update readme.md

README.md

@@ -917,11 +917,11 @@ gt::gt(thyroid_active, rowname_col = "substance") |>
     title = "Summary table of results from statistical analysis of all 36 validation studies of the ring test of the XETA test guideline. This table shows the results of the automatic analysis carried out with the data_prep() function of the xeredar R-package. Furthermore, this table summarises the results of the original analysis carried out by John Green using SAS. As both approaches led to exactly the same conclusions, only one table is shown. In case a substance was identified to be Thyroid active, the respective cell is colored green, whereas when a substance was identified to be Thyroid inactive, the cell was colored blue. For the study applying testosterone in the french lab, the writing is colored red, because in the original table in the validation document, this substance was incorrectly classified as Thyroid active due to a data transfer mistake. Furthermore, for the study applying testosterone in the belgium lab, the writing is colored red, as well, because in the validation document, a slip in the column led to incorrectly categorizing the respective results as carried out by the japanese lab2.")
 ```
 
-</style>
+
 <table class="gt_table" data-quarto-disable-processing="false" data-quarto-bootstrap="false">
   <thead>
     <tr class="gt_heading">
-      <td colspan="8" class="gt_heading gt_title gt_font_normal gt_bottom_border" style>Summary table of results from statistical analysis of all 36 validation studies of the ring test of the XETA test guideline. This table shows the results of the automatic analysis carried out with the data_prep() function of the xeredar R-package. Furthermore, this table summarises the results of the original analysis carried out by John Green using SAS. As both approaches led to exactly the same conclusions, only one table is shown. In case a substance was identified to be Thyroid active, the respective cell is colored green, whereas when a substance was identified to be Thyroid inactive, the cell was colored blue. For the study applying testosterone in the french lab, the writing is colored red, because in the original table in the validation document, this substance was incorrectly classified as Thyroid active due to a data transfer mistake. Furthermore, for the study applying testosterone in the belgium lab, the writing is colored red, as well, because in the validation document, a slip in the column led to incorrectly categorizing the respective results as carried out by the japanese lab2.</td>
+      <td colspan="8" class="gt_heading gt_title gt_font_normal gt_bottom_border" style>Summary table of results from statistical analysis of all 36 validation studies of the ring test of the XETA test guideline. This table shows the results of the automatic analysis carried out with the data_prep() function of the xeredar R-package. Furthermore, this table summarises the results of the original analysis carried out by John Green using SAS. As both approaches led to exactly the same conclusions, only one table is shown. The only two differences between the reported table in the validation document of the TG and the here depicted results are due to misunderstandings of the SAS output and slips of the pen about the identity of the lab, carrying out the study. For the study applying testosterone in the french lab this substance was incorrectly classified as Thyroid active in the table of the validation document due to data transfer mistake from the SAS output to the final table. Furthermore, for the study applying testosterone in the belgium lab a slip in the column led to incorrectly categorizing the respective results as carried out by the japanese lab2 in the table of the validation document.</td>
     </tr>
     &#10;    <tr class="gt_col_headings gt_spanner_row">
       <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="2" colspan="1" scope="col" id="Chemical">Chemical</th>
@@ -1049,6 +1049,73 @@ gt::gt(thyroid_active, rowname_col = "substance") |>
 </table>
 </div>
 
+# The shiny app
+
+xeredar contains an integrated shiny app that is available to the users
+by writing `run_app()` into the console. The only requirement to use the
+app is the successful installation of xeredar. When the app started, the
+user has a couple of options to analyse the data. These options can be
+adjusted by clicking on the little gear sign next to *Inputs*. The
+following options are available:
+
+- **Use d’Agostino test?**
+  - The default here is that this is not selected meaning the
+    Shapiro-Wilk test is utilized to check for residual normality.
+    However, the RADAR TG mentions the d’Agostino test which is why it
+    is also available to the users.
+- **Apply 10% Trimming**
+  - The default here is that this is selected, meaning that 10% Trimming
+    is conducted when the ANOVA assumptions are not fulfilled by the raw
+    data. Please be aware that this does not mean that 10% Trimming is
+    always conducted. It is only conducted, when the raw data is
+    violating the residual normality and variance homogeneity
+    assumptions, tested with the respective test with an adjustable
+    alpha level.
+- **Remove outliers**
+  - The default here is that this is selected, meaning that outlier
+    removal is conducted when the ANOVA assumptions are not fulfilled by
+    the raw data or by 10% Trimming, if it is selected above.
+- **Try Box-Cox transformation**
+  - The default here is that this is selected, meaning that box-cox
+    transformation is carried out when the ANOVA assumptions are not
+    fulfilled by the raw or processed data (10% Trimming or outlier
+    removal) nor by log- or square-root transformation. Box-Cox
+    transformation is not mentioned in any of the TGs which is why it is
+    left to the choice of the user.
+- **alpha for residual normality and variance homogeneity tests**
+  - The default here is 0.05. In the TGs the alpha level is discussed so
+    the user is adviced to inspect the requirements of the respective
+    study to analyze.
+
+The next option in the little box on the top-left of the app is to set a
+hook or remove the hook to decide whether the exposure well ID is
+regarded as random term in the underlying mixed ANOVA model. In case a
+REACTIV study is investigated the hook should be removed. For RADAR and
+XETA, the hook should be placed as long as information about the
+exposure well ID was documented. Of course, reducing the complexity of
+the random term might also make sense for XETA and RADAR studies in case
+no variance is explained by the exposure well-ID. However, this choice
+is left to the user.
+
+When own data is supposed to be analyzed xlsx files with either spiked
+or unspiked data can be uploaded. Please make sure that the uploaded
+data fulfills the Data requirements explained above. In case of
+insecurity, inspect the uploaded data structure of the pre-loaded
+example data.
+
+The app contains several output boxes about the required data
+processing, a conclusion table, the uploaded data, residual diagnostics
+plots, boxplots, a data summary table, the output of the residual
+normality and homogeneity tests, the monotonicity test result, the
+Dunnett’s and increasing and decreasing Williams test result tables
+along with the summary table of the underlying mixed ANOVA model.
+
+The depicted information can be downloaded in a simple report by
+clicking on the button \*\* Word report\*\*. It takes a couple of
+seconds until the final docx file is produced and ready to download.
+Avoid clicking the button several times as this can lead to long waiting
+times and the production of several reports.
+
 # References
 
 OECD. 2019a. Validation Report of the Xenopus Eleutheroembryonic Thyroid

Readme.Rmd

@@ -407,6 +407,28 @@ gt::gt(thyroid_active, rowname_col = "substance") |>
 
