diff --git a/DESCRIPTION b/DESCRIPTION index f0101c3b..3e721c3d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -23,6 +23,7 @@ Imports: magrittr, pander, pkgconfig, + reformulas, rlang, sandwich, tibble diff --git a/R/colors.R b/R/colors.R index 24f2cd11..eafb14ee 100644 --- a/R/colors.R +++ b/R/colors.R @@ -48,7 +48,7 @@ #' @references #' #' Paul Tol's site is what is used to derive 4 of the 6 `jtools`-specific -#' qualitative palettes: \url{https://personal.sron.nl/~pault/} +#' qualitative palettes: \url{https://sronpersonalpages.nl/~pault/} #' #' Okabe and Ito's palette inspired "CUD Bright", though "CUD Bright" is not #' exactly the same. "CUD" is the same. diff --git a/R/gscale.R b/R/gscale.R index 78033d96..c89cb242 100644 --- a/R/gscale.R +++ b/R/gscale.R @@ -90,7 +90,7 @@ #' #' Gelman, A. (2008). Scaling regression inputs by dividing by two standard #' deviations. \emph{Statistics in Medicine}, \emph{27}, 2865–2873. -#' \url{http://www.stat.columbia.edu/~gelman/research/published/standardizing7.pdf} +#' \url{https://sites.stat.columbia.edu/gelman/research/published/standardizing7.pdf} #' #' Grotenhuis, M. te, Pelzer, B., Eisinga, R., Nieuwenhuis, R., #' Schmidt-Catran, A., & Konig, R. (2017). When size matters: Advantages of diff --git a/R/lme4_utils.R b/R/lme4_utils.R index a8c9669b..36bd46aa 100644 --- a/R/lme4_utils.R +++ b/R/lme4_utils.R @@ -196,7 +196,7 @@ noReForm <- function(re.form) { reOnly <- function(f, response = FALSE) { response <- if (response && length(f) == 3) { f[[2]] } else { NULL } - reformulate(paste0("(", vapply(lme4::findbars(f), safeDeparse, + reformulate(paste0("(", vapply(reformulas::findbars(f), safeDeparse, ""), ")"), response = response) } @@ -238,7 +238,7 @@ mkNewReTrms <- function(object, newdata, re.form = NULL, na.action = na.pass, 0) { newdata <- newdata[-fit.na.action, ] } - ReTrms <- lme4::mkReTrms(lme4::findbars(re.form[[2]]), rfd) + ReTrms <- reformulas::mkReTrms(reformulas::findbars(re.form[[2]]), rfd) ReTrms <- within(ReTrms, Lambdat@x <- unname(lme4::getME(object, "theta")[Lind])) if (!allow.new.levels && any(vapply(ReTrms$flist, anyNA, diff --git a/R/mer_utils.r b/R/mer_utils.r index 63a2ee07..877af076 100644 --- a/R/mer_utils.r +++ b/R/mer_utils.r @@ -284,7 +284,7 @@ get.random.formula <- function(model, rhs) { random.formula <- if (any(class(model) %in% c("lmerMod", "lmerModLmerTest", "glmerMod", "glmmTMB"))) { - paste("(", lme4::findbars(formula(model)), ")", collapse = " + ") + paste("(", reformulas::findbars(formula(model)), ")", collapse = " + ") } diff --git a/man/gscale.Rd b/man/gscale.Rd index 5ffd1edc..01f8047a 100644 --- a/man/gscale.Rd +++ b/man/gscale.Rd @@ -150,7 +150,7 @@ if (requireNamespace("survey")) { \references{ Gelman, A. (2008). Scaling regression inputs by dividing by two standard deviations. \emph{Statistics in Medicine}, \emph{27}, 2865–2873. -\url{http://www.stat.columbia.edu/~gelman/research/published/standardizing7.pdf} +\url{https://sites.stat.columbia.edu/gelman/research/published/standardizing7.pdf} Grotenhuis, M. te, Pelzer, B., Eisinga, R., Nieuwenhuis, R., Schmidt-Catran, A., & Konig, R. (2017). When size matters: Advantages of diff --git a/man/jtools_colors.Rd b/man/jtools_colors.Rd index aa12dbdf..b9297677 100644 --- a/man/jtools_colors.Rd +++ b/man/jtools_colors.Rd @@ -51,7 +51,7 @@ see all of those options). } \references{ Paul Tol's site is what is used to derive 4 of the 6 \code{jtools}-specific -qualitative palettes: \url{https://personal.sron.nl/~pault/} +qualitative palettes: \url{https://sronpersonalpages.nl/~pault/} Okabe and Ito's palette inspired "CUD Bright", though "CUD Bright" is not exactly the same. "CUD" is the same. diff --git a/vignettes/summ.Rmd b/vignettes/summ.Rmd index 8e3459ad..eb97d4f2 100644 --- a/vignettes/summ.Rmd +++ b/vignettes/summ.Rmd @@ -155,7 +155,7 @@ you would get if you did `scale(log(us_gross))` rather than You can also choose a different number of standard deviations to divide by for standardization. -[Andrew Gelman](http://www.stat.columbia.edu/~gelman/research/published/standardizing7.pdf) +[Andrew Gelman](https://sites.stat.columbia.edu/gelman/research/published/standardizing7.pdf) has been a proponent of dividing by 2 standard deviations; if you want to do things that way, give the argument `n.sd = 2`.