Merge pull request #342 from Merck/341-re-organize-the-pkgdown-website

re-org vignettes and references

.lintr

@@ -11,7 +11,7 @@ exclusions:
     list(
       "inst/",
       "tests/testthat/old_function/",
-      "vignettes/articles/usage-gs-spending-bound.Rmd" = list(
+      "vignettes/articles/story-seven-test-types.Rmd" = list(
         object_name_linter = Inf
       ),
       "data-raw/simu_test_gs_design_combo.R" = list(

R/fixed_design_ahr.R

@@ -16,25 +16,39 @@
 #  You should have received a copy of the GNU General Public License
 #  along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-#' Fixed design using average hazard ratio under non-proportional hazards
+#' Fixed design under non-proportional hazards
 #'
-#' Computes fixed design sample size (given power) or power (given sample size)
-#' for AHR method.
-#' Returns a list with a basic summary.
+#' @description
+#' Computes fixed design sample size (given power)
+#' or power (given sample size) by:
+#' - [fixed_design_ahr()] - Average hazard ratio method.
+#' - [fixed_design_fh()] - Weighted logrank test with Fleming-Harrington
+#'   weights (Farrington and Manning, 1990).
+#' - [fixed_design_mb()] - Weighted logrank test with Magirr-Burman weights.
+#' - [fixed_design_lf()] - Lachin-Foulkes method (Lachin and Foulkes, 1986).
+#' - [fixed_design_maxcombo()] - MaxCombo method.
+#' - [fixed_design_rmst()] - RMST method.
+#' - [fixed_design_milestone()] - Milestone method.
+#'
+#' Additionally, [fixed_design_rd()] provides fixed design for binary endpoint
+#' with treatment effect measuring in risk difference.
 #'
 #' @inheritParams gs_design_ahr
 #' @inheritParams gs_power_ahr
 #' @param power Power (`NULL` to compute power or strictly between 0
 #'   and `1 - alpha` otherwise).
 #' @param study_duration Study duration.
 #'
-#' @return A table.
-#'
 #' @importFrom dplyr filter
 #'
+#' @returns A list of design characteristic summary.
+#'
 #' @export
 #'
+#' @rdname fixed_design
+#'
 #' @examples
+#' # AHR method ----
 #' library(dplyr)
 #'
 #' # Example 1: given power and compute sample size
@@ -64,6 +78,7 @@
 #'   study_duration = 36
 #' )
 #' x %>% summary()
+#'
 fixed_design_ahr <- function(
     enroll_rate,
     fail_rate,

R/fixed_design_fh.R

@@ -16,12 +16,6 @@
 #  You should have received a copy of the GNU General Public License
 #  along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-#' Fixed design using Fleming-Harrington method
-#'
-#' Computes fixed design sample size (given power) or power (given sample size)
-#' for Fleming-Harrington method (Farrington and Manning, 1990).
-#' Returns a list with a basic summary.
-#'
 #' @inheritParams gs_design_wlr
 #' @inheritParams gs_power_wlr
 #' @param power Power (`NULL` to compute power or strictly between 0
@@ -30,13 +24,14 @@
 #' @param rho test parameter in Fleming-Harrington method.
 #' @param gamma test parameter in Fleming-Harrington method.
 #'
-#' @return A table.
-#'
 #' @importFrom dplyr filter
 #'
 #' @export
 #'
+#' @rdname fixed_design
+#'
 #' @examples
+#' # WLR test with FH weights ----
 #' library(dplyr)
 #'
 #' # Example 1: given power and compute sample size
@@ -68,6 +63,7 @@
 #'   rho = 1, gamma = 1
 #' )
 #' x %>% summary()
+#'
 fixed_design_fh <- function(
     alpha = 0.025,
     power = NULL,

R/fixed_design_lf.R

@@ -16,24 +16,19 @@
 #  You should have received a copy of the GNU General Public License
 #  along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-#' Fixed design using Lachin-Foulkes method
-#'
-#' Computes fixed design sample size (given power) or power (given sample size)
-#' for Lachin-Foulkes method (Lachin and Foulkes, 1986).
-#' Returns a list with a basic summary.
-#'
 #' @param alpha One-sided Type I error (strictly between 0 and 1).
 #' @param power Power (`NULL` to compute power or strictly between 0
 #'   and `1 - alpha` otherwise).
 #' @param ratio Experimental:Control randomization ratio.
 #' @param study_duration Study duration.
 #' @inheritParams gs_design_ahr
 #'
-#' @return A table.
-#'
 #' @export
 #'
+#' @rdname fixed_design
+#'
 #' @examples
+#' # LF method ----
 #' library(dplyr)
 #'
 #' # Example 1: given power and compute sample size
@@ -63,6 +58,7 @@
 #'   study_duration = 36
 #' )
 #' x %>% summary()
+#'
 fixed_design_lf <- function(
     alpha = 0.025,
     power = NULL,

