-
+
Arguments -
+Arguments
--
-
- d - +
- d
a tibble created by `createGrid`
-- parallel - +
- parallel
use parallelisation if available
-- cores - +
- cores
the number of cores to use when parallelising. If <code>NA</code>, all available cores are requested
-- minChunkSize - +
- minChunkSize
The minimum size of the grid before paralellisation is attempted
-
- Usage Notes
-
-
+
-
+
+
+
-
-
diff --git a/main/reference/createGrid.html b/main/reference/createGrid.html
index 2ba60e1..d510ecf 100644
--- a/main/reference/createGrid.html
+++ b/main/reference/createGrid.html
@@ -1,19 +1,5 @@
-
-
-
-
-
-
-Usage Notes -
+Usage Notes
Regardless of the value of `parallel`, parallelisation is only @@ -117,15 +82,13 @@
Usage Notes
- Examples
-
+ Examples
x <- createGrid(p0 = 0.1, p1 = 0.30, alpha = 0.1, beta = 0.1, nMin = 24, nMax = 32) %>%
augmentGrid(parallel = FALSE)
x <- createGrid(p0 = 0.1, p1 = 0.30, alpha = 0.1, beta = 0.1, nMin = 24, nMax = 32) %>%
augmentGrid(parallel = FALSE)
Create a grid of candidate designs
-
Usage -
+Usage
-
+Arguments -
+Arguments
--
-
- p0 - +
- p0
the response rate under the null hypothesis
-- p1 - +
- p1
the response rate under the alternate hypothesis
-- alpha - +
- alpha
the desired (one-sided) type 1 error rate
-- beta - +
- beta
the desired type 2 error rate
-- power - +
- power
an alternative to
beta
-- nMin - +
- nMin
the lower bound for the search grid. If
NA,searchBoundsis called to provide an appropriate value
-- nMax - +
- nMax
the lower bound for the search grid. If
NA,searchBoundsis called to provide an appropriate value
-- mander - +
- mander
is a Mander & Thompson or a Simon's design required?
-
-
+
-
+
+
+
-
-
diff --git a/main/reference/index.html b/main/reference/index.html
index e444d5d..ee5b060 100644
--- a/main/reference/index.html
+++ b/main/reference/index.html
@@ -1,17 +1,5 @@
-
-
-
-
-
-
-Examples -
+Examples
# Standard use for a Simon's 2-stage design
x <- createGrid(p0 = 0.1, p1 = 0.5, alpha = 0.1, beta = 0.1, mander = FALSE)
# Custom search bounds for a Mander & Thompson design
@@ -142,8 +103,7 @@ Examples
-
Package index
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+
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+
+
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diff --git a/main/reference/obtainDesign.html b/main/reference/obtainDesign.html
index f788b1c..ff44d48 100644
--- a/main/reference/obtainDesign.html
+++ b/main/reference/obtainDesign.html
@@ -1,25 +1,11 @@
-
-
-
-
-
-
--
-
- +
-
augmentGrid() - Augment a grid of candidate designs with type 1 and type 2 error probabilities, expected sample sizes and probabilities of early termination -
- +
-
createGrid() - Create a grid of candidate designs -
- +
-
obtainDesign() - Finds optimal and minimax designs for either Simon's 2-stage or Mander & Thompson studies -
- +
-
powerPlot() - Plot the power curve(s) for the given design(s) -
- +
-
searchBounds() - Obtain default bounds for the construction of the search grid. -
-
-
-
-
-
-
-
-
Finds optimal and minimax designs for either Simon's 2-stage or Mander &
- Usage
-
+ Usage
- Arguments
-
+ Arguments
-
-- grid
-
+- grid
Optional. A tibble created by createGrid. If NULL,
then p0, p1, alpha and beta must be specified
and createGrid is called to generate the required grid. If not
@@ -100,45 +71,37 @@
Argumentsp0
-
+- p0
the response rate under the null hypothesis
- p1
-
+- p1
the response rate under the alternate hypothesis
- alpha
-
+- alpha
the desired (one-sided) type 1 error rate
- beta
-
+- beta
the desired type 2 error rate
- fullGrid
-
+- fullGrid
should the full grid of all possible designs be returned, or
simply the optimal and minimax solutions? For a Mander and Thompson design,
optimal and minimax designs are returned for both the null and alternate
hypotheses. See Usage Notes below.
- ...
-
+- ...
passed to `createGrid` or `augmentGrid`. In particular
mander=TRUE for a Mander & Thompson design or mander=FALSE for
a Simon's 2-stage design.
-
+
- Value
-
+ Value
a tibble created by createGrid. If
fullGrid == FALSE the table contains an additional column,
Criterion indicating the type of design. Possible values for
@@ -147,8 +110,7 @@
Value
Thompson designs.
- Usage notes
-
+ Usage notes
If grid is not NULL it is possible that none of the candidate
@@ -162,8 +124,7 @@
Usage notes
- Examples
-
+ Examples
# \donttest{
# Standard use (Simon's 2-stage design)
createGrid(p0 = 0.05, p1 = 0.25, alpha = 0.05, beta = 0.2, mander = FALSE) %>%
@@ -194,8 +155,7 @@ Examples
-
+
-
+
+
+
-
-
diff --git a/main/reference/pipe.html b/main/reference/pipe.html
index c999ddc..67c08b1 100644
--- a/main/reference/pipe.html
+++ b/main/reference/pipe.html
@@ -1,19 +1,5 @@
-
-
-
-
-
-
-Pipe operator — %>% • mtdesign
-
-
-
-
-
-
-
-
-
+
+Pipe operator — %>% • mtdesign
Skip to contents
@@ -29,23 +15,12 @@
+
@@ -63,37 +38,29 @@ Pipe operator
+
-
+
-
+
+
+
-
-
diff --git a/main/reference/powerPlot.html b/main/reference/powerPlot.html
index 21298e5..e2a7daa 100644
--- a/main/reference/powerPlot.html
+++ b/main/reference/powerPlot.html
@@ -1,19 +1,5 @@
-
-
-
-
-
-
-Plot the power curve(s) for the given design(s) — powerPlot • mtdesign
-
-
-
-
-
-
-
-
-
+
+Plot the power curve(s) for the given design(s) — powerPlot • mtdesign
Skip to contents
@@ -29,23 +15,12 @@
+
@@ -63,51 +38,42 @@ Plot the power curve(s) for the given design(s)
+
- Examples
-
+ Examples
createGrid(p0 = 0.05, p1 = 0.25, alpha = 0.05, beta = 0.2, mander = FALSE) %>%
augmentGrid(cores = 2) %>%
obtainDesign() %>%
powerPlot(probs = seq(0, 0.5, 0.025))
#> Warning: one argument not used by format 'Parallelisation has been requested, but the grid size [72814] is less than the minimum chunk size [1e+05]. Parallelisation will not occur'
-#> pkgdown 2024-10-31 15:51:49 INFO pkgdown::build_site: Parallelisation has been requested, but the grid size [72814] is less than the minimum chunk size [1e+05]. Parallelisation will not occur
+#> pkgdown 2024-11-01 13:52:51 INFO pkgdown::build_site: Parallelisation has been requested, but the grid size [72814] is less than the minimum chunk size [1e+05]. Parallelisation will not occur
-
+
-
+
+
+
-
-
diff --git a/main/reference/searchBounds.html b/main/reference/searchBounds.html
index e5ccd4c..472397b 100644
--- a/main/reference/searchBounds.html
+++ b/main/reference/searchBounds.html
@@ -1,21 +1,7 @@
-
-
-
-
-
-
-Obtain default bounds for the construction of the search grid. — searchBounds • mtdesign
-
-
-
-
-
-
-
-
-
+
+Obtain default bounds for the construction of the search grid. — searchBounds • mtdesign
Skip to contents
@@ -31,23 +17,12 @@
+
@@ -66,54 +41,43 @@ Obtain default bounds for the construction of the search grid.
+
- Value
-
+ Value
a list with three elements: "n" - the single stage sample size from
Fleiss et al; "min" - the lower bound, 0.8*n; "max" - the upper bound, 2*n.
floor() and ceiling() are applied as appropriate.
