diff --git a/README.Rmd b/README.Rmd
index 46ecb16..d6ab5d1 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -9,6 +9,7 @@ always_allow_html: yes
```{r, include = FALSE, cache = FALSE}
+library(cTOST)
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
@@ -34,34 +35,124 @@ asciicast::init_knitr_engine(
[](https://www.r-pkg.org/pkg/cTOST)
-## `cTOST` Overview
+## 1. `cTOST` Overview
-This R package contains the functions to test equivalence in univariate and multivariate settings based on the Two One-Sided Tests (TOST). In addition, the package contains different corrective procedures applied to the standard TOST in order to adjust the size of the procedure at the desired nominal level leading to more powerful procedures. This package implements the $\alpha$-TOST and $\delta$-TOST methods proposed in Boulaguiem et al. (2024a) and in Boulaguiem et al. (2024b).
+This R package contains functions for testing equivalence in both univariate and multivariate settings, based on the Two One-Sided Tests (TOST). The `cTOST` package implements the $\alpha$-TOST and $\delta$-TOST methods proposed by Boulaguiem et al. (2024a, 2024b). These two corrective procedures that can be applied to the standard TOST to adjust the size of the procedure to the desired nominal level, resulting in more powerful procedures.
-## Install Instructions
+## 2. Install Instructions
-The `cTOST` package is available on GitHub at the moment. It is subject to ongoing updates that may lead to stability issues.
+The `cTOST` package is available on cran and on GitHub. The version on GitHub is subject to ongoing updates that may lead to stability issues.
-In order to install the package, it is required to pre-install the `devtools` dependency. Run the following command if you do not have it already installed:
+The package can from cran as follows:
-```{r, eval=FALSE}
-install.packages("devtools")
+```{r, eval = F}
+install.packages("cTOST")
```
-The package is then installed with the following command:
+The package can also be install from GitHub using the `devtools` package:
```{r, eval=FALSE}
+install.packages("devtools")
devtools::install_github("stephaneguerrier/cTOST")
```
Note that Windows users are assumed that have Rtools installed (if this is not the case, please visit this [link](https://cran.r-project.org/bin/windows/Rtools/).
-## How to use
+## 3. How to use
+
+We provide here a few examples on the usage of the `cTOST` package. More information can be found here: ???
+
+### 3.1. Univariate settings
+
+To illustrate the use of the proposed method in the univariate settings, we consider the `skin` dataset analyzed in Boulaguiem et al. (2024a), which can be loaded as follows:
+
+```{r}
+data(skin)
+theta_hat = diff(apply(skin,2,mean))
+nu = nrow(skin) - 1
+sig_hat = sd(apply(skin,1,diff))/sqrt(nu)
+```
+
+### 3.1.1. Standard TOST
+
+The standard TOST can be used as follows:
+
+```{r, eval = F}
+stost = tost(theta = theta_hat, sigma = sig_hat, nu = nu, delta = log(1.25))
+stost
+```
+
+```{asciicast}
+library(cTOST)
+data(skin)
+theta_hat = diff(apply(skin,2,mean))
+nu = nrow(skin) - 1
+sig_hat = sd(apply(skin,1,diff))/sqrt(nu)
+stost = tost(theta = theta_hat, sigma = sig_hat, nu = nu, delta = log(1.25))
+stost
+```
+
+#### 3.1.2. $\alpha$-TOST
+
+The $\alpha$-TOST can be used through the function `ctost` as follows:
+
+```{r, eval = F}
+atost = ctost(theta = theta_hat, sigma = sig_hat, nu = nu,
+ delta = log(1.25), method = "alpha")
+atost
+```
+
+```{asciicast}
+library(cTOST)
+data(skin)
+theta_hat = diff(apply(skin,2,mean))
+nu = nrow(skin) - 1
+sig_hat = sd(apply(skin,1,diff))/sqrt(nu)
+atost = ctost(theta = theta_hat, sigma = sig_hat, nu = nu, delta = log(1.25), method = "alpha")
+atost
+```
+
+It is possible to compare the results of the $\alpha$-TOST (or $\delta$-TOST, see below) with the standard TOST as follows:
+
+```{r, eval = F}
+compare_to_tost(atost)
+```
+
+```{asciicast}
+library(cTOST)
+data(skin)
+theta_hat = diff(apply(skin,2,mean))
+nu = nrow(skin) - 1
+sig_hat = sd(apply(skin,1,diff))/sqrt(nu)
+atost = ctost(theta = theta_hat, sigma = sig_hat, nu = nu, delta = log(1.25), method = "alpha")
+compare_to_tost(atost)
+```
+
+### 3.1.3. $\delta$-TOST
+
+The $\delta$-TOST can be used through the function `ctost` as follows:
+
+```{r}
+dtost = ctost(theta = theta_hat, sigma = sig_hat, nu = nu,
+ delta = log(1.25), method = "delta")
+dtost
+```
+
+```{asciicast}
+library(cTOST)
+data(skin)
+theta_hat = diff(apply(skin,2,mean))
+nu = nrow(skin) - 1
+sig_hat = sd(apply(skin,1,diff))/sqrt(nu)
+dtost = ctost(theta = theta_hat, sigma = sig_hat, nu = nu, delta = log(1.25), method = "delta")
+dtost
+```
-TO DO
+### 3.2. Multivariate settings
+COMING SOON
-## How to cite
+## 4. How to cite
```{}
@Manual{boulaguiem2024ctost,
@@ -73,11 +164,11 @@ TO DO
}
```
-## License
+## 5. License
The license this source code is released under is the GNU AFFERO GENERAL PUBLIC LICENSE (AGPL) v3.0. Please see the LICENSE file for full text. Otherwise, please consult [GNU](https://www.gnu.org/licenses/agpl-3.0.en.html) which will provide a synopsis of the restrictions placed upon the code.
