wviechtb / metafor

Compare a9c18bd ... +10 ... 7e5376e

Coverage Reach
rma.mv.r rma.uni.r rma.glmm.r escalc.r to.long.r to.table.r misc.func.hidden.mv.r misc.func.hidden.r forest.rma.r rma.mh.r funnel.rma.r funnel.default.r forest.default.r reporter.rma.uni.r confint.rma.mv.r profile.rma.mv.r plot.infl.rma.uni.r forest.cumul.rma.r predict.rma.r rma.peto.r print.rma.mv.r confint.rma.uni.r permutest.rma.uni.r llplot.r plot.gosh.rma.r labbe.rma.r radial.rma.r print.rma.uni.r ranef.rma.mv.r influence.rma.uni.r addpoly.default.r anova.rma.r rstudent.rma.mv.r print.rma.glmm.r gosh.rma.r cumul.rma.uni.r trimfill.rma.uni.r to.wide.r summary.escalc.r hc.rma.uni.r cumul.rma.mh.r dfbetas.rma.mv.r profile.rma.uni.r misc.func.hidden.escalc.r qqnorm.rma.uni.r misc.func.hidden.prof.r transf.r cooks.distance.rma.mv.r cumul.rma.peto.r regtest.default.r leave1out.rma.uni.r plot.cumul.rma.r rstandard.rma.mv.r leave1out.rma.mh.r leave1out.rma.peto.r misc.func.hidden.glmm.r robust.rma.mv.r print.rma.mh.r robust.rma.uni.r baujat.rma.r plot.rma.uni.r misc.func.hidden.uni.r fsn.r contrmat.r regtest.rma.r ranef.rma.uni.r methods.escalc.r blup.rma.uni.r print.anova.rma.r methods.list.rma.r plot.profile.rma.r print.list.rma.r print.regtest.rma.r rstudent.rma.mh.r rstandard.rma.uni.r residuals.rma.r vcov.rma.r rstudent.rma.peto.r print.rma.peto.r print.robust.rma.r qqnorm.rma.peto.r qqnorm.rma.mh.r vif.rma.r confint.rma.mh.r confint.rma.peto.r weights.rma.mv.r ranktest.default.r weights.rma.mh.r addpoly.rma.r print.permutest.rma.uni.r hatvalues.rma.uni.r plot.rma.mh.r plot.rma.peto.r print.fsn.r hatvalues.rma.mv.r simulate.rma.r weights.rma.peto.r print.gosh.rma.r weights.rma.uni.r update.rma.r print.escalc.r fitstats.rma.r rstandard.rma.mh.r rstandard.rma.peto.r fitted.rma.r print.vif.rma.r print.confint.rma.r AIC.rma.r model.matrix.rma.r ranktest.rma.r print.infl.rma.uni.r print.hc.rma.uni.r print.list.confint.rma.r BIC.rma.r zzz.r logLik.rma.r print.ranktest.rma.r bldiag.r coef.summary.rma.r formula.rma.r deviance.rma.r replmiss.r coef.rma.r summary.rma.r coef.permutest.rma.uni.r print.profile.rma.r print.summary.rma.r nobs.rma.r df.residual.rma.r confint.rma.glmm.r weights.rma.glmm.r plot.rma.glmm.r qqnorm.rma.glmm.r qqnorm.rma.mv.r radial.r gosh.r cooks.distance.rma.uni.r labbe.r ranktest.r reporter.r blup.r hc.r baujat.r permutest.r addpoly.r funnel.r leave1out.r dfbetas.rma.uni.r regtest.r metafor.news.r vif.r rstudent.rma.uni.r forest.r cumul.r robust.r trimfill.r fitstats.r

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Showing 38 of 182 files from the diff.
Other files ignored by Codecov
.travis.yml has changed.
docs/index.html has changed.
docs/pkgdown.yml has changed.
man/gosh.Rd has changed.
docs/authors.html has changed.
man/rma.mv.Rd has changed.
docs/404.html has changed.
README.md has changed.
man/vif.Rd has changed.
NEWS.md has changed.
NEWS has changed.
DESCRIPTION has changed.