-
+
-
+
+
+
-
-
diff --git a/main/search.json b/main/search.json
index 775ba1b..5ca4b27 100644
--- a/main/search.json
+++ b/main/search.json
@@ -1 +1 @@
-[{"path":"https://openpharma.github.io/mtdesign/main/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc. .","code":" Copyright (C) This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see Copyright (C) This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://openpharma.github.io/mtdesign/main/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"John Kirkpatrick. Author, maintainer.","code":""},{"path":"https://openpharma.github.io/mtdesign/main/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Kirkpatrick J (2024). mtdesign: Mander Thompson Designs. R package version 0.1.2, https://github.com/openpharma/mtdesign.","code":"@Manual{, title = {mtdesign: Mander and Thompson Designs}, author = {John Kirkpatrick}, year = {2024}, note = {R package version 0.1.2}, url = {https://github.com/openpharma/mtdesign}, }"},{"path":[]},{"path":"https://openpharma.github.io/mtdesign/main/index.html","id":"introduction","dir":"","previous_headings":"","what":"Introduction","title":"Mander and Thompson Designs","text":"package mtdesign provides implementations Simon (1989) Mander & Thompson (2010). implementations Simon’s methods available - example, ph2simon function clinfun package (Seshan 2018), provide easy access non-optimal solutions way mtdesign . aware R-based implementations Mander & Thompson’s extension Simon.","code":""},{"path":"https://openpharma.github.io/mtdesign/main/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Mander and Thompson Designs","text":"available CRAN, can install mtdesign usual way: install.packages(\"mtdesign\") can install development version mtdesign GitHub : devtools::install_github(\"openpharma/mtdesign\")","code":""},{"path":"https://openpharma.github.io/mtdesign/main/index.html","id":"set-up-vignette-environment","dir":"","previous_headings":"","what":"Set up vignette environment","title":"Mander and Thompson Designs","text":"","code":"# By policy, on CRAN, use only two cores, no matter how many are available. if (requireNamespace(\"parallel\", quietly = TRUE)) { maxCores <- parallel::detectCores() maxCores <- ifelse(identical(Sys.getenv(\"NOT_CRAN\"), \"true\"), maxCores, min(maxCores, 2)) } else { maxCores <- 1 }"},{"path":"https://openpharma.github.io/mtdesign/main/index.html","id":"example","dir":"","previous_headings":"","what":"Example","title":"Mander and Thompson Designs","text":"Suppose treatments response rate less 5% interest response rate least 25% worthy development. Simon’s 2-stage design seek efficacy signal significance level 5% power 80% required. table shows optimal design requirements 0/9 2/17. expected sample size 12.0 probability early termination 63%. significance level actually achieved 4.7% power level achieved 100% - 18.8% = 81.2%. power curves designs easily plotted. Obtaining equivalent Mander & Thompson designs requires small change calls.","code":"library(mtdesign) library(knitr) library(dplyr) #> #> Attaching package: 'dplyr' #> The following objects are masked from 'package:stats': #> #> filter, lag #> The following objects are masked from 'package:base': #> #> intersect, setdiff, setequal, union simonDesign <- obtainDesign(p0 = 0.05, p1 = 0.25, alpha = 0.05, beta = 0.2, mander = FALSE, parallel = FALSE) simonDesign %>% select(-Alpha, -Beta, -p0, -p1, -PETAlt, -AveSizeAlt) %>% kable(digits = c(0, 0, 0, 0, 3, 3, 2, 1, NA)) powerPlot(simonDesign) manderDesign <- obtainDesign( p0 = 0.05, p1 = 0.25, alpha = 0.05, beta = 0.2, cores = maxCores ) manderDesign %>% select(-Alpha, -Beta, -p0, -p1) %>% kable(digits = c(0, 0, 0, 0, 3, 3, 2, 2, 2, 1, NA)) powerPlot(manderDesign)"},{"path":"https://openpharma.github.io/mtdesign/main/index.html","id":"constrained-designs","dir":"","previous_headings":"Example","what":"Constrained designs","title":"Mander and Thompson Designs","text":"Suppose trial, whatever reason, restricted using 8 participants stage. shown , optimal Simon’s two stage design 0/9 2/17. ’s close n1 = 8, n = 16. (slightly) sub-optimal design n1 = 8, n = 16? , isn’t. close can get? Best sub-optimal design required significance level Best sub-optimal design required power choice lies design achieves required significance level power 77.1% one required power significance level 15.1%. designs accept null hypothesis responders seen first group eight participants. differ critical value end stage 2: 1 maintain power, 2 maintain significance level. power curve designs can compared globally optimal design.","code":"x <- createGrid(p0 = 0.05, p1 = 0.25, alpha = 0.05, beta = 0.2, mander = FALSE) y <- x %>% filter(nStage1 == 8, nTotal == 16) z <- y %>% obtainDesign(cores = maxCores) #> Warning: No acceptable designs were found. if (nrow(z) == 0) { print(\"No acceptable designs were found.\") } else { select(-Alpha, -Beta, -p0, -p1, -PETAlt, -AveSizeAlt) %>% z() %>% select(-Alpha, -Beta, -p0, -p1, -PETAlt, -AveSizeAlt) %>% kable(digits = c(0, 0, 0, 0, 3, 3, 2, 1, NA)) } #> [1] \"No acceptable designs were found.\" z1 <- y %>% augmentGrid() bestSize <- z1 %>% filter(Type1 < Alpha) %>% slice_min(Type2) bestSize %>% select(-Alpha, -Beta, -p0, -p1, -PETAlt, -AveSizeAlt) %>% kable( caption = \"Best sub-optimal design with required significance level\", digits = c(0, 0, 0, 0, 3, 3, 2, 1, NA) ) bestPower <- z1 %>% filter(Type2 < Beta) %>% slice_min(Type1) bestPower %>% select(-Alpha, -Beta, -p0, -p1, -PETAlt, -AveSizeAlt) %>% kable( caption = \"Best sub-optimal design with required power\", digits = c(0, 0, 0, 0, 3, 3, 2, 1, NA) ) plotData1 <- simonDesign %>% filter(Criterion == \"optimal\") %>% bind_rows(list(bestSize, bestPower)) powerPlot(plotData1)"},{"path":"https://openpharma.github.io/mtdesign/main/index.html","id":"package-structure","dir":"","previous_headings":"","what":"Package structure","title":"Mander and Thompson Designs","text":"mtdesign package consists three main functions: createGrid creates grid (nStage1, rFutility, nTotal rTotal Simon’s design nStage1, rFutility, rSuccess, nTotal rTotal Mander & Thompson design) brute force search required design(s) conducted augmentGridtakes grid created createGrid adds columns probability early termination, Type 1 error, Type 2 error expected sample size . obtainDesign takes augmented grid identifies optimal minimax designs","code":""},{"path":"https://openpharma.github.io/mtdesign/main/index.html","id":"error-and-warning-messages-and-logging","dir":"","previous_headings":"","what":"Error and warning messages and logging","title":"Mander and Thompson Designs","text":"mtdesign package supports logging via futile.logger package (Rowe 2016). functions simply report Entry Exit DEBUG level. augmentGrid function reports steps parallelisation process TRACE level.","code":""},{"path":"https://openpharma.github.io/mtdesign/main/index.html","id":"parallelisation","dir":"","previous_headings":"","what":"Parallelisation","title":"Mander and Thompson Designs","text":"known closed form solution obtaining solutions either Simon’s original equations Mander & Thompson’s extensions. mtdesign package uses brute force approach evaluate operating characteristics reasonable potential designs. grids can quickly become large, particularly Mander & Thompson designs. example, createGrid(0.2, 0.4, alpha=0.1, beta=0.1) creates grid almost 11 million candidate designs. mtdesign uses paralellisation attempt speed evaluation candidate designs. augmentGrid function allows users control parallelisation process: parallel parameter defaults TRUE defines whether paralellisation used. cores parameter specifies many cores used. default value, NA tells mtdesign use available (defined parallel::detectCores()), cores. minChunkSize determines smallest grid candidate designs trigger paralellisation. default value 100000. parallel package required parallelisation. parallelisation needed (ie grid size exceeds minChunkSize) requested parallel package installed, error message thrown augmentation grid stops. paralellisation requested grid contains one million rows, warning produced.","code":""},{"path":"https://openpharma.github.io/mtdesign/main/index.html","id":"troubleshooting","dir":"","previous_headings":"","what":"Troubleshooting","title":"Mander and Thompson Designs","text":", installing using mtdesign package, get error regarding syntax error .hpp file, similar following issue likely mismatch g++ compiler used headers supplied BH package. two solutions know : Upgrade g++ Downgrade version BH package using. appropriate package version depends version g++ compiler using.","code":".../BH/include/boost/math/tools/fraction.hpp:84:48: error: ‘long double’ is not a class, struct, or union type using value_type = typename T::value_type;"},{"path":[]},{"path":"https://openpharma.github.io/mtdesign/main/reference/augmentGrid.html","id":null,"dir":"Reference","previous_headings":"","what":"Augment a grid of candidate designs with type 1 and type 2 error probabilities, expected sample sizes and probabilities of early termination — augmentGrid","title":"Augment a grid of candidate designs with type 1 and type 2 error probabilities, expected sample sizes and probabilities of early termination — augmentGrid","text":"Augment grid candidate designs type 1 type 2 error probabilities, expected sample sizes probabilities early termination","code":""},{"path":"https://openpharma.github.io/mtdesign/main/reference/augmentGrid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Augment a grid of candidate designs with type 1 and type 2 error probabilities, expected sample sizes and probabilities of early termination — augmentGrid","text":"","code":"augmentGrid(d, parallel = TRUE, cores = NA, minChunkSize = 1e+05)"},{"path":"https://openpharma.github.io/mtdesign/main/reference/augmentGrid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Augment a grid of candidate designs with type 1 and type 2 error probabilities, expected sample sizes and probabilities of early termination — augmentGrid","text":"d tibble created `createGrid` parallel use parallelisation available cores number cores use parallelising. NA<\/code>, available cores requested minChunkSize minimum size grid paralellisation attempted","code":""},{"path":"https://openpharma.github.io/mtdesign/main/reference/augmentGrid.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Augment a grid of candidate designs with type 1 and type 2 error probabilities, expected sample sizes and probabilities of early termination — augmentGrid","text":"augmented grid tibble","code":""},{"path":"https://openpharma.github.io/mtdesign/main/reference/augmentGrid.html","id":"usage-notes","dir":"Reference","previous_headings":"","what":"Usage Notes","title":"Augment a grid of candidate designs with type 1 and type 2 error probabilities, expected sample sizes and probabilities of early termination — augmentGrid","text":"Regardless value `parallel`, parallelisation used size grid greater chunkSize<\/code>. paralellisation requested needed, exception thrown parallel package available.","code":""},{"path":"https://openpharma.github.io/mtdesign/main/reference/augmentGrid.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Augment a grid of candidate designs with type 1 and type 2 error probabilities, expected sample sizes and probabilities of early termination — augmentGrid","text":"","code":"x <- createGrid(p0 = 0.1, p1 = 0.30, alpha = 0.1, beta = 0.1, nMin = 24, nMax = 32) %>% augmentGrid(parallel = FALSE)"},{"path":"https://openpharma.github.io/mtdesign/main/reference/createGrid.