-## References
+## 6. References
Boulaguiem, Y., Quartier, J., Lapteva, M., Kalia, Y. N., Victoria-Feser, M. P., Guerrier, S. & Couturier, D. L., "*Finite Sample Adjustments for Average Equivalence Testing*", Statistics in Medicine, 2024a, [https://doi.org/10.1002/sim.9993]( https://doi.org/10.1002/sim.9993).
diff --git a/README.md b/README.md
index 566fc6a..18e08b3 100644
--- a/README.md
+++ b/README.md
@@ -14,32 +14,32 @@ downloads](http://cranlogs.r-pkg.org/badges/cTOST)](https://www.r-pkg.org/pkg/cT
downloads](https://cranlogs.r-pkg.org/badges/grand-total/cTOST)](https://www.r-pkg.org/pkg/cTOST)
-## `cTOST` Overview
+## 1. `cTOST` Overview
-This R package contains the functions to test equivalence in univariate
-and multivariate settings based on the Two One-Sided Tests (TOST). In
-addition, the package contains different corrective procedures applied
-to the standard TOST in order to adjust the size of the procedure at the
-desired nominal level leading to more powerful procedures. This package
-implements the $\alpha$-TOST and $\delta$-TOST methods proposed in
-Boulaguiem et al. (2024a) and in Boulaguiem et al. (2024b).
+This R package contains functions for testing equivalence in both
+univariate and multivariate settings, based on the Two One-Sided Tests
+(TOST). The `cTOST` package implements the $\alpha$-TOST and
+$\delta$-TOST methods proposed by Boulaguiem et al. (2024a, 2024b).
+These two corrective procedures that can be applied to the standard TOST
+to adjust the size of the procedure to the desired nominal level,
+resulting in more powerful procedures.
-## Install Instructions
+## 2. Install Instructions
-The `cTOST` package is available on GitHub at the moment. It is subject
-to ongoing updates that may lead to stability issues.
+The `cTOST` package is available on cran and on GitHub. The version on
+GitHub is subject to ongoing updates that may lead to stability issues.
-In order to install the package, it is required to pre-install the
-`devtools` dependency. Run the following command if you do not have it
-already installed:
+The package can from cran as follows:
``` r
-install.packages("devtools")
+install.packages("cTOST")
```
-The package is then installed with the following command:
+The package can also be install from GitHub using the `devtools`
+package:
``` r
+install.packages("devtools")
devtools::install_github("stephaneguerrier/cTOST")
```
@@ -47,11 +47,82 @@ Note that Windows users are assumed that have Rtools installed (if this
is not the case, please visit this
[link](https://cran.r-project.org/bin/windows/Rtools/).
-## How to use
+## 3. How to use
+
+We provide here a few examples on the usage of the `cTOST` package. More
+information can be found here: ???