 ```
 
+# The shiny app
+
+xeredar contains an integrated shiny app that is available to the users by writing `run_app()` into the console. The only requirement to use the app is the successful installation of xeredar. When the app started, the user has a couple of options to analyse the data. These options can be adjusted by clicking on the little gear sign next to *Inputs*. The following options are available: 
+
+- **Use d'Agostino test?**
+  - The default here is that this is not selected meaning the Shapiro-Wilk test is utilized to check for residual normality. However, the RADAR TG mentions the d'Agostino test which is why it is also available to the users. 
+- **Apply 10% Trimming**
+  - The default here is that this is selected, meaning that 10% Trimming is conducted when the ANOVA assumptions are not fulfilled by the raw data. Please be aware that this does not mean that 10% Trimming is always conducted. It is only conducted, when the raw data is violating the residual normality and variance homogeneity assumptions, tested with the respective test with an adjustable alpha level. 
+- **Remove outliers**
+  - The default here is that this is selected, meaning that outlier removal is conducted when the ANOVA assumptions are not fulfilled by the raw data or by 10% Trimming, if it is selected above. 
+- **Try Box-Cox transformation**
+  - The default here is that this is selected, meaning that box-cox transformation is carried out when the ANOVA assumptions are not fulfilled by the raw or processed data (10% Trimming or outlier removal) nor by log- or square-root transformation. Box-Cox transformation is not mentioned in any of the TGs which is why it is left to the choice of the user.
+- **alpha for residual normality and variance homogeneity tests**
+  - The default here is 0.05. In the TGs the alpha level is discussed so the user is adviced to inspect the requirements of the respective study to analyze. 
+
+The next option in the little box on the top-left of the app is to set a hook or remove the hook to decide whether the exposure well ID is regarded as random term in the underlying mixed ANOVA model. In case a REACTIV study is investigated the hook should be removed. For RADAR and XETA, the hook should be placed as long as information about the exposure well ID was documented. Of course, reducing the complexity of the random term might also make sense for XETA and RADAR studies in case no variance is explained by the exposure well-ID. However, this choice is left to the user. 
+
+When own data is supposed to be analyzed xlsx files with either spiked or unspiked data can be uploaded. Please make sure that the uploaded data fulfills the Data requirements explained above. In case of insecurity, inspect the uploaded data structure of the pre-loaded example data.
+
+The app contains several output boxes about the required data processing, a conclusion table, the uploaded data, residual diagnostics plots, boxplots, a data summary table, the output of the residual normality and homogeneity tests, the monotonicity test result, the Dunnett's and increasing and decreasing Williams test result tables along with the summary table of the underlying mixed ANOVA model. 
+
+The depicted information can be downloaded in a simple report by clicking on the button ** Word report**. It takes a couple of seconds until the final docx file is produced and ready to download. Avoid clicking the button several times as this can lead to long waiting times and the production of several reports.
 