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a grid of candidate designs — createGrid","title":"Create a grid of candidate designs — createGrid","text":"Create grid candidate designs","code":""},{"path":"https://openpharma.github.io/mtdesign/main/reference/createGrid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a grid of candidate designs — createGrid","text":"","code":"createGrid( p0, p1, alpha = 0.1, beta = NA, power = ifelse(is.na(beta), 0.9, 1 - beta), nMin = NA, nMax = NA, mander = TRUE )"},{"path":"https://openpharma.github.io/mtdesign/main/reference/createGrid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a grid of candidate designs — createGrid","text":"p0 response rate null hypothesis p1 response rate alternate hypothesis alpha desired (one-sided) type 1 error rate beta desired type 2 error rate power alternative beta nMin lower bound search grid. NA, searchBounds called provide appropriate value nMax lower bound search grid. NA, searchBounds called provide appropriate value mander Mander & Thompson Simon's design required?","code":""},{"path":"https://openpharma.github.io/mtdesign/main/reference/createGrid.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a grid of candidate designs — createGrid","text":"tibble. See Usage notes list description columns.","code":""},{"path":"https://openpharma.github.io/mtdesign/main/reference/createGrid.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a grid of candidate designs — createGrid","text":"","code":"# Standard use for a Simon's 2-stage design x <- createGrid(p0 = 0.1, p1 = 0.5, alpha = 0.1, beta = 0.1, mander = FALSE) # Custom search bounds for a Mander & Thompson design y <- createGrid(p0 = 0.1, p1 = 0.4, alpha = 0.1, beta = 0.1, nMin = 20, nMax = 30)"},{"path":"https://openpharma.github.io/mtdesign/main/reference/obtainDesign.html","id":null,"dir":"Reference","previous_headings":"","what":"Finds optimal and minimax designs for either Simon's 2-stage or Mander & Thompson studies — obtainDesign","title":"Finds optimal and minimax designs for either Simon's 2-stage or Mander & Thompson studies — obtainDesign","text":"obtainDesign essentially wrapper calls createGrid augmentGrid followed simple filtering candidate designs identify optimal minimax designs.","code":""},{"path":"https://openpharma.github.io/mtdesign/main/reference/obtainDesign.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Finds optimal and minimax designs for either Simon's 2-stage or Mander & Thompson studies — obtainDesign","text":"","code":"obtainDesign( grid = NULL, p0 = NA, p1 = NA, alpha = ifelse(is.null(grid), 0.05, NA), beta = ifelse(is.null(grid), 0.1, NA), fullGrid = FALSE, ... )"},{"path":"https://openpharma.github.io/mtdesign/main/reference/obtainDesign.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Finds optimal and minimax designs for either Simon's 2-stage or Mander & Thompson studies — obtainDesign","text":"grid Optional. tibble created createGrid. NULL, p0, p1, alpha beta must specified createGrid called generate required grid. NULL p0, p1, alpha beta ignored p0 response rate null hypothesis p1 response rate alternate hypothesis alpha desired (one-sided) type 1 error rate beta desired type 2 error rate fullGrid full grid possible designs returned, simply optimal minimax solutions? Mander Thompson design, optimal minimax designs returned null alternate hypotheses. See Usage Notes . ... passed `createGrid` `augmentGrid`. particular mander=TRUE Mander & Thompson design mander=FALSE Simon's 2-stage design.","code":""},{"path":"https://openpharma.github.io/mtdesign/main/reference/obtainDesign.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Finds optimal and minimax designs for either Simon's 2-stage or Mander & Thompson studies — obtainDesign","text":"tibble created createGrid. fullGrid == FALSE table contains additional column, Criterion indicating type design. Possible values Criterion \"optimal\" \"minimax\" Simon's designs \"optimalNull\", \"optimalAlt\", \"minimaxNull\" \"minimaxAlt\" Mander & Thompson designs.","code":""},{"path":"https://openpharma.github.io/mtdesign/main/reference/obtainDesign.html","id":"usage-notes","dir":"Reference","previous_headings":"","what":"Usage notes","title":"Finds optimal and minimax designs for either Simon's 2-stage or Mander & Thompson studies — obtainDesign","text":"grid NULL possible none candidate designs acceptable (, satisfy significance level power requirements). case fullGrid == FALSE, empty tibble returned. versbose == TRUE warning message also printed. fullGrid == TRUE full grid designs considered returned. can interrogated find optimal designs constraints - example fixed stage sizes.","code":""},{"path":"https://openpharma.github.io/mtdesign/main/reference/obtainDesign.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Finds optimal and minimax designs for either Simon's 2-stage or Mander & Thompson studies — obtainDesign","text":"","code":"# \\donttest{ # Standard use (Simon's 2-stage design) createGrid(p0 = 0.05, p1 = 0.25, alpha = 0.05, beta = 0.2, mander = FALSE) %>% augmentGrid(parallel = FALSE) %>% obtainDesign() #> # A tibble: 2 × 15 #> nTotal nStage1 rTotal rFutility p0 p1 Alpha Beta Type1 Type2 PETNull #> #> 1 17 9 2 0 0.05 0.25 0.05 0.2 0.0466 0.188 0.630 #> 2 16 12 2 0 0.05 0.25 0.05 0.2 0.0427 0.199 0.540 #> # ℹ 4 more variables: PETAlt , AveSizeNull , AveSizeAlt , #> # Criterion # Constrained stage sizes createGrid(p0 = 0.25, p1 = 0.45, alpha = 0.05, beta = 0.2) %>% dplyr::filter(nStage1 == 8) %>% augmentGrid(parallel = FALSE) %>% obtainDesign() #> # A tibble: 4 × 16 #> nTotal nStage1 rTotal rFutility rSuccess p0 p1 Alpha Beta Type1 Type2 #> #> 1 39 8 14 1 5 0.25 0.45 0.05 0.2 0.0430 0.196 #> 2 36 8 13 0 5 0.25 0.45 0.05 0.2 0.0482 0.184 #> 3 36 8 13 0 5 0.25 0.45 0.05 0.2 0.0482 0.184 #> 4 36 8 13 0 5 0.25 0.45 0.05 0.2 0.0482 0.184 #> # ℹ 5 more variables: PETNull , PETAlt , AveSizeNull , #> # AveSizeAlt , Criterion # }"},{"path":"https://openpharma.github.io/mtdesign/main/reference/pipe.html","id":null,"dir":"Reference","previous_headings":"","what":"Pipe operator — %>%","title":"Pipe operator — %>%","text":"See magrittr::%>% details.","code":""},{"path":"https://openpharma.github.io/mtdesign/main/reference/pipe.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pipe operator — %>%","text":"","code":"lhs %>% rhs"},{"path":"https://openpharma.github.io/mtdesign/main/reference/pipe.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pipe operator — %>%","text":"lhs value magrittr placeholder. rhs function call using magrittr semantics.","code":""},{"path":"https://openpharma.github.io/mtdesign/main/reference/pipe.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pipe operator — %>%","text":"result calling `rhs(lhs)`.","code":""},{"path":"https://openpharma.github.io/mtdesign/main/reference/powerPlot.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot the power curve(s) for the given design(s) — powerPlot","title":"Plot the power curve(s) for the given design(s) — powerPlot","text":"Plot power curve(s) given design(s)","code":""},{"path":"https://openpharma.github.io/mtdesign/main/reference/powerPlot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot the power curve(s) for the given design(s) — powerPlot","text":"","code":"powerPlot(grid, probs = seq(0, 1, 0.01))"},{"path":"https://openpharma.github.io/mtdesign/main/reference/powerPlot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot the power curve(s) for the given design(s) — powerPlot","text":"grid tibble containing designs plotted probs response rates rejection probabilities plotted","code":""},{"path":"https://openpharma.github.io/mtdesign/main/reference/powerPlot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot the power curve(s) for the given design(s) — powerPlot","text":"ggplot object containing power curve(s)","code":""},{"path":"https://openpharma.github.io/mtdesign/main/reference/powerPlot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot the power curve(s) for the given design(s) — powerPlot","text":"","code":"createGrid(p0 = 0.05, p1 = 0.25, alpha = 0.05, beta = 0.2, mander = FALSE) %>% augmentGrid(cores = 2) %>% obtainDesign() %>% powerPlot(probs = seq(0, 0.5, 0.025)) #> Warning: one argument not used by format 'Parallelisation has been requested, but the grid size [72814] is less than the minimum chunk size [1e+05]. Parallelisation will not occur' #> pkgdown 2024-10-31 15:51:49 INFO pkgdown::build_site: Parallelisation has been requested, but the grid size [72814] is less than the minimum chunk size [1e+05]. Parallelisation will not occur"},{"path":"https://openpharma.github.io/mtdesign/main/reference/searchBounds.html","id":null,"dir":"Reference","previous_headings":"","what":"Obtain default bounds for the construction of the search grid. — searchBounds","title":"Obtain default bounds for the construction of the search grid. — searchBounds","text":"formula used continuity corrected Normal approximation Fleiss et al (2003).","code":""},{"path":"https://openpharma.github.io/mtdesign/main/reference/searchBounds.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Obtain default bounds for the construction of the search grid. — searchBounds","text":"","code":"searchBounds(p0, p1, alpha = 0.05, beta = 0.2, twoSided = TRUE)"},{"path":"https://openpharma.github.io/mtdesign/main/reference/searchBounds.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Obtain default bounds for the construction of the search grid. — searchBounds","text":"p0 response rate null hypothesis p1 response rate alternate hypothesis alpha desired (one-sided) type 1 error rate beta desired type 2 error rate twoSided two- one-sided significance level?","code":""},{"path":"https://openpharma.github.io/mtdesign/main/reference/searchBounds.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Obtain default bounds for the construction of the search grid. — searchBounds","text":"list three elements: \"n\" - single stage sample size Fleiss et al; \"min\" - lower bound, 0.8*n; \"max\" - upper bound, 2*n. floor() ceiling() applied appropriate.","code":""}]