+
+### 3.1. Univariate settings
+
+To illustrate the use of the proposed method in the univariate settings,
+we consider the `skin` dataset analyzed in Boulaguiem et al. (2024a),
+which can be loaded as follows:
+
+``` r
+data(skin)
+theta_hat = diff(apply(skin,2,mean))
+nu = nrow(skin) - 1
+sig_hat = sd(apply(skin,1,diff))/sqrt(nu)
+```
+
+### 3.1.1. Standard TOST
+
+The standard TOST can be used as follows:
+
+``` r
+stost = tost(theta = theta_hat, sigma = sig_hat, nu = nu, delta = log(1.25))
+stost
+```
+
+
+
+#### 3.1.2. $\alpha$-TOST
+
+The $\alpha$-TOST can be used through the function `ctost` as follows:
+
+``` r
+atost = ctost(theta = theta_hat, sigma = sig_hat, nu = nu,
+ delta = log(1.25), method = "alpha")
+atost
+```
+
+
+
+It is possible to compare the results of the $\alpha$-TOST (or
+$\delta$-TOST, see below) with the standard TOST as follows:
+
+``` r
+compare_to_tost(atost)
+```
+
+
+
+### 3.1.3. $\delta$-TOST
+
+The $\delta$-TOST can be used through the function `ctost` as follows:
+
+``` r
+dtost = ctost(theta = theta_hat, sigma = sig_hat, nu = nu,
+ delta = log(1.25), method = "delta")
+dtost
+#> ✖ Can't accept (bio)equivalence
+#> Corr. Equiv. Region: |----------------0----------------|
+#> Estim. Inter.: (--------------x---------------)
+#> CI = (-0.21174 ; 0.25715)
+#>
+#> Method: delta-TOST
+#> alpha = 0.05; Equiv. lim. = +/- 0.22314
+#> Corrected Equiv. lim. = +/- 0.25473
+#> Mean = 0.02270; Stand. dev. = 0.13428; df = 16
+```
+
+
+
+### 3.2. Multivariate settings
-TO DO
+COMING SOON
-## How to cite
+## 4. How to cite
@Manual{boulaguiem2024ctost,
title = {cTOST: Finite Sample Correction of The TOST in The Univariate Framework},
@@ -61,7 +132,7 @@ TO DO
url = {https://github.com/stephaneguerrier},
}
-## License
+## 5. License
The license this source code is released under is the GNU AFFERO GENERAL
PUBLIC LICENSE (AGPL) v3.0. Please see the LICENSE file for full text.
@@ -69,7 +140,7 @@ Otherwise, please consult
[GNU](https://www.gnu.org/licenses/agpl-3.0.en.html) which will provide
a synopsis of the restrictions placed upon the code.
-## References
+## 6. References
Boulaguiem, Y., Quartier, J., Lapteva, M., Kalia, Y. N., Victoria-Feser,
M. P., Guerrier, S. & Couturier, D. L., “*Finite Sample Adjustments for
diff --git a/README_files/figure-gfm/unnamed-chunk-10.svg b/README_files/figure-gfm/unnamed-chunk-10.svg
index 4b34504..4bd4109 100644
--- a/README_files/figure-gfm/unnamed-chunk-10.svg
+++ b/README_files/figure-gfm/unnamed-chunk-10.svg
@@ -1 +1 @@
-
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+
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diff --git a/README_files/figure-gfm/unnamed-chunk-12.svg b/README_files/figure-gfm/unnamed-chunk-12.svg
index 4bd4109..f63426d 100644
--- a/README_files/figure-gfm/unnamed-chunk-12.svg
+++ b/README_files/figure-gfm/unnamed-chunk-12.svg
@@ -1 +1 @@
-
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+
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diff --git a/README_files/figure-gfm/unnamed-chunk-6.svg b/README_files/figure-gfm/unnamed-chunk-6.svg
new file mode 100644
index 0000000..0715490
--- /dev/null
+++ b/README_files/figure-gfm/unnamed-chunk-6.svg
@@ -0,0 +1 @@
+
\ No newline at end of file
diff --git a/README_files/figure-gfm/unnamed-chunk-8.svg b/README_files/figure-gfm/unnamed-chunk-8.svg
index 231c7cf..4b34504 100644
--- a/README_files/figure-gfm/unnamed-chunk-8.svg
+++ b/README_files/figure-gfm/unnamed-chunk-8.svg
@@ -1 +1 @@
-
\ No newline at end of file
+
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diff --git a/_pkgdown.yml b/_pkgdown.yml
index 7e0564a..41bec2e 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -6,8 +6,7 @@ reference:
- title: TOST functions
contents:
- tost
- - dtost
- - atost
+ - ctost
- title: Data
contents:
- skin
diff --git a/docs/articles/get_started.html b/docs/articles/get_started.html
index fb6d58e..945d05d 100644
--- a/docs/articles/get_started.html
+++ b/docs/articles/get_started.html
@@ -52,12 +52,6 @@
-
This R package contains the functions to test equivalence in univariate and multivariate settings based on the Two One-Sided Tests (TOST). In addition, the package contains different corrective procedures applied to the standard TOST in order to adjust the size of the procedure at the desired nominal level leading to more powerful procedures. This package implements the α-TOST and δ-TOST methods proposed in Boulaguiem et al. (2024a) and in Boulaguiem et al. (2024b).
-
Install Instructions
+
2. Install Instructions
The cTOST package is available on GitHub at the moment. It is subject to ongoing updates that may lead to stability issues.