@@ -2052,20 +2052,41 @@
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      res <- list(b=beta, beta=beta, se=se, zval=zval, pval=pval, ci.lb=ci.lb, ci.ub=ci.ub, vb=vb,
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                  tau2=tau2, se.tau2=se.tau2, sigma2=sigma2,
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                  k=k, k.f=k.f, k.yi=k.yi, k.eff=k.eff, k.all=k.all, p=p, p.eff=p.eff, parms=parms, m=m,
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                  QE.Wld=QE.Wld, QEp.Wld=QEp.Wld, QE.LRT=QE.LRT, QEp.LRT=QEp.LRT, QE.df=QE.df, QM=QM, QMp=QMp, I2=I2, H2=H2, vt=vt,
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                  int.only=int.only, int.incl=int.incl,
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                  I2=I2, H2=H2, vt=vt,
2056 +
                  QE.Wld=QE.Wld, QEp.Wld=QEp.Wld, QE.LRT=QE.LRT, QEp.LRT=QEp.LRT, QE.df=QE.df, QM=QM, QMp=QMp,
2057 +
                  k=k, k.f=k.f, k.yi=k.yi, k.eff=k.eff, k.all=k.all, p=p, p.eff=p.eff, parms=parms,
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                  int.only=int.only, int.incl=int.incl, intercept=intercept,
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                  yi=yi, vi=vi, X=X, yi.f=yi.f, vi.f=vi.f, X.f=X.f,
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                  ai=ai, bi=bi, ci=ci, di=di, ai.f=ai.f, bi.f=bi.f, ci.f=ci.f, di.f=di.f,
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                  x1i=x1i, x2i=x2i, t1i=t1i, t2i=t2i, x1i.f=x1i.f, x2i.f=x2i.f, t1i.f=t1i.f, t2i.f=t2i.f,
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                  xi=xi, mi=mi, ti=ti, xi.f=xi.f, mi.f=mi.f, ti.f=ti.f, ni=ni, ni.f=ni.f,
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                  ids=ids, not.na=not.na, subset=subset, not.na.yivi=not.na.yivi, slab=slab, slab.null=slab.null,
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                  measure=measure, method=method, model=model, weighted=weighted, test=test, dfs=dfs, btt=btt, intercept=intercept, digits=digits, level=level, control=control, verbose=verbose,
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                  measure=measure, method=method, model=model, weighted=weighted,
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                  test=test, dfs=dfs, btt=btt, m=m,
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                  digits=digits, level=level, control=control, verbose=verbose,
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                  add=add, to=to, drop00=drop00,
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                  fit.stats=fit.stats, formula.yi=NULL, formula.mods=formula.mods, version=packageVersion("metafor"), call=mf)
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                  fit.stats=fit.stats,
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                  formula.yi=NULL, formula.mods=formula.mods, version=packageVersion("metafor"), call=mf)
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   }
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   if (!is.null(ddd$outlist)) {
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      if (ddd$outlist == "minimal") {
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         res <- list(b=beta, beta=beta, se=se, zval=zval, pval=pval, ci.lb=ci.lb, ci.ub=ci.ub, vb=vb,
2076 +
                     tau2=tau2, se.tau2=se.tau2, sigma2=sigma2,
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                     I2=I2, H2=H2,
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                     QE.Wld=QE.Wld, QEp.Wld=QEp.Wld, QE.LRT=QE.LRT, QEp.LRT=QEp.LRT, QE.df=QE.df, QEp=QEp, QM=QM, QMp=QMp,
2079 +
                     k=k, k.eff=k.eff, p=p, p.eff=p.eff, parms=parms,
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                     int.only=int.only,
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                     measure=measure, method=method, model=model,
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                     test=test, dfs=dfs, btt=btt, m=m,
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                     digits=digits,
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                     fit.stats=fit.stats)
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      } else {
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         res <- eval(parse(text=paste0("list(", ddd$outlist, ")")))
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      }
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   }
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   time.end <- proc.time()
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   res$time <- unname(time.end - time.start)[3]
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@@ -2075,14 +2096,6 @@
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   if (verbose || .isTRUE(ddd$time))
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      cat("\n")
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   if (!is.null(ddd$outlist)) {
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      if (ddd$outlist == "minimal") {
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         res <- list(b=beta, beta=beta, se=se, zval=zval, pval=pval, ci.lb=ci.lb, ci.ub=ci.ub, vb=vb, int.only=int.only, digits=digits, k=k, k.eff=k.eff, p=p, p.eff=p.eff, parms=parms, m=m, tau2=tau2, se.tau2=se.tau2, sigma2=sigma2, method=method, fit.stats=fit.stats, model=model, QE.Wld=QE.Wld, QEp.Wld=QEp.Wld, QE.LRT=QE.LRT, QEp.LRT=QEp.LRT, QE.df=QE.df, QEp=QEp, QM=QM, QMp=QMp, I2=I2, H2=H2, btt=btt, test=test, dfs=dfs, measure=measure)
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      } else {
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         res <- eval(parse(text=paste0("list(", ddd$outlist, ")")))
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      }
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   }
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   class(res) <- c("rma.glmm", "rma")
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   return(res)
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@@ -56,12 +56,12 @@
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   ### note: skipping NA cases
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   if (progbar)
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      pbar <- txtProgressBar(min=0, max=x$k.f, style=3)
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      pbar <- pbapply::startpb(min=0, max=x$k.f)
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   for (i in seq_len(x$k.f)) {
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      if (progbar)
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         setTxtProgressBar(pbar, i)
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         pbapply::setpb(pbar, i)
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      if (!not.na[i])
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         next
@@ -83,7 +83,7 @@
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   }
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   if (progbar)
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      close(pbar)
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      pbapply::closepb(pbar)
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   #########################################################################
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@@ -31,12 +31,12 @@
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   ### note: skipping NA tables
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   if (progbar)
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      pbar <- txtProgressBar(min=0, max=x$k.f, style=3)
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      pbar <- pbapply::startpb(min=0, max=x$k.f)
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   for (i in seq_len(x$k.f)) {
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      if (progbar)
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         setTxtProgressBar(pbar, i)
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         pbapply::setpb(pbar, i)
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      if (!x$not.na[i])
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         next
@@ -52,7 +52,7 @@
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   }
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   if (progbar)
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      close(pbar)
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      pbapply::closepb(pbar)
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   resid <- x$yi.f - delpred
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   resid[abs(resid) < 100 * .Machine$double.eps] <- 0