+[{"path":"https://openpharma.github.io/mtdesign/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc. .","code":" Copyright (C) This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see Copyright (C) This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://openpharma.github.io/mtdesign/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"John Kirkpatrick. Author, maintainer.","code":""},{"path":"https://openpharma.github.io/mtdesign/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Kirkpatrick J (2024). mtdesign: Mander Thompson Designs. R package version 0.1.2, https://github.com/openpharma/mtdesign.","code":"@Manual{, title = {mtdesign: Mander and Thompson Designs}, author = {John Kirkpatrick}, year = {2024}, note = {R package version 0.1.2}, url = {https://github.com/openpharma/mtdesign}, }"},{"path":[]},{"path":"https://openpharma.github.io/mtdesign/index.html","id":"introduction","dir":"","previous_headings":"","what":"Introduction","title":"Mander and Thompson Designs","text":"package mtdesign provides implementations Simon (1989) Mander & Thompson (2010). implementations Simon’s methods available - example, ph2simon function clinfun package (Seshan 2018), provide easy access non-optimal solutions way mtdesign . aware R-based implementations Mander & Thompson’s extension Simon.","code":""},{"path":"https://openpharma.github.io/mtdesign/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Mander and Thompson Designs","text":"available CRAN, can install mtdesign usual way: install.packages(\"mtdesign\") can install development version mtdesign GitHub : devtools::install_github(\"openpharma/mtdesign\")","code":""},{"path":"https://openpharma.github.io/mtdesign/index.html","id":"set-up-vignette-environment","dir":"","previous_headings":"","what":"Set up vignette environment","title":"Mander and Thompson Designs","text":"","code":"# By policy, on CRAN, use only two cores, no matter how many are available. if (requireNamespace(\"parallel\", quietly = TRUE)) { maxCores <- parallel::detectCores() maxCores <- ifelse(identical(Sys.getenv(\"NOT_CRAN\"), \"true\"), maxCores, min(maxCores, 2)) } else { maxCores <- 1 }"},{"path":"https://openpharma.github.io/mtdesign/index.html","id":"example","dir":"","previous_headings":"","what":"Example","title":"Mander and Thompson Designs","text":"Suppose treatments response rate less 5% interest response rate least 25% worthy development. Simon’s 2-stage design seek efficacy signal significance level 5% power 80% required. table shows optimal design requirements 0/9 2/17. expected sample size 12.0 probability early termination 63%. significance level actually achieved 4.7% power level achieved 100% - 18.8% = 81.2%. power curves designs easily plotted. Obtaining equivalent Mander & Thompson designs requires small change calls.","code":"library(mtdesign) library(knitr) library(dplyr) #> #> Attaching package: 'dplyr' #> The following objects are masked from 'package:stats': #> #> filter, lag #> The following objects are masked from 'package:base': #> #> intersect, setdiff, setequal, union simonDesign <- obtainDesign(p0 = 0.05, p1 = 0.25, alpha = 0.05, beta = 0.2, mander = FALSE, parallel = FALSE) simonDesign %>% select(-Alpha, -Beta, -p0, -p1, -PETAlt, -AveSizeAlt) %>% kable(digits = c(0, 0, 0, 0, 3, 3, 2, 1, NA)) powerPlot(simonDesign) manderDesign <- obtainDesign( p0 = 0.05, p1 = 0.25, alpha = 0.05, beta = 0.2, cores = maxCores ) manderDesign %>% select(-Alpha, -Beta, -p0, -p1) %>% kable(digits = c(0, 0, 0, 0, 3, 3, 2, 2, 2, 1, NA)) powerPlot(manderDesign)"},{"path":"https://openpharma.github.io/mtdesign/index.html","id":"constrained-designs","dir":"","previous_headings":"Example","what":"Constrained designs","title":"Mander and Thompson Designs","text":"Suppose trial, whatever reason, restricted using 8 participants stage. shown , optimal Simon’s two stage design 0/9 2/17. ’s close n1 = 8, n = 16. (slightly) sub-optimal design n1 = 8, n = 16? , isn’t. close can get? Best sub-optimal design required significance level Best sub-optimal design required power choice lies design achieves required significance level power 77.1% one required power significance level 15.1%. designs accept null hypothesis responders seen first group eight participants. differ critical value end stage 2: 1 maintain power, 2 maintain significance level. power curve designs can compared globally optimal design.","code":"x <- createGrid(p0 = 0.05, p1 = 0.25, alpha = 0.05, beta = 0.2, mander = FALSE) y <- x %>% filter(nStage1 == 8, nTotal == 16) z <- y %>% obtainDesign(cores = maxCores) #> Warning: No acceptable designs were found. if (nrow(z) == 0) { print(\"No acceptable designs were found.\") } else { select(-Alpha, -Beta, -p0, -p1, -PETAlt, -AveSizeAlt) %>% z() %>% select(-Alpha, -Beta, -p0, -p1, -PETAlt, -AveSizeAlt) %>% kable(digits = c(0, 0, 0, 0, 3, 3, 2, 1, NA)) } #> [1] \"No acceptable designs were found.\" z1 <- y %>% augmentGrid() bestSize <- z1 %>% filter(Type1 < Alpha) %>% slice_min(Type2) bestSize %>% select(-Alpha, -Beta, -p0, -p1, -PETAlt, -AveSizeAlt) %>% kable( caption = \"Best sub-optimal design with required significance level\", digits = c(0, 0, 0, 0, 3, 3, 2, 1, NA) ) bestPower <- z1 %>% filter(Type2 < Beta) %>% slice_min(Type1) bestPower %>% select(-Alpha, -Beta, -p0, -p1, -PETAlt, -AveSizeAlt) %>% kable( caption = \"Best sub-optimal design with required power\", digits = c(0, 0, 0, 0, 3, 3, 2, 1, NA) ) plotData1 <- simonDesign %>% filter(Criterion == \"optimal\") %>% bind_rows(list(bestSize, bestPower)) powerPlot(plotData1)"},{"path":"https://openpharma.github.io/mtdesign/index.html","id":"package-structure","dir":"","previous_headings":"","what":"Package structure","title":"Mander and Thompson Designs","text":"mtdesign package consists three main functions: createGrid creates grid (nStage1, rFutility, nTotal rTotal Simon’s design nStage1, rFutility, rSuccess, nTotal rTotal Mander & Thompson design) brute force search required design(s) conducted augmentGridtakes grid created createGrid adds columns probability early termination, Type 1 error, Type 2 error expected sample size . obtainDesign takes augmented grid identifies optimal minimax designs","code":""},{"path":"https://openpharma.github.io/mtdesign/index.html","id":"error-and-warning-messages-and-logging","dir":"","previous_headings":"","what":"Error and warning messages and logging","title":"Mander and Thompson Designs","text":"mtdesign package supports logging via futile.logger package (Rowe 2016). functions simply report Entry Exit DEBUG level. augmentGrid function reports steps parallelisation process TRACE level.","code":""},{"path":"https://openpharma.github.io/mtdesign/index.html","id":"parallelisation","dir":"","previous_headings":"","what":"Parallelisation","title":"Mander and Thompson Designs","text":"known closed form solution obtaining solutions either Simon’s original equations Mander & Thompson’s extensions. mtdesign package uses brute force approach evaluate operating characteristics reasonable potential designs. grids can quickly become large, particularly Mander & Thompson designs. example, createGrid(0.2, 0.4, alpha=0.1, beta=0.1) creates grid almost 11 million candidate designs. mtdesign uses paralellisation attempt speed evaluation candidate designs. augmentGrid function allows users control parallelisation process: parallel parameter defaults TRUE defines whether paralellisation used. cores parameter specifies many cores used. default value, NA tells mtdesign use available (defined parallel::detectCores()), cores. minChunkSize determines smallest grid candidate designs trigger paralellisation. default value 100000. parallel package required parallelisation. parallelisation needed (ie grid size exceeds minChunkSize) requested parallel package installed, error message thrown augmentation grid stops. paralellisation requested grid contains one million rows, warning produced.","code":""},{"path":"https://openpharma.github.io/mtdesign/index.html","id":"troubleshooting","dir":"","previous_headings":"","what":"Troubleshooting","title":"Mander and Thompson Designs","text":", installing using mtdesign package, get error regarding syntax error .hpp file, similar following issue likely mismatch g++ compiler used headers supplied BH package. two solutions know : Upgrade g++ Downgrade version BH package using. appropriate package version depends version g++ compiler using.","code":".../BH/include/boost/math/tools/fraction.hpp:84:48: error: ‘long double’ is not a class, struct, or union type using value_type = typename T::value_type;"},{"path":[]},{"path":"https://openpharma.github.io/mtdesign/reference/augmentGrid.html","id":null,"dir":"Reference","previous_headings":"","what":"Augment a grid of candidate designs with type 1 and type 2 error probabilities, expected sample sizes and probabilities of early termination — augmentGrid","title":"Augment a grid of candidate designs with type 1 and type 2 error probabilities, expected sample sizes and probabilities of early termination — augmentGrid","text":"Augment grid candidate designs type 1 type 2 error probabilities, expected sample sizes probabilities early termination","code":""},{"path":"https://openpharma.github.io/mtdesign/reference/augmentGrid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Augment a grid of candidate designs with type 1 and type 2 error probabilities, expected sample sizes and probabilities of early termination — augmentGrid","text":"","code":"augmentGrid(d, parallel = TRUE, cores = NA, minChunkSize = 1e+05)"},{"path":"https://openpharma.github.io/mtdesign/reference/augmentGrid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Augment a grid of candidate designs with type 1 and type 2 error probabilities, expected sample sizes and probabilities of early termination — augmentGrid","text":"d tibble created `createGrid` parallel use parallelisation available cores number cores use parallelising. NA<\/code>, available cores requested minChunkSize minimum size grid paralellisation attempted","code":""},{"path":"https://openpharma.github.io/mtdesign/reference/augmentGrid.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Augment a grid of candidate designs with type 1 and type 2 error probabilities, expected sample sizes and probabilities of early termination — augmentGrid","text":"augmented grid tibble","code":""},{"path":"https://openpharma.github.io/mtdesign/reference/augmentGrid.html","id":"usage-notes","dir":"Reference","previous_headings":"","what":"Usage Notes","title":"Augment a grid of candidate designs with type 1 and type 2 error probabilities, expected sample sizes and probabilities of early termination — augmentGrid","text":"Regardless value `parallel`, parallelisation used size grid greater chunkSize<\/code>. paralellisation requested needed, exception thrown parallel package available.","code":""},{"path":"https://openpharma.github.io/mtdesign/reference/augmentGrid.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Augment a grid of candidate designs with type 1 and type 2 error probabilities, expected sample sizes and probabilities of early termination — augmentGrid","text":"","code":"x <- createGrid(p0 = 0.1, p1 = 0.30, alpha = 0.1, beta = 0.1, nMin = 24, nMax = 32) %>% augmentGrid(parallel = FALSE)"},{"path":"https://openpharma.github.io/mtdesign/reference/createGrid.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a grid of candidate designs — createGrid","title":"Create a grid of candidate designs — createGrid","text":"Create grid candidate designs","code":""},{"path":"https://openpharma.github.io/mtdesign/reference/createGrid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a grid of candidate designs — createGrid","text":"","code":"createGrid( p0, p1, alpha = 0.1, beta = NA, power = ifelse(is.na(beta), 0.9, 1 - beta), nMin = NA, nMax = NA, mander = TRUE )"},{"path":"https://openpharma.github.io/mtdesign/reference/createGrid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a grid of candidate designs — createGrid","text":"p0 response rate null hypothesis p1 response rate alternate hypothesis alpha desired (one-sided) type 1 error rate beta desired type 2 error rate power alternative beta nMin lower bound search grid. NA, searchBounds called provide appropriate value nMax lower bound search grid. NA, searchBounds called provide appropriate value mander Mander & Thompson Simon's design required?","code":""},{"path":"https://openpharma.github.io/mtdesign/reference/createGrid.