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Test fixes
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@robalexclark
robalexclark committed Oct 20, 2021
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4 changes: 4 additions & 0 deletions SilveR.IntegrationTests/ExpectedResults/EquivalenceTOSTTest/ETT21.html
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</style>
<link rel="stylesheet" type="text/css" href='r2html.css'>

<h1> InVivoStat Equivalence TOST Test Analysis</h1>

<p class='character'>Unfortunately not all combinations of the levels of the treatment factors are present in the experimental design. We recommend you manually create a new factor corresponding to the combinations of the levels of the treatment factors.</p>
277 changes: 277 additions & 0 deletions SilveR.IntegrationTests/ExpectedResults/EquivalenceTOSTTest/ETT22.html
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2 changes: 1 addition & 1 deletion SilveR.IntegrationTests/ExpectedResults/EquivalenceTOSTTest/ETT40.html
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Expand Up @@ -57,7 +57,7 @@ <h2> Model coefficients</h2>

<h2> Table of the back-transformed geometric means with 95% confidence intervals</h2>

<p class='character'>As the response was log transformed prior to analysis the least square (predicted) means are presented on the log scale. These results can be back transformed onto the original scale. These are known as the back-transformed geometric means.</p>
<p class='character'>As the response was log transformed prior to analysis the means are presented back transformed onto the original scale. These are known as the back-transformed geometric means.</p>


<p align="left">
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2 changes: 1 addition & 1 deletion SilveR.IntegrationTests/ExpectedResults/EquivalenceTOSTTest/ETT41.html
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Expand Up @@ -57,7 +57,7 @@ <h2> Model coefficients</h2>

<h2> Table of the back-transformed geometric means with 95% confidence intervals</h2>

<p class='character'>As the response was log transformed prior to analysis the least square (predicted) means are presented on the log scale. These results can be back transformed onto the original scale. These are known as the back-transformed geometric means.</p>
<p class='character'>As the response was log transformed prior to analysis the means are presented back transformed onto the original scale. These are known as the back-transformed geometric means.</p>


<p align="left">
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2 changes: 1 addition & 1 deletion SilveR.IntegrationTests/ExpectedResults/EquivalenceTOSTTest/ETT42.html
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Expand Up @@ -57,7 +57,7 @@ <h2> Model coefficients</h2>

<h2> Table of the back-transformed geometric means with 95% confidence intervals</h2>

<p class='character'>As the response was log transformed prior to analysis the least square (predicted) means are presented on the log scale. These results can be back transformed onto the original scale. These are known as the back-transformed geometric means.</p>
<p class='character'>As the response was log transformed prior to analysis the means are presented back transformed onto the original scale. These are known as the back-transformed geometric means.</p>


<p align="left">
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2 changes: 1 addition & 1 deletion SilveR.IntegrationTests/ExpectedResults/EquivalenceTOSTTest/ETT43.html
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Expand Up @@ -57,7 +57,7 @@ <h2> Model coefficients</h2>

<h2> Table of the back-transformed geometric means with 95% confidence intervals</h2>

<p class='character'>As the response was log transformed prior to analysis the least square (predicted) means are presented on the log scale. These results can be back transformed onto the original scale. These are known as the back-transformed geometric means.</p>
<p class='character'>As the response was log transformed prior to analysis the means are presented back transformed onto the original scale. These are known as the back-transformed geometric means.</p>


<p align="left">
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2 changes: 1 addition & 1 deletion SilveR.IntegrationTests/ExpectedResults/EquivalenceTOSTTest/ETT49.html
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Expand Up @@ -57,7 +57,7 @@ <h2> Model coefficients</h2>

<h2> Table of the back-transformed geometric means with 95% confidence intervals</h2>

<p class='character'>As the response was log transformed prior to analysis the least square (predicted) means are presented on the log scale. These results can be back transformed onto the original scale. These are known as the back-transformed geometric means.</p>
<p class='character'>As the response was log transformed prior to analysis the means are presented back transformed onto the original scale. These are known as the back-transformed geometric means.</p>


<p align="left">
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2 changes: 1 addition & 1 deletion SilveR.IntegrationTests/ExpectedResults/EquivalenceTOSTTest/ETT50.html
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Expand Up @@ -57,7 +57,7 @@ <h2> Model coefficients</h2>

<h2> Table of the back-transformed geometric means with 95% confidence intervals</h2>

<p class='character'>As the response was log transformed prior to analysis the least square (predicted) means are presented on the log scale. These results can be back transformed onto the original scale. These are known as the back-transformed geometric means.</p>
<p class='character'>As the response was log transformed prior to analysis the means are presented back transformed onto the original scale. These are known as the back-transformed geometric means.</p>


<p align="left">
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941 changes: 941 additions & 0 deletions SilveR.IntegrationTests/ExpectedResults/EquivalenceTOSTTest/ETT55.html
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905 changes: 905 additions & 0 deletions SilveR.IntegrationTests/ExpectedResults/EquivalenceTOSTTest/ETT56.html
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909 changes: 909 additions & 0 deletions SilveR.IntegrationTests/ExpectedResults/EquivalenceTOSTTest/ETT57.html
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945 changes: 945 additions & 0 deletions SilveR.IntegrationTests/ExpectedResults/EquivalenceTOSTTest/ETT58.html
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2 changes: 1 addition & 1 deletion SilveR.IntegrationTests/SilveR.IntegrationTests.csproj
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Expand Up @@ -7,7 +7,7 @@

<ItemGroup>
<PackageReference Include="ExcelDataReader" Version="3.6.0" />
<PackageReference Include="Microsoft.AspNetCore.Mvc.Testing" Version="5.0.9" />
<PackageReference Include="Microsoft.AspNetCore.Mvc.Testing" Version="5.0.11" />
<PackageReference Include="Microsoft.NET.Test.Sdk" Version="16.11.0" />
<PackageReference Include="xunit" Version="2.4.1" />
<PackageReference Include="xunit