@@ -70,17 +70,17 @@
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   svb <- chol2inv(chol(x$vb[btt,btt,drop=FALSE]))
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   if (parallel=="no") {
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   if (parallel == "no") {
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      cook.d <- rep(NA_real_, n)
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      if (progbar)
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         pbar <- txtProgressBar(min=0, max=n, style=3)
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         pbar <- pbapply::startpb(min=0, max=n)
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      for (i in seq_len(n)) {
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         if (progbar)
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            setTxtProgressBar(pbar, i)
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            pbapply::setpb(pbar, i)
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         incl <- cluster %in% ids[i]
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@@ -126,18 +126,18 @@
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      }
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      if (progbar)
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         close(pbar)
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         pbapply::closepb(pbar)
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   }
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   if (parallel=="snow" || parallel == "multicore") {
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   if (parallel == "snow" || parallel == "multicore") {
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      if (!requireNamespace("parallel", quietly=TRUE))
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         stop(mstyle$stop("Please install the 'parallel' package for parallel processing."))
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      ncpus <- as.integer(ncpus)
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      if (ncpus < 1)
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      if (ncpus < 1L)
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         stop(mstyle$stop("Argument 'ncpus' must be >= 1."))
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      if (parallel == "multicore")

@@ -67,12 +67,12 @@
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   ### also: it is possible that model fitting fails, so that generates more NAs (these NAs will always be shown in output)
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   if (progbar)
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      pbar <- txtProgressBar(min=0, max=x$k.f, style=3)
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      pbar <- pbapply::startpb(min=0, max=x$k.f)
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   for (i in seq_len(x$k.f)) {
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      if (progbar)
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         setTxtProgressBar(pbar, i)
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         pbapply::setpb(pbar, i)
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      if (!not.na[i])
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         next
@@ -97,7 +97,7 @@
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   }
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   if (progbar)
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      close(pbar)
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      pbapply::closepb(pbar)
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   ### for first 'not.na' element, I2 and H2 would be NA (since k=1), but set to 0 and 1, respectively
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Everything is accounted for!

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What changes does Codecov check for?
Lines, not adjusted in diff, that have changed coverage data.
Files that introduced coverage data that had none before.
Files that have missing coverage data that once were tracked.
Files Coverage
R -0.09% 70.78%
Project Totals (157 files) 70.78%
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