In order to install the package, it is required to pre-install the devtools dependency. Run the following command if you do not have it already installed:
@Manual{boulaguiem2024ctost,
- title = {cTOST: Finite Sample Correction of The TOST in The Univariate Framework},
- author = {Boulaguiem, Y. and Insolia, L. and Couturier, D.-L. and Guerrier, S.},
- year = {2024},
- note = {R package version 1.1.0},
- url = {https://github.com/stephaneguerrier},
-}
+
@Manual{boulaguiem2024ctost,
+ title = {cTOST: Finite Sample Correction of The TOST in The Univariate Framework},
+ author = {Boulaguiem, Y. and Insolia, L. and Couturier, D.-L. and Guerrier, S.},
+ year = {2024},
+ note = {R package version 1.1.0},
+ url = {https://github.com/stephaneguerrier},
+}
+
+#### 3.1.2. $\alpha$-TOST
+
+The $\alpha$-TOST can be used through the function `ctost` as follows:
+
+``` r
+atost = ctost(theta = theta_hat, sigma = sig_hat, nu = nu,
+ delta = log(1.25), method = "alpha")
+atost
+```
+
+
+
+It is possible to compare the results of the $\alpha$-TOST (or
+$\delta$-TOST, see below) with the standard TOST as follows:
+
+``` r
+compare_to_tost(atost)
+```
+
+
+
+### 3.1.3. $\delta$-TOST
+
+The $\delta$-TOST can be used through the function `ctost` as follows:
+
+``` r
+dtost = ctost(theta = theta_hat, sigma = sig_hat, nu = nu,
+ delta = log(1.25), method = "delta")
+dtost
+#> ✖ Can't accept (bio)equivalence
+#> Corr. Equiv. Region: |----------------0----------------|
+#> Estim. Inter.: (--------------x---------------)
+#> CI = (-0.21174 ; 0.25715)
+#>
+#> Method: delta-TOST
+#> alpha = 0.05; Equiv. lim. = +/- 0.22314
+#> Corrected Equiv. lim. = +/- 0.25473
+#> Mean = 0.02270; Stand. dev. = 0.13428; df = 16
+```
+
+
+
+### 3.2. Multivariate settings
-TO DO
+COMING SOON
-## How to cite
+## 4. How to cite
@Manual{boulaguiem2024ctost,
title = {cTOST: Finite Sample Correction of The TOST in The Univariate Framework},
@@ -61,7 +132,7 @@ TO DO
url = {https://github.com/stephaneguerrier},
}
-## License
+## 5. License
The license this source code is released under is the GNU AFFERO GENERAL
PUBLIC LICENSE (AGPL) v3.0. Please see the LICENSE file for full text.
@@ -69,7 +140,7 @@ Otherwise, please consult
[GNU](https://www.gnu.org/licenses/agpl-3.0.en.html) which will provide
a synopsis of the restrictions placed upon the code.
-## References
+## 6. References
Boulaguiem, Y., Quartier, J., Lapteva, M., Kalia, Y. N., Victoria-Feser,
M. P., Guerrier, S. & Couturier, D. L., “*Finite Sample Adjustments for
diff --git a/README_files/figure-gfm/unnamed-chunk-10.svg b/README_files/figure-gfm/unnamed-chunk-10.svg
index 4b34504..4bd4109 100644
--- a/README_files/figure-gfm/unnamed-chunk-10.svg
+++ b/README_files/figure-gfm/unnamed-chunk-10.svg
@@ -1 +1 @@
-
\ No newline at end of file
+
\ No newline at end of file
diff --git a/README_files/figure-gfm/unnamed-chunk-12.svg b/README_files/figure-gfm/unnamed-chunk-12.svg
index 4bd4109..f63426d 100644
--- a/README_files/figure-gfm/unnamed-chunk-12.svg
+++ b/README_files/figure-gfm/unnamed-chunk-12.svg
@@ -1 +1 @@
-
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+
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diff --git a/README_files/figure-gfm/unnamed-chunk-6.svg b/README_files/figure-gfm/unnamed-chunk-6.svg
new file mode 100644
index 0000000..0715490
--- /dev/null
+++ b/README_files/figure-gfm/unnamed-chunk-6.svg
@@ -0,0 +1 @@
+
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diff --git a/README_files/figure-gfm/unnamed-chunk-8.svg b/README_files/figure-gfm/unnamed-chunk-8.svg
index 231c7cf..4b34504 100644
--- a/README_files/figure-gfm/unnamed-chunk-8.svg
+++ b/README_files/figure-gfm/unnamed-chunk-8.svg
@@ -1 +1 @@
-
\ No newline at end of file
+
\ No newline at end of file
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 7e0564a..41bec2e 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -6,8 +6,7 @@ reference:
- title: TOST functions
contents:
- tost
- - dtost
- - atost
+ - ctost
- title: Data
contents:
- skin
diff --git a/docs/articles/get_started.html b/docs/articles/get_started.html
index fb6d58e..945d05d 100644
--- a/docs/articles/get_started.html
+++ b/docs/articles/get_started.html
@@ -52,12 +52,6 @@
-