fix cmdcheck notes

R/globals.R

@@ -9,4 +9,5 @@ utils::globalVariables(c("y", "year", "smooth_vals", "smooth_num",
                          "param_name", "outcome", "mgcv_plottable",
                          "term", "data_test", "object", "row_num", "trends_test",
                          "trend", "trend_series", "trend_y", ".", "gam",
-                         "group", "mod", "row_id", "byvar"))
+                         "group", "mod", "row_id", "byvar", "direction",
+                         "index..time..index"))

R/mvgam_formulae.R

@@ -20,7 +20,8 @@
 #' \code{\link[mgcv]{t2}},
 #' time-varying effects using \code{\link{dynamic}},
 #' monotonically increasing (using `s(x, bs = 'moi')`) or
-#' or decreasing splines (using `s(x, bs = 'mod')`; see \code{\link{monotonic}} for
+#' or decreasing splines (using `s(x, bs = 'mod')`;
+#' see \code{\link{smooth.construct.moi.smooth.spec}} for
 #' details), as well as
 #' Gaussian Process functions using \code{\link[brms]{gp}},
 #' can be added to the right hand side (and \code{.} is not supported in \code{mvgam} formulae).
@@ -35,8 +36,7 @@
 #' \code{\link[mgcv]{jagam}},
 #' \code{\link[mgcv]{gam}},
 #' \code{\link[mgcv]{s}},
-#' \code{\link[stats]{formula}},
-#' \code{\link{monotonic}}
+#' \code{\link[stats]{formula}}
 #' @author Nicholas J Clark
 #' @name mvgam_formulae
 NULL

R/trends.R

@@ -708,7 +708,7 @@ extract_trend_pars = function(object, keep_all_estimates = TRUE,
   if(attr(object$model_data, 'trend_model') %in% c('PWlinear', 'PWlogistic')){
     out$delta_trend <- lapply(seq_along(levels(object$obs_data$series)), function(series){
       if(object$fit_engine == 'stan'){
-        delta_estimates <- mvgam:::mcmc_chains(object$model_output, 'delta_trend')[,seq(series,
+        delta_estimates <- mcmc_chains(object$model_output, 'delta_trend')[,seq(series,
                                                                           dim(mcmc_chains(object$model_output,
                                                                                           'delta_trend'))[2],
                                                                           by = NCOL(object$ytimes))]