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a grid of candidate designs — createGrid","text":"tibble. See Usage notes list description columns.","code":""},{"path":"https://openpharma.github.io/mtdesign/reference/createGrid.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a grid of candidate designs — createGrid","text":"","code":"# Standard use for a Simon's 2-stage design x <- createGrid(p0 = 0.1, p1 = 0.5, alpha = 0.1, beta = 0.1, mander = FALSE) # Custom search bounds for a Mander & Thompson design y <- createGrid(p0 = 0.1, p1 = 0.4, alpha = 0.1, beta = 0.1, nMin = 20, nMax = 30)"},{"path":"https://openpharma.github.io/mtdesign/reference/obtainDesign.html","id":null,"dir":"Reference","previous_headings":"","what":"Finds optimal and minimax designs for either Simon's 2-stage or Mander & Thompson studies — obtainDesign","title":"Finds optimal and minimax designs for either Simon's 2-stage or Mander & Thompson studies — obtainDesign","text":"obtainDesign essentially wrapper calls createGrid augmentGrid followed simple filtering candidate designs identify optimal minimax designs.","code":""},{"path":"https://openpharma.github.io/mtdesign/reference/obtainDesign.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Finds optimal and minimax designs for either Simon's 2-stage or Mander & Thompson studies — obtainDesign","text":"","code":"obtainDesign( grid = NULL, p0 = NA, p1 = NA, alpha = ifelse(is.null(grid), 0.05, NA), beta = ifelse(is.null(grid), 0.1, NA), fullGrid = FALSE, ... )"},{"path":"https://openpharma.github.io/mtdesign/reference/obtainDesign.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Finds optimal and minimax designs for either Simon's 2-stage or Mander & Thompson studies — obtainDesign","text":"grid Optional. tibble created createGrid. NULL, p0, p1, alpha beta must specified createGrid called generate required grid. NULL p0, p1, alpha beta ignored p0 response rate null hypothesis p1 response rate alternate hypothesis alpha desired (one-sided) type 1 error rate beta desired type 2 error rate fullGrid full grid possible designs returned, simply optimal minimax solutions? Mander Thompson design, optimal minimax designs returned null alternate hypotheses. See Usage Notes . ... passed `createGrid` `augmentGrid`. particular mander=TRUE Mander & Thompson design mander=FALSE Simon's 2-stage design.","code":""},{"path":"https://openpharma.github.io/mtdesign/reference/obtainDesign.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Finds optimal and minimax designs for either Simon's 2-stage or Mander & Thompson studies — obtainDesign","text":"tibble created createGrid. fullGrid == FALSE table contains additional column, Criterion indicating type design. Possible values Criterion \"optimal\" \"minimax\" Simon's designs \"optimalNull\", \"optimalAlt\", \"minimaxNull\" \"minimaxAlt\" Mander & Thompson designs.","code":""},{"path":"https://openpharma.github.io/mtdesign/reference/obtainDesign.html","id":"usage-notes","dir":"Reference","previous_headings":"","what":"Usage notes","title":"Finds optimal and minimax designs for either Simon's 2-stage or Mander & Thompson studies — obtainDesign","text":"grid NULL possible none candidate designs acceptable (, satisfy significance level power requirements). case fullGrid == FALSE, empty tibble returned. versbose == TRUE warning message also printed. fullGrid == TRUE full grid designs considered returned. can interrogated find optimal designs constraints - example fixed stage sizes.","code":""},{"path":"https://openpharma.github.io/mtdesign/reference/obtainDesign.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Finds optimal and minimax designs for either Simon's 2-stage or Mander & Thompson studies — obtainDesign","text":"","code":"# \\donttest{ # Standard use (Simon's 2-stage design) createGrid(p0 = 0.05, p1 = 0.25, alpha = 0.05, beta = 0.2, mander = FALSE) %>% augmentGrid(parallel = FALSE) %>% obtainDesign() #> # A tibble: 2 × 15 #> nTotal nStage1 rTotal rFutility p0 p1 Alpha Beta Type1 Type2 PETNull #> #> 1 17 9 2 0 0.05 0.25 0.05 0.2 0.0466 0.188 0.630 #> 2 16 12 2 0 0.05 0.25 0.05 0.2 0.0427 0.199 0.540 #> # ℹ 4 more variables: PETAlt , AveSizeNull , AveSizeAlt , #> # Criterion # Constrained stage sizes createGrid(p0 = 0.25, p1 = 0.45, alpha = 0.05, beta = 0.2) %>% dplyr::filter(nStage1 == 8) %>% augmentGrid(parallel = FALSE) %>% obtainDesign() #> # A tibble: 4 × 16 #> nTotal nStage1 rTotal rFutility rSuccess p0 p1 Alpha Beta Type1 Type2 #> #> 1 39 8 14 1 5 0.25 0.45 0.05 0.2 0.0430 0.196 #> 2 36 8 13 0 5 0.25 0.45 0.05 0.2 0.0482 0.184 #> 3 36 8 13 0 5 0.25 0.45 0.05 0.2 0.0482 0.184 #> 4 36 8 13 0 5 0.25 0.45 0.05 0.2 0.0482 0.184 #> # ℹ 5 more variables: PETNull , PETAlt , AveSizeNull , #> # AveSizeAlt , Criterion # }"},{"path":"https://openpharma.github.io/mtdesign/reference/pipe.html","id":null,"dir":"Reference","previous_headings":"","what":"Pipe operator — %>%","title":"Pipe operator — %>%","text":"See magrittr::%>% details.","code":""},{"path":"https://openpharma.github.io/mtdesign/reference/pipe.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pipe operator — %>%","text":"","code":"lhs %>% rhs"},{"path":"https://openpharma.github.io/mtdesign/reference/pipe.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pipe operator — %>%","text":"lhs value magrittr placeholder. rhs function call using magrittr semantics.","code":""},{"path":"https://openpharma.github.io/mtdesign/reference/pipe.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pipe operator — %>%","text":"result calling `rhs(lhs)`.","code":""},{"path":"https://openpharma.github.io/mtdesign/reference/powerPlot.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot the power curve(s) for the given design(s) — powerPlot","title":"Plot the power curve(s) for the given design(s) — powerPlot","text":"Plot power curve(s) given design(s)","code":""},{"path":"https://openpharma.github.io/mtdesign/reference/powerPlot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot the power curve(s) for the given design(s) — powerPlot","text":"","code":"powerPlot(grid, probs = seq(0, 1, 0.01))"},{"path":"https://openpharma.github.io/mtdesign/reference/powerPlot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot the power curve(s) for the given design(s) — powerPlot","text":"grid tibble containing designs plotted probs response rates rejection probabilities plotted","code":""},{"path":"https://openpharma.github.io/mtdesign/reference/powerPlot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot the power curve(s) for the given design(s) — powerPlot","text":"ggplot object containing power curve(s)","code":""},{"path":"https://openpharma.github.io/mtdesign/reference/powerPlot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot the power curve(s) for the given design(s) — powerPlot","text":"","code":"createGrid(p0 = 0.05, p1 = 0.25, alpha = 0.05, beta = 0.2, mander = FALSE) %>% augmentGrid(cores = 2) %>% obtainDesign() %>% powerPlot(probs = seq(0, 0.5, 0.025)) #> Warning: one argument not used by format 'Parallelisation has been requested, but the grid size [72814] is less than the minimum chunk size [1e+05]. Parallelisation will not occur' #> pkgdown 2024-11-01 13:52:51 INFO pkgdown::build_site: Parallelisation has been requested, but the grid size [72814] is less than the minimum chunk size [1e+05]. Parallelisation will not occur"},{"path":"https://openpharma.github.io/mtdesign/reference/searchBounds.html","id":null,"dir":"Reference","previous_headings":"","what":"Obtain default bounds for the construction of the search grid. — searchBounds","title":"Obtain default bounds for the construction of the search grid. — searchBounds","text":"formula used continuity corrected Normal approximation Fleiss et al (2003).","code":""},{"path":"https://openpharma.github.io/mtdesign/reference/searchBounds.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Obtain default bounds for the construction of the search grid. — searchBounds","text":"","code":"searchBounds(p0, p1, alpha = 0.05, beta = 0.2, twoSided = TRUE)"},{"path":"https://openpharma.github.io/mtdesign/reference/searchBounds.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Obtain default bounds for the construction of the search grid. — searchBounds","text":"p0 response rate null hypothesis p1 response rate alternate hypothesis alpha desired (one-sided) type 1 error rate beta desired type 2 error rate twoSided two- one-sided significance level?","code":""},{"path":"https://openpharma.github.io/mtdesign/reference/searchBounds.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Obtain default bounds for the construction of the search grid. — searchBounds","text":"list three elements: \"n\" - single stage sample size Fleiss et al; \"min\" - lower bound, 0.8*n; \"max\" - upper bound, 2*n. floor() ceiling() applied appropriate.","code":""}]
Usage -
+Usage
-
+Arguments -
+Arguments
--
-
- grid - +
- grid
Optional. A tibble created by
createGrid. IfNULL, thenp0,p1,alphaandbetamust be specified andcreateGridis called to generate the required grid. If not @@ -100,45 +71,37 @@Argumentsp0 - +
- p0
the response rate under the null hypothesis
- p1 -
+- p1
the response rate under the alternate hypothesis
- alpha -
+- alpha
the desired (one-sided) type 1 error rate
- beta -
+- beta
the desired type 2 error rate
- fullGrid -
+- fullGrid
should the full grid of all possible designs be returned, or simply the optimal and minimax solutions? For a Mander and Thompson design, optimal and minimax designs are returned for both the null and alternate hypotheses. See Usage Notes below.
- ... -
+- ...
passed to `createGrid` or `augmentGrid`. In particular
mander=TRUEfor a Mander & Thompson design ormander=FALSEfor a Simon's 2-stage design.
Value -
+Value
a tibble created by createGrid. If
fullGrid == FALSE the table contains an additional column,
Criterion indicating the type of design. Possible values for
@@ -147,8 +110,7 @@
Value Thompson designs.
Usage notes -
+Usage notes
If grid is not NULL it is possible that none of the candidate
@@ -162,8 +124,7 @@
Usage notes
- Examples
-
+ Examples
# \donttest{
# Standard use (Simon's 2-stage design)
createGrid(p0 = 0.05, p1 = 0.25, alpha = 0.05, beta = 0.2, mander = FALSE) %>%
@@ -194,8 +155,7 @@ Examples
-
+
# \donttest{
# Standard use (Simon's 2-stage design)
createGrid(p0 = 0.05, p1 = 0.25, alpha = 0.05, beta = 0.2, mander = FALSE) %>%
@@ -194,8 +155,7 @@ Examples
-
Examples -
+Examples
createGrid(p0 = 0.05, p1 = 0.25, alpha = 0.05, beta = 0.2, mander = FALSE) %>%
augmentGrid(cores = 2) %>%
obtainDesign() %>%
powerPlot(probs = seq(0, 0.5, 0.025))
#> Warning: one argument not used by format 'Parallelisation has been requested, but the grid size [72814] is less than the minimum chunk size [1e+05]. Parallelisation will not occur'
-#> pkgdown 2024-10-31 15:51:49 INFO pkgdown::build_site: Parallelisation has been requested, but the grid size [72814] is less than the minimum chunk size [1e+05]. Parallelisation will not occur
+#> pkgdown 2024-11-01 13:52:51 INFO pkgdown::build_site: Parallelisation has been requested, but the grid size [72814] is less than the minimum chunk size [1e+05]. Parallelisation will not occur
Value -
+Value
a list with three elements: "n" - the single stage sample size from
Fleiss et al; "min" - the lower bound, 0.8*n; "max" - the upper bound, 2*n.
floor() and ceiling() are applied as appropriate.
