From 6dd0cf5253b9db2cf5a37a0727806e86d7360b60 Mon Sep 17 00:00:00 2001
From: FBartos <f.bartos96@gmail.com>
Date: Wed, 25 Oct 2023 16:39:49 +0200
Subject: [PATCH] update documentation

---
 DESCRIPTION               | 2 +-
 R/main.R                  | 5 +++--
 R/zcurve_EM.R             | 2 +-
 R/zcurve_density.R        | 4 ++--
 man/control_EM.Rd         | 2 +-
 man/control_density.Rd    | 2 +-
 man/control_density_v1.Rd | 2 +-
 man/plot.zcurve.Rd        | 2 ++
 man/zcurve.Rd             | 2 +-
 9 files changed, 13 insertions(+), 10 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 3ad7f90..d323d92 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -17,7 +17,7 @@ License: GPL-3
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 Imports: 
     Rcpp (>= 1.0.2),
     nleqslv,
diff --git a/R/main.R b/R/main.R
index 55f5985..2d499ef 100644
--- a/R/main.R
+++ b/R/main.R
@@ -66,7 +66,7 @@
 #'   "max_iter" = 9999,
 #'   "alpha"    = .10
 #'   )
-#' \donttest{m1.EM <- zcurve(OSC.z, method = "EM", bootstrap = FALSE, control = ctr1)}
+#' \dontrun{m1.EM <- zcurve(OSC.z, method = "EM", bootstrap = FALSE, control = ctr1)}
 #' # see '?control_EM' and '?control_density' for more information about different
 #' # z-curves specifications
 #' @seealso [summary.zcurve()], [plot.zcurve()], [control_EM], [control_density]
@@ -556,7 +556,7 @@ print.summary.zcurve <- function(x, ...){
 #' @export plot.zcurve
 #' @rawNamespace S3method(plot, zcurve)
 #' 
-#' @examples 
+#' @examples \dontrun{
 #' # simulate some z-statistics and fit a z-curve
 #' z <- abs(rnorm(300,3))
 #' m.EM <- zcurve(z, method = "EM", bootstrap = 100)
@@ -569,6 +569,7 @@ print.summary.zcurve <- function(x, ...){
 #' 
 #' # change the location of the annotation to the left
 #' plot(m.EM, annotation = TRUE, CI = TRUE, x_text = 0)
+#' }
 #' @seealso [zcurve()]
 plot.zcurve          <- function(x, annotation = FALSE, CI = FALSE, extrapolate = FALSE, plot_type = "base",
                                  y.anno = c(.95, .88, .78, .71, .61, .53, .43, .35), x.anno = .6, cex.anno = 1, ...){
diff --git a/R/zcurve_EM.R b/R/zcurve_EM.R
index 46cdb7c..22a6e78 100644
--- a/R/zcurve_EM.R
+++ b/R/zcurve_EM.R
@@ -234,7 +234,7 @@
 #'    fit_reps  = 50,
 #'    mu = c(0, 1.5, 3, 4.5, 6)
 #' )
-#' \donttest{zcurve(OSC.z, method = "EM", control = ctrl)}
+#' \dontrun{zcurve(OSC.z, method = "EM", control = ctrl)}
 #' 
 #' @seealso [zcurve()], [control_density]
 NULL
diff --git a/R/zcurve_density.R b/R/zcurve_density.R
index c13d46e..2b84958 100644
--- a/R/zcurve_density.R
+++ b/R/zcurve_density.R
@@ -193,7 +193,7 @@
 #'    version   = 1,
 #'    max_iter  = 300
 #' )
-#' \donttest{zcurve(OSC.z, method = "density", control = ctrl)}
+#' \dontrun{zcurve(OSC.z, method = "density", control = ctrl)}
 #' 
 #' @seealso [zcurve()], [control_density], [control_EM]
 NULL
@@ -349,7 +349,7 @@ NULL
 #'    max_iter  = 300,
 #'    criterion = 1e-4
 #' )
-#' \donttest{zcurve(OSC.z, method = "density", control = ctrl)}
+#' \dontrun{zcurve(OSC.z, method = "density", control = ctrl)}
 #' 
 #' @seealso [zcurve()], [control_density_v1], [control_EM]
 NULL
diff --git a/man/control_EM.Rd b/man/control_EM.Rd
index b2c4a85..5353d78 100644
--- a/man/control_EM.Rd
+++ b/man/control_EM.Rd
@@ -64,7 +64,7 @@ ctrl <- list(
    fit_reps  = 50,
    mu = c(0, 1.5, 3, 4.5, 6)
 )
-\donttest{zcurve(OSC.z, method = "EM", control = ctrl)}
+\dontrun{zcurve(OSC.z, method = "EM", control = ctrl)}
 
 }
 \references{
diff --git a/man/control_density.Rd b/man/control_density.Rd
index 2104f3f..3422f9d 100644
--- a/man/control_density.Rd
+++ b/man/control_density.Rd
@@ -77,7 +77,7 @@ ctrl <- list(
    max_iter  = 300,
    criterion = 1e-4
 )
-\donttest{zcurve(OSC.z, method = "density", control = ctrl)}
+\dontrun{zcurve(OSC.z, method = "density", control = ctrl)}
 
 }
 \references{
diff --git a/man/control_density_v1.Rd b/man/control_density_v1.Rd
index 7227abc..b4e89d6 100644
--- a/man/control_density_v1.Rd
+++ b/man/control_density_v1.Rd
@@ -45,7 +45,7 @@ ctrl <- list(
    version   = 1,
    max_iter  = 300
 )
-\donttest{zcurve(OSC.z, method = "density", control = ctrl)}
+\dontrun{zcurve(OSC.z, method = "density", control = ctrl)}
 
 }
 \references{
diff --git a/man/plot.zcurve.Rd b/man/plot.zcurve.Rd
index 0d5c97f..80c87a6 100644
--- a/man/plot.zcurve.Rd
+++ b/man/plot.zcurve.Rd
@@ -48,6 +48,7 @@ of annotations relative to the figure's width.}
 Plot fitted z-curve object
 }
 \examples{
+\dontrun{
 # simulate some z-statistics and fit a z-curve
 z <- abs(rnorm(300,3))
 m.EM <- zcurve(z, method = "EM", bootstrap = 100)
@@ -61,6 +62,7 @@ plot(m.EM, annotation = TRUE, CI = TRUE)
 # change the location of the annotation to the left
 plot(m.EM, annotation = TRUE, CI = TRUE, x_text = 0)
 }
+}
 \seealso{
 \code{\link[=zcurve]{zcurve()}}
 }
diff --git a/man/zcurve.Rd b/man/zcurve.Rd
index 12b5254..ec0141c 100644
--- a/man/zcurve.Rd
+++ b/man/zcurve.Rd
@@ -94,7 +94,7 @@ ctr1 <- list(
   "max_iter" = 9999,
   "alpha"    = .10
   )
-\donttest{m1.EM <- zcurve(OSC.z, method = "EM", bootstrap = FALSE, control = ctr1)}
+\dontrun{m1.EM <- zcurve(OSC.z, method = "EM", bootstrap = FALSE, control = ctr1)}
 # see '?control_EM' and '?control_density' for more information about different
 # z-curves specifications
 }