 # References
 

vignettes/User_guide.Rmd

@@ -282,6 +282,28 @@ xeredar::data_summary(reactiv_spiked_result) |>
 
 ```
 
+# The shiny app
+
+xeredar contains an integrated shiny app that is available to the users by writing `run_app()` into the console. The only requirement to use the app is the successful installation of xeredar. When the app started, the user has a couple of options to analyse the data. These options can be adjusted by clicking on the little gear sign next to *Inputs*. The following options are available: 
+
+- **Use d'Agostino test?**
+  - The default here is that this is not selected meaning the Shapiro-Wilk test is utilized to check for residual normality. However, the RADAR TG mentions the d'Agostino test which is why it is also available to the users. 
+- **Apply 10% Trimming**
+  - The default here is that this is selected, meaning that 10% Trimming is conducted when the ANOVA assumptions are not fulfilled by the raw data. Please be aware that this does not mean that 10% Trimming is always conducted. It is only conducted, when the raw data is violating the residual normality and variance homogeneity assumptions, tested with the respective test with an adjustable alpha level. 
+- **Remove outliers**
+  - The default here is that this is selected, meaning that outlier removal is conducted when the ANOVA assumptions are not fulfilled by the raw data or by 10% Trimming, if it is selected above. 
+- **Try Box-Cox transformation**
+  - The default here is that this is selected, meaning that box-cox transformation is carried out when the ANOVA assumptions are not fulfilled by the raw or processed data (10% Trimming or outlier removal) nor by log- or square-root transformation. Box-Cox transformation is not mentioned in any of the TGs which is why it is left to the choice of the user.
+- **alpha for residual normality and variance homogeneity tests**
+  - The default here is 0.05. In the TGs the alpha level is discussed so the user is adviced to inspect the requirements of the respective study to analyze. 
+
+The next option in the little box on the top-left of the app is to set a hook or remove the hook to decide whether the exposure well ID is regarded as random term in the underlying mixed ANOVA model. In case a REACTIV study is investigated the hook should be removed. For RADAR and XETA, the hook should be placed as long as information about the exposure well ID was documented. Of course, reducing the complexity of the random term might also make sense for XETA and RADAR studies in case no variance is explained by the exposure well-ID. However, this choice is left to the user. 
+
+When own data is supposed to be analyzed xlsx files with either spiked or unspiked data can be uploaded. Please make sure that the uploaded data fulfills the Data requirements explained above. In case of insecurity, inspect the uploaded data structure of the pre-loaded example data.
+
+The app contains several output boxes about the required data processing, a conclusion table, the uploaded data, residual diagnostics plots, boxplots, a data summary table, the output of the residual normality and homogeneity tests, the monotonicity test result, the Dunnett's and increasing and decreasing Williams test result tables along with the summary table of the underlying mixed ANOVA model. 
+
+The depicted information can be downloaded in a simple report by clicking on the button ** Word report**. It takes a couple of seconds until the final docx file is produced and ready to download. Avoid clicking the button several times as this can lead to long waiting times and the production of several reports.
 # Validation