NA<\/code>, available cores requested minChunkSize minimum size grid paralellisation attempted","code":""},{"path":"https://openpharma.github.io/mtdesign/main/reference/augmentGrid.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Augment a grid of candidate designs with type 1 and type 2 error probabilities, expected sample sizes and probabilities of early termination — augmentGrid","text":"augmented grid tibble","code":""},{"path":"https://openpharma.github.io/mtdesign/main/reference/augmentGrid.html","id":"usage-notes","dir":"Reference","previous_headings":"","what":"Usage Notes","title":"Augment a grid of candidate designs with type 1 and type 2 error probabilities, expected sample sizes and probabilities of early termination — augmentGrid","text":"Regardless value `parallel`, parallelisation used size grid greater chunkSize<\/code>. paralellisation requested needed, exception thrown parallel package available.","code":""},{"path":"https://openpharma.github.io/mtdesign/main/reference/augmentGrid.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Augment a grid of candidate designs with type 1 and type 2 error probabilities, expected sample sizes and probabilities of early termination — augmentGrid","text":"","code":"x <- createGrid(p0 = 0.1, p1 = 0.30, alpha = 0.1, beta = 0.1, nMin = 24, nMax = 32) %>% augmentGrid(parallel = FALSE)"},{"path":"https://openpharma.github.io/mtdesign/main/reference/createGrid.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a grid of candidate designs — createGrid","title":"Create a grid of candidate designs — createGrid","text":"Create grid candidate designs","code":""},{"path":"https://openpharma.github.io/mtdesign/main/reference/createGrid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a grid of candidate designs — createGrid","text":"","code":"createGrid( p0, p1, alpha = 0.1, beta = NA, power = ifelse(is.na(beta), 0.9, 1 - beta), nMin = NA, nMax = NA, mander = TRUE )"},{"path":"https://openpharma.github.io/mtdesign/main/reference/createGrid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a grid of candidate designs — createGrid","text":"p0 response rate null hypothesis p1 response rate alternate hypothesis alpha desired (one-sided) type 1 error rate beta desired type 2 error rate power alternative beta nMin lower bound search grid. NA, searchBounds called provide appropriate value nMax lower bound search grid. NA, searchBounds called provide appropriate value mander Mander & Thompson Simon's design required?","code":""},{"path":"https://openpharma.github.io/mtdesign/main/reference/createGrid.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a grid of candidate designs — createGrid","text":"tibble. See Usage notes list description columns.","code":""},{"path":"https://openpharma.github.io/mtdesign/main/reference/createGrid.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a grid of candidate designs — createGrid","text":"","code":"# Standard use for a Simon's 2-stage design x <- createGrid(p0 = 0.1, p1 = 0.5, alpha = 0.1, beta = 0.1, mander = FALSE) # Custom search bounds for a Mander & Thompson design y <- createGrid(p0 = 0.1, p1 = 0.4, alpha = 0.1, beta = 0.1, nMin = 20, nMax = 30)"},{"path":"https://openpharma.github.io/mtdesign/main/reference/obtainDesign.html","id":null,"dir":"Reference","previous_headings":"","what":"Finds optimal and minimax designs for either Simon's 2-stage or Mander & Thompson studies — obtainDesign","title":"Finds optimal and minimax designs for either Simon's 2-stage or Mander & Thompson studies — obtainDesign","text":"obtainDesign essentially wrapper calls createGrid augmentGrid followed simple filtering candidate designs identify optimal minimax designs.","code":""},{"path":"https://openpharma.github.io/mtdesign/main/reference/obtainDesign.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Finds optimal and minimax designs for either Simon's 2-stage or Mander & Thompson studies — obtainDesign","text":"","code":"obtainDesign( grid = NULL, p0 = NA, p1 = NA, alpha = ifelse(is.null(grid), 0.05, NA), beta = ifelse(is.null(grid), 0.1, NA), fullGrid = FALSE, ... )"},{"path":"https://openpharma.github.io/mtdesign/main/reference/obtainDesign.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Finds optimal and minimax designs for either Simon's 2-stage or Mander & Thompson studies — obtainDesign","text":"grid Optional. tibble created createGrid. NULL, p0, p1, alpha beta must specified createGrid called generate required grid. NULL p0, p1, alpha beta ignored p0 response rate null hypothesis p1 response rate alternate hypothesis alpha desired (one-sided) type 1 error rate beta desired type 2 error rate fullGrid full grid possible designs returned, simply optimal minimax solutions? Mander Thompson design, optimal minimax designs returned null alternate hypotheses. See Usage Notes . ... passed `createGrid` `augmentGrid`. particular mander=TRUE Mander & Thompson design mander=FALSE Simon's 2-stage design.","code":""},{"path":"https://openpharma.github.io/mtdesign/main/reference/obtainDesign.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Finds optimal and minimax designs for either Simon's 2-stage or Mander & Thompson studies — obtainDesign","text":"tibble created createGrid. fullGrid == FALSE table contains additional column, Criterion indicating type design. Possible values Criterion \"optimal\" \"minimax\" Simon's designs \"optimalNull\", \"optimalAlt\", \"minimaxNull\" \"minimaxAlt\" Mander & Thompson designs.","code":""},{"path":"https://openpharma.github.io/mtdesign/main/reference/obtainDesign.html","id":"usage-notes","dir":"Reference","previous_headings":"","what":"Usage notes","title":"Finds optimal and minimax designs for either Simon's 2-stage or Mander & Thompson studies — obtainDesign","text":"grid NULL possible none candidate designs acceptable (, satisfy significance level power requirements). case fullGrid == FALSE, empty tibble returned. versbose == TRUE warning message also printed. fullGrid == TRUE full grid designs considered returned. can interrogated find optimal designs constraints - example fixed stage sizes.","code":""},{"path":"https://openpharma.github.io/mtdesign/main/reference/obtainDesign.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Finds optimal and minimax designs for either Simon's 2-stage or Mander & Thompson studies — obtainDesign","text":"","code":"# \\donttest{ # Standard use (Simon's 2-stage design) createGrid(p0 = 0.05, p1 = 0.25, alpha = 0.05, beta = 0.2, mander = FALSE) %>% augmentGrid(parallel = FALSE) %>% obtainDesign() #> # A tibble: 2 × 15 #> nTotal nStage1 rTotal rFutility p0 p1 Alpha Beta Type1 Type2 PETNull #> #> 1 17 9 2 0 0.05 0.25 0.05 0.2 0.0466 0.188 0.630 #> 2 16 12 2 0 0.05 0.25 0.05 0.2 0.0427 0.199 0.540 #> # ℹ 4 more variables: PETAlt , AveSizeNull , AveSizeAlt , #> # Criterion # Constrained stage sizes createGrid(p0 = 0.25, p1 = 0.45, alpha = 0.05, beta = 0.2) %>% dplyr::filter(nStage1 == 8) %>% augmentGrid(parallel = FALSE) %>% obtainDesign() #> # A tibble: 4 × 16 #> nTotal nStage1 rTotal rFutility rSuccess p0 p1 Alpha Beta Type1 Type2 #> #> 1 39 8 14 1 5 0.25 0.45 0.05 0.2 0.0430 0.196 #> 2 36 8 13 0 5 0.25 0.45 0.05 0.2 0.0482 0.184 #> 3 36 8 13 0 5 0.25 0.45 0.05 0.2 0.0482 0.184 #> 4 36 8 13 0 5 0.25 0.45 0.05 0.2 0.0482 0.184 #> # ℹ 5 more variables: PETNull , PETAlt , AveSizeNull , #> # AveSizeAlt , Criterion # }"},{"path":"https://openpharma.github.io/mtdesign/main/reference/pipe.html","id":null,"dir":"Reference","previous_headings":"","what":"Pipe operator — %>%","title":"Pipe operator — %>%","text":"See magrittr::%>% details.","code":""},{"path":"https://openpharma.github.io/mtdesign/main/reference/pipe.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pipe operator — %>%","text":"","code":"lhs %>% rhs"},{"path":"https://openpharma.github.io/mtdesign/main/reference/pipe.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pipe operator — %>%","text":"lhs value magrittr placeholder. rhs function call using magrittr semantics.","code":""},{"path":"https://openpharma.github.io/mtdesign/main/reference/pipe.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pipe operator — %>%","text":"result calling `rhs(lhs)`.","code":""},{"path":"https://openpharma.github.io/mtdesign/main/reference/powerPlot.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot the power curve(s) for the given design(s) — powerPlot","title":"Plot the power curve(s) for the given design(s) — powerPlot","text":"Plot power curve(s) given design(s)","code":""},{"path":"https://openpharma.github.io/mtdesign/main/reference/powerPlot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot the power curve(s) for the given design(s) — powerPlot","text":"","code":"powerPlot(grid, probs = seq(0, 1, 0.01))"},{"path":"https://openpharma.github.io/mtdesign/main/reference/powerPlot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot the power curve(s) for the given design(s) — powerPlot","text":"grid tibble containing designs plotted probs response rates rejection probabilities plotted","code":""},{"path":"https://openpharma.github.io/mtdesign/main/reference/powerPlot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot the power curve(s) for the given design(s) — powerPlot","text":"ggplot object containing power curve(s)","code":""},{"path":"https://openpharma.github.io/mtdesign/main/reference/powerPlot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot the power curve(s) for the given design(s) — powerPlot","text":"","code":"createGrid(p0 = 0.05, p1 = 0.25, alpha = 0.05, beta = 0.2, mander = FALSE) %>% augmentGrid(cores = 2) %>% obtainDesign() %>% powerPlot(probs = seq(0, 0.5, 0.025)) #> Warning: one argument not used by format 'Parallelisation has been requested, but the grid size [72814] is less than the minimum chunk size [1e+05]. Parallelisation will not occur' #> pkgdown 2024-10-31 15:51:49 INFO pkgdown::build_site: Parallelisation has been requested, but the grid size [72814] is less than the minimum chunk size [1e+05]. Parallelisation will not occur"},{"path":"https://openpharma.github.io/mtdesign/main/reference/searchBounds.html","id":null,"dir":"Reference","previous_headings":"","what":"Obtain default bounds for the construction of the search grid. — searchBounds","title":"Obtain default bounds for the construction of the search grid. — searchBounds","text":"formula used continuity corrected Normal approximation Fleiss et al (2003).","code":""},{"path":"https://openpharma.github.io/mtdesign/main/reference/searchBounds.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Obtain default bounds for the construction of the search grid. — searchBounds","text":"","code":"searchBounds(p0, p1, alpha = 0.05, beta = 0.2, twoSided = TRUE)"},{"path":"https://openpharma.github.io/mtdesign/main/reference/searchBounds.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Obtain default bounds for the construction of the search grid. — searchBounds","text":"p0 response rate null hypothesis p1 response rate alternate hypothesis alpha desired (one-sided) type 1 error rate beta desired type 2 error rate twoSided two- one-sided significance level?","code":""},{"path":"https://openpharma.github.io/mtdesign/main/reference/searchBounds.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Obtain default bounds for the construction of the search grid. — searchBounds","text":"list three elements: \"n\" - single stage sample size Fleiss et al; \"min\" - lower bound, 0.8*n; \"max\" - upper bound, 2*n. floor() ceiling() applied appropriate.","code":""}]