R/fixed_design_maxcombo.R

@@ -16,12 +16,6 @@
 #  You should have received a copy of the GNU General Public License
 #  along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-#' Fixed design using MaxCombo method
-#'
-#' Computes fixed design sample size (given power) or power (given sample size)
-#' for MaxCombo method.
-#' Returns a list with a basic summary.
-#'
 #' @param alpha One-sided Type I error (strictly between 0 and 1).
 #' @param power Power (`NULL` to compute power or strictly between 0
 #'   and `1 - alpha` otherwise).
@@ -32,11 +26,12 @@
 #' @param tau A vector of numbers paring with gamma and rho for maxcombo test.
 #' @inheritParams gs_design_combo
 #'
-#' @return A table.
-#'
 #' @export
 #'
+#' @rdname fixed_design
+#'
 #' @examples
+#' # MaxCombo test ----
 #' library(dplyr)
 #'
 #' # Example 1: given power and compute sample size
@@ -68,6 +63,7 @@
 #'   rho = c(0, 0.5), gamma = c(0, 0), tau = c(-1, -1)
 #' )
 #' x %>% summary()
+#'
 fixed_design_maxcombo <- function(
     alpha = 0.025,
     power = NULL,

R/fixed_design_mb.R

@@ -16,12 +16,6 @@
 #  You should have received a copy of the GNU General Public License
 #  along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-#' Fixed design using Magirr-Burman method
-#'
-#' Computes fixed design sample size (given power) or power (given sample size)
-#' for Magirr-Burman method.
-#' Returns a list with a basic summary.
-#'
 #' @inheritParams gs_design_wlr
 #' @inheritParams gs_power_wlr
 #' @param power Power (`NULL` to compute power or strictly between 0
@@ -30,11 +24,12 @@
 #' @param study_duration Study duration.
 #' @param tau Test parameter of Magirr-Burman method.
 #'
-#' @return A table.
-#'
 #' @export
 #'
+#' @rdname fixed_design
+#'
 #' @examples
+#' # WLR test with MB weights ----
 #' library(dplyr)
 #'
 #' # Example 1: given power and compute sample size
@@ -66,6 +61,7 @@
 #'   tau = 4
 #' )
 #' x %>% summary()
+#'
 fixed_design_mb <- function(
     alpha = 0.025,
     power = NULL,

R/fixed_design_milestone.R

@@ -16,12 +16,6 @@
 #  You should have received a copy of the GNU General Public License
 #  along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-#' Fixed design using milestone method
-#'
-#' Computes fixed design sample size (given power) or power (given sample size)
-#' for milestone method (Yung and Liu, 2020).
-#' Returns a list with a basic summary.
-#'
 #' @inheritParams gs_design_ahr
 #' @param alpha One-sided Type I error (strictly between 0 and 1).
 #' @param power Power (`NULL` to compute power or strictly between 0
@@ -30,11 +24,12 @@
 #' @param study_duration Study duration.
 #' @param tau Test parameter of milestone method.
 #'
-#' @return A table.
-#'
 #' @export
 #'
+#' @rdname fixed_design
+#'
 #' @examples
+#' # Milestone method ----
 #' library(dplyr)
 #'
 #' # Example 1: given power and compute sample size
@@ -66,6 +61,7 @@
 #'   tau = 18
 #' )
 #' x %>% summary()
+#'
 fixed_design_milestone <- function(
     alpha = 0.025,
     power = NULL,

R/fixed_design_rd.R

@@ -16,12 +16,6 @@
 #  You should have received a copy of the GNU General Public License
 #  along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-#' Fixed design for binary outcome measuring in risk difference
-#'
-#' Computes fixed design sample size (given power) or power (given sample size)
-#' for binary outcome measuring in risk difference (Mehrotra and Railkar, 2000).
-#' Returns a list with a basic summary.
-#'
 #' @param alpha One-sided Type I error (strictly between 0 and 1).
 #' @param power Power (`NULL` to compute power or strictly between 0
 #'   and `1 - alpha` otherwise).
@@ -32,11 +26,12 @@
 #' computed to achieve the targeted power
 #' @param ratio Experimental:Control randomization ratio.
 #'
-#' @return A table.
-#'
 #' @export
 #'
+#' @rdname fixed_design
+#'
 #' @examples
+#' # Binary endpoint with risk differences ----
 #' library(dplyr)
 #'
 #' # Example 1: given power and compute sample size
@@ -52,6 +47,7 @@
 #'   rd0 = 0, n = 2000, ratio = 1
 #' )
 #' x %>% summary()
+#'
 fixed_design_rd <- function(
     alpha = 0.025,
     power = NULL,

R/fixed_design_rmst.R

@@ -16,12 +16,6 @@
 #  You should have received a copy of the GNU General Public License
 #  along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-#' Fixed design using RMST method
-#'
-#' Computes fixed design sample size (given power) or power (given sample size)
-#' for RMST methods (Yung and Liu, 2020).
-#' Returns a list with a basic summary.
-#'
 #' @inheritParams gs_design_ahr
 #' @param alpha One-sided Type I error (strictly between 0 and 1).
 #' @param power Power (`NULL` to compute power or strictly between 0
@@ -30,11 +24,12 @@
 #' @param study_duration Study duration.
 #' @param tau Test parameter in RMST.
 #'
-#' @return A table.
-#'
 #' @export
 #'
+#' @rdname fixed_design
+#'
 #' @examples
+#' # RMST method ----
 #' library(dplyr)
 #'
 #' # Example 1: given power and compute sample size

_pkgdown.yml

@@ -147,6 +147,7 @@ articles:
   - articles/story-design-with-spending
   - articles/story-spending-time-example
   - articles/story-power-evaluation-with-spending-bound
+  - articles/story-seven-test-types
 
 - title: "Design by AHR"
   desc: >