts of the output when the \href{https://cran.r-project.org/package=crayon}{crayon} package is loaded and a terminal is used that supports \sQuote{ANSI} color/highlight codes (unset by default). See \link[=misc-options]{here} for details. Can also be a logical and set to \code{FALSE} to switch off output styling when the \code{crayon} package is loaded.} \item{\code{theme}}{character string to specify how plots created by the package should be themed. The default is \code{"default"}, which means that the default foreground and background colors of plotting devices are used. Alternative options are \code{"light"} and \code{"dark"}, which forces plots to be drawn with a light or dark background, respectively. See \link[=misc-options]{here} for further details. RStudio users can also set this to \code{"auto"}, in which case plotting colors are chosen depending on the RStudio theme used (for some themes, using \code{"auto2"} might be aesthetically more pleasing). One can also use \code{setmfopt(theme="custom", fg=, bg=)} to set the foreground and background colors to custom choices (depending on the colors chosen, using \code{"custom2"} might be aesthetically more pleasing).} } diff --git a/man/misc-options.Rd b/man/misc-options.Rd index f971cece6..23976ad38 100644 --- a/man/misc-options.Rd +++ b/man/misc-options.Rd @@ -123,6 +123,8 @@ summary(res)} Note that support for 256 different colors and text formatting (such as underlined and bold text) differs across terminals. + To switch off output styling when the \code{crayon} package is loaded, use \code{setmfopt(style=FALSE}). + } \subsection{Removing Empty Lines Before and After the Output}{