+[{"path":"https://openpharma.github.io/mtdesign/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc. .","code":" Copyright (C) This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see Copyright (C) This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://openpharma.github.io/mtdesign/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"John Kirkpatrick. Author, maintainer.","code":""},{"path":"https://openpharma.github.io/mtdesign/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Kirkpatrick J (2024). mtdesign: Mander Thompson Designs. R package version 0.1.2, https://github.com/openpharma/mtdesign.","code":"@Manual{, title = {mtdesign: Mander and Thompson Designs}, author = {John Kirkpatrick}, year = {2024}, note = {R package version 0.1.2}, url = {https://github.com/openpharma/mtdesign}, }"},{"path":[]},{"path":"https://openpharma.github.io/mtdesign/index.html","id":"introduction","dir":"","previous_headings":"","what":"Introduction","title":"Mander and Thompson Designs","text":"package mtdesign provides implementations Simon (1989) Mander & Thompson (2010). implementations Simon’s methods available - example, ph2simon function clinfun package (Seshan 2018), provide easy access non-optimal solutions way mtdesign . aware R-based implementations Mander & Thompson’s extension Simon.","code":""},{"path":"https://openpharma.github.io/mtdesign/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Mander and Thompson Designs","text":"available CRAN, can install mtdesign usual way: install.packages(\"mtdesign\") can install development version mtdesign GitHub : devtools::install_github(\"openpharma/mtdesign\")","code":""},{"path":"https://openpharma.github.io/mtdesign/index.html","id":"set-up-vignette-environment","dir":"","previous_headings":"","what":"Set up vignette environment","title":"Mander and Thompson Designs","text":"","code":"# By policy, on CRAN, use only two cores, no matter how many are available. if (requireNamespace(\"parallel\", quietly = TRUE)) { maxCores <- parallel::detectCores() maxCores <- ifelse(identical(Sys.getenv(\"NOT_CRAN\"), \"true\"), maxCores, min(maxCores, 2)) } else { maxCores <- 1 }"},{"path":"https://openpharma.github.io/mtdesign/index.html","id":"example","dir":"","previous_headings":"","what":"Example","title":"Mander and Thompson Designs","text":"Suppose treatments response rate less 5% interest response rate least 25% worthy development. Simon’s 2-stage design seek efficacy signal significance level 5% power 80% required. table shows optimal design requirements 0/9 2/17. expected sample size 12.0 probability early termination 63%. significance level actually achieved 4.7% power level achieved 100% - 18.8% = 81.2%. power curves designs easily plotted. Obtaining equivalent Mander & Thompson designs requires small change calls.","code":"library(mtdesign) library(knitr) library(dplyr) #> #> Attaching package: 'dplyr' #> The following objects are masked from 'package:stats': #> #> filter, lag #> The following objects are masked from 'package:base': #> #> intersect, setdiff, setequal, union simonDesign <- obtainDesign(p0 = 0.05, p1 = 0.25, alpha = 0.05, beta = 0.2, mander = FALSE, parallel = FALSE) simonDesign %>% select(-Alpha, -Beta, -p0, -p1, -PETAlt, -AveSizeAlt) %>% kable(digits = c(0, 0, 0, 0, 3, 3, 2, 1, NA)) powerPlot(simonDesign) manderDesign <- obtainDesign( p0 = 0.05, p1 = 0.25, alpha = 0.05, beta = 0.2, cores = maxCores ) manderDesign %>% select(-Alpha, -Beta, -p0, -p1) %>% kable(digits = c(0, 0, 0, 0, 3, 3, 2, 2, 2, 1, NA)) powerPlot(manderDesign)"},{"path":"https://openpharma.github.io/mtdesign/index.html","id":"constrained-designs","dir":"","previous_headings":"Example","what":"Constrained designs","title":"Mander and Thompson Designs","text":"Suppose trial, whatever reason, restricted using 8 participants stage. shown , optimal Simon’s two stage design 0/9 2/17. ’s close n1 = 8, n = 16. (slightly) sub-optimal design n1 = 8, n = 16? , isn’t. close can get? Best sub-optimal design required significance level Best sub-optimal design required power choice lies design achieves required significance level power 77.1% one required power significance level 15.1%. designs accept null hypothesis responders seen first group eight participants. differ critical value end stage 2: 1 maintain power, 2 maintain significance level. power curve designs can compared globally optimal design.","code":"x <- createGrid(p0 = 0.05, p1 = 0.25, alpha = 0.05, beta = 0.2, mander = FALSE) y <- x %>% filter(nStage1 == 8, nTotal == 16) z <- y %>% obtainDesign(cores = maxCores) #> Warning: No acceptable designs were found. if (nrow(z) == 0) { print(\"No acceptable designs were found.\") } else { select(-Alpha, -Beta, -p0, -p1, -PETAlt, -AveSizeAlt) %>% z() %>% select(-Alpha, -Beta, -p0, -p1, -PETAlt, -AveSizeAlt) %>% kable(digits = c(0, 0, 0, 0, 3, 3, 2, 1, NA)) } #> [1] \"No acceptable designs were found.\" z1 <- y %>% augmentGrid() bestSize <- z1 %>% filter(Type1 < Alpha) %>% slice_min(Type2) bestSize %>% select(-Alpha, -Beta, -p0, -p1, -PETAlt, -AveSizeAlt) %>% kable( caption = \"Best sub-optimal design with required significance level\", digits = c(0, 0, 0, 0, 3, 3, 2, 1, NA) ) bestPower <- z1 %>% filter(Type2 < Beta) %>% slice_min(Type1) bestPower %>% select(-Alpha, -Beta, -p0, -p1, -PETAlt, -AveSizeAlt) %>% kable( caption = \"Best sub-optimal design with required power\", digits = c(0, 0, 0, 0, 3, 3, 2, 1, NA) ) plotData1 <- simonDesign %>% filter(Criterion == \"optimal\") %>% bind_rows(list(bestSize, bestPower)) powerPlot(plotData1)"},{"path":"https://openpharma.github.io/mtdesign/index.html","id":"package-structure","dir":"","previous_headings":"","what":"Package structure","title":"Mander and Thompson Designs","text":"mtdesign package consists three main functions: createGrid creates grid (nStage1, rFutility, nTotal rTotal Simon’s design nStage1, rFutility, rSuccess, nTotal rTotal Mander & Thompson design) brute force search required design(s) conducted augmentGridtakes grid created createGrid adds columns probability early termination, Type 1 error, Type 2 error expected sample size . obtainDesign takes augmented grid identifies optimal minimax designs","code":""},{"path":"https://openpharma.github.io/mtdesign/index.html","id":"error-and-warning-messages-and-logging","dir":"","previous_headings":"","what":"Error and warning messages and logging","title":"Mander and Thompson Designs","text":"mtdesign package supports logging via futile.logger package (Rowe 2016). functions simply report Entry Exit DEBUG level. augmentGrid function reports steps parallelisation process TRACE level.","code":""},{"path":"https://openpharma.github.io/mtdesign/index.html","id":"parallelisation","dir":"","previous_headings":"","what":"Parallelisation","title":"Mander and Thompson Designs","text":"known closed form solution obtaining solutions either Simon’s original equations Mander & Thompson’s extensions. mtdesign package uses brute force approach evaluate operating characteristics reasonable potential designs. grids can quickly become large, particularly Mander & Thompson designs. example, createGrid(0.2, 0.4, alpha=0.1, beta=0.1) creates grid almost 11 million candidate designs. mtdesign uses paralellisation attempt speed evaluation candidate designs. augmentGrid function allows users control parallelisation process: parallel parameter defaults TRUE defines whether paralellisation used. cores parameter specifies many cores used. default value, NA tells mtdesign use available (defined parallel::detectCores()), cores. minChunkSize determines smallest grid candidate designs trigger paralellisation. default value 100000. parallel package required parallelisation. parallelisation needed (ie grid size exceeds minChunkSize) requested parallel package installed, error message thrown augmentation grid stops. paralellisation requested grid contains one million rows, warning produced.","code":""},{"path":"https://openpharma.github.io/mtdesign/index.html","id":"troubleshooting","dir":"","previous_headings":"","what":"Troubleshooting","title":"Mander and Thompson Designs","text":", installing using mtdesign package, get error regarding syntax error .hpp file, similar following issue likely mismatch g++ compiler used headers supplied BH package. two solutions know : Upgrade g++ Downgrade version BH package using. appropriate package version depends version g++ compiler using.","code":".../BH/include/boost/math/tools/fraction.hpp:84:48: error: ‘long double’ is not a class, struct, or union type using value_type = typename T::value_type;"},{"path":[]},{"path":"https://openpharma.github.io/mtdesign/reference/augmentGrid.html","id":null,"dir":"Reference","previous_headings":"","what":"Augment a grid of candidate designs with type 1 and type 2 error probabilities, expected sample sizes and probabilities of early termination — augmentGrid","title":"Augment a grid of candidate designs with type 1 and type 2 error probabilities, expected sample sizes and probabilities of early termination — augmentGrid","text":"Augment grid candidate designs type 1 type 2 error probabilities, expected sample sizes probabilities early termination","code":""},{"path":"https://openpharma.github.io/mtdesign/reference/augmentGrid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Augment a grid of candidate designs with type 1 and type 2 error probabilities, expected sample sizes and probabilities of early termination — augmentGrid","text":"","code":"augmentGrid(d, parallel = TRUE, cores = NA, minChunkSize = 1e+05)"},{"path":"https://openpharma.github.io/mtdesign/reference/augmentGrid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Augment a grid of candidate designs with type 1 and type 2 error probabilities, expected sample sizes and probabilities of early termination — augmentGrid","text":"d tibble created `createGrid` parallel use parallelisation available cores number cores use parallelising. NA<\/code>, available cores requested minChunkSize minimum size grid paralellisation attempted","code":""},{"path":"https://openpharma.github.io/mtdesign/reference/augmentGrid.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Augment a grid of candidate designs with type 1 and type 2 error probabilities, expected sample sizes and probabilities of early termination — augmentGrid","text":"augmented grid tibble","code":""},{"path":"https://openpharma.github.io/mtdesign/reference/augmentGrid.html","id":"usage-notes","dir":"Reference","previous_headings":"","what":"Usage Notes","title":"Augment a grid of candidate designs with type 1 and type 2 error probabilities, expected sample sizes and probabilities of early termination — augmentGrid","text":"Regardless value `parallel`, parallelisation used size grid greater chunkSize<\/code>. paralellisation requested needed, exception thrown parallel package available.","code":""},{"path":"https://openpharma.github.io/mtdesign/reference/augmentGrid.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Augment a grid of candidate designs with type 1 and type 2 error probabilities, expected sample sizes and probabilities of early termination — augmentGrid","text":"","code":"x <- createGrid(p0 = 0.1, p1 = 0.30, alpha = 0.1, beta = 0.1, nMin = 24, nMax = 32) %>% augmentGrid(parallel = FALSE)"},{"path":"https://openpharma.github.io/mtdesign/reference/createGrid.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a grid of candidate designs — createGrid","title":"Create a grid of candidate designs — createGrid","text":"Create grid candidate designs","code":""},{"path":"https://openpharma.github.io/mtdesign/reference/createGrid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a grid of candidate designs — createGrid","text":"","code":"createGrid( p0, p1, alpha = 0.1, beta = NA, power = ifelse(is.na(beta), 0.9, 1 - beta), nMin = NA, nMax = NA, mander = TRUE )"},{"path":"https://openpharma.github.io/mtdesign/reference/createGrid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a grid of candidate designs — createGrid","text":"p0 response rate null hypothesis p1 response rate alternate hypothesis alpha desired (one-sided) type 1 error rate beta desired type 2 error rate power alternative beta nMin lower bound search grid. NA, searchBounds called provide appropriate value nMax lower bound search grid. NA, searchBounds called provide appropriate value mander Mander & Thompson Simon's design required?","code":""},{"path":"https://openpharma.github.io/mtdesign/reference/createGrid.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a grid of candidate designs — createGrid","text":"tibble. See Usage notes list description columns.","code":""},{"path":"https://openpharma.github.io/mtdesign/reference/createGrid.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a grid of candidate designs — createGrid","text":"","code":"# Standard use for a Simon's 2-stage design x <- createGrid(p0 = 0.1, p1 = 0.5, alpha = 0.1, beta = 0.1, mander = FALSE) # Custom search bounds for a Mander & Thompson design y <- createGrid(p0 = 0.1, p1 = 0.4, alpha = 0.1, beta = 0.1, nMin = 20, nMax = 30)"},{"path":"https://openpharma.github.io/mtdesign/reference/obtainDesign.html","id":null,"dir":"Reference","previous_headings":"","what":"Finds optimal and minimax designs for either Simon's 2-stage or Mander & Thompson studies — obtainDesign","title":"Finds optimal and minimax designs for either Simon's 2-stage or Mander & Thompson studies — obtainDesign","text":"obtainDesign essentially wrapper calls createGrid augmentGrid followed simple filtering candidate designs identify optimal minimax designs.","code":""},{"path":"https://openpharma.github.io/mtdesign/reference/obtainDesign.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Finds optimal and minimax designs for either Simon's 2-stage or Mander & Thompson studies — obtainDesign","text":"","code":"obtainDesign( grid = NULL, p0 = NA, p1 = NA, alpha = ifelse(is.null(grid), 0.05, NA), beta = ifelse(is.null(grid), 0.1, NA), fullGrid = FALSE, ... )"},{"path":"https://openpharma.github.io/mtdesign/reference/obtainDesign.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Finds optimal and minimax designs for either Simon's 2-stage or Mander & Thompson studies — obtainDesign","text":"grid Optional. tibble created createGrid. NULL, p0, p1, alpha beta must specified createGrid called generate required grid. NULL p0, p1, alpha beta ignored p0 response rate null hypothesis p1 response rate alternate hypothesis alpha desired (one-sided) type 1 error rate beta desired type 2 error rate fullGrid full grid possible designs returned, simply optimal minimax solutions? Mander Thompson design, optimal minimax designs returned null alternate hypotheses. See Usage Notes . ... passed `createGrid` `augmentGrid`. particular mander=TRUE Mander & Thompson design mander=FALSE Simon's 2-stage design.","code":""},{"path":"https://openpharma.github.io/mtdesign/reference/obtainDesign.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Finds optimal and minimax designs for either Simon's 2-stage or Mander & Thompson studies — obtainDesign","text":"tibble created createGrid. fullGrid == FALSE table contains additional column, Criterion indicating type design. Possible values Criterion \"optimal\" \"minimax\" Simon's designs \"optimalNull\", \"optimalAlt\", \"minimaxNull\" \"minimaxAlt\" Mander & Thompson designs.","code":""},{"path":"https://openpharma.github.io/mtdesign/reference/obtainDesign.html","id":"usage-notes","dir":"Reference","previous_headings":"","what":"Usage notes","title":"Finds optimal and minimax designs for either Simon's 2-stage or Mander & Thompson studies — obtainDesign","text":"grid NULL possible none candidate designs acceptable (, satisfy significance level power requirements). case fullGrid == FALSE, empty tibble returned. versbose == TRUE warning message also printed. fullGrid == TRUE full grid designs considered returned. can interrogated find optimal designs constraints - example fixed stage sizes.","code":""},{"path":"https://openpharma.github.io/mtdesign/reference/obtainDesign.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Finds optimal and minimax designs for either Simon's 2-stage or Mander & Thompson studies — obtainDesign","text":"","code":"# \\donttest{ # Standard use (Simon's 2-stage design) createGrid(p0 = 0.05, p1 = 0.25, alpha = 0.05, beta = 0.2, mander = FALSE) %>% augmentGrid(parallel = FALSE) %>% obtainDesign() #> # A tibble: 2 × 15 #> nTotal nStage1 rTotal rFutility p0 p1 Alpha Beta Type1 Type2 PETNull #> #> 1 17 9 2 0 0.05 0.25 0.05 0.2 0.0466 0.188 0.630 #> 2 16 12 2 0 0.05 0.25 0.05 0.2 0.0427 0.199 0.540 #> # ℹ 4 more variables: PETAlt , AveSizeNull , AveSizeAlt , #> # Criterion # Constrained stage sizes createGrid(p0 = 0.25, p1 = 0.45, alpha = 0.05, beta = 0.2) %>% dplyr::filter(nStage1 == 8) %>% augmentGrid(parallel = FALSE) %>% obtainDesign() #> # A tibble: 4 × 16 #> nTotal nStage1 rTotal rFutility rSuccess p0 p1 Alpha Beta Type1 Type2 #> #> 1 39 8 14 1 5 0.25 0.45 0.05 0.2 0.0430 0.196 #> 2 36 8 13 0 5 0.25 0.45 0.05 0.2 0.0482 0.184 #> 3 36 8 13 0 5 0.25 0.45 0.05 0.2 0.0482 0.184 #> 4 36 8 13 0 5 0.25 0.45 0.05 0.2 0.0482 0.184 #> # ℹ 5 more variables: PETNull , PETAlt , AveSizeNull , #> # AveSizeAlt , Criterion # }"},{"path":"https://openpharma.github.io/mtdesign/reference/pipe.html","id":null,"dir":"Reference","previous_headings":"","what":"Pipe operator — %>%","title":"Pipe operator — %>%","text":"See magrittr::%>% details.","code":""},{"path":"https://openpharma.github.io/mtdesign/reference/pipe.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pipe operator — %>%","text":"","code":"lhs %>% rhs"},{"path":"https://openpharma.github.io/mtdesign/reference/pipe.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pipe operator — %>%","text":"lhs value magrittr placeholder. rhs function call using magrittr semantics.","code":""},{"path":"https://openpharma.github.io/mtdesign/reference/pipe.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pipe operator — %>%","text":"result calling `rhs(lhs)`.","code":""},{"path":"https://openpharma.github.io/mtdesign/reference/powerPlot.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot the power curve(s) for the given design(s) — powerPlot","title":"Plot the power curve(s) for the given design(s) — powerPlot","text":"Plot power curve(s) given design(s)","code":""},{"path":"https://openpharma.github.io/mtdesign/reference/powerPlot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot the power curve(s) for the given design(s) — powerPlot","text":"","code":"powerPlot(grid, probs = seq(0, 1, 0.01))"},{"path":"https://openpharma.github.io/mtdesign/reference/powerPlot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot the power curve(s) for the given design(s) — powerPlot","text":"grid tibble containing designs plotted probs response rates rejection probabilities plotted","code":""},{"path":"https://openpharma.github.io/mtdesign/reference/powerPlot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot the power curve(s) for the given design(s) — powerPlot","text":"ggplot object containing power curve(s)","code":""},{"path":"https://openpharma.github.io/mtdesign/reference/powerPlot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot the power curve(s) for the given design(s) — powerPlot","text":"","code":"createGrid(p0 = 0.05, p1 = 0.25, alpha = 0.05, beta = 0.2, mander = FALSE) %>% augmentGrid(cores = 2) %>% obtainDesign() %>% powerPlot(probs = seq(0, 0.5, 0.025)) #> Warning: one argument not used by format 'Parallelisation has been requested, but the grid size [72814] is less than the minimum chunk size [1e+05]. Parallelisation will not occur' #> pkgdown 2024-11-01 13:52:51 INFO pkgdown::build_site: Parallelisation has been requested, but the grid size [72814] is less than the minimum chunk size [1e+05]. Parallelisation will not occur"},{"path":"https://openpharma.github.io/mtdesign/reference/searchBounds.html","id":null,"dir":"Reference","previous_headings":"","what":"Obtain default bounds for the construction of the search grid. — searchBounds","title":"Obtain default bounds for the construction of the search grid. — searchBounds","text":"formula used continuity corrected Normal approximation Fleiss et al (2003).","code":""},{"path":"https://openpharma.github.io/mtdesign/reference/searchBounds.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Obtain default bounds for the construction of the search grid. — searchBounds","text":"","code":"searchBounds(p0, p1, alpha = 0.05, beta = 0.2, twoSided = TRUE)"},{"path":"https://openpharma.github.io/mtdesign/reference/searchBounds.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Obtain default bounds for the construction of the search grid. — searchBounds","text":"p0 response rate null hypothesis p1 response rate alternate hypothesis alpha desired (one-sided) type 1 error rate beta desired type 2 error rate twoSided two- one-sided significance level?","code":""},{"path":"https://openpharma.github.io/mtdesign/reference/searchBounds.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Obtain default bounds for the construction of the search grid. — searchBounds","text":"list three elements: \"n\" - single stage sample size Fleiss et al; \"min\" - lower bound, 0.8*n; \"max\" - upper bound, 2*n. floor() ceiling() applied appropriate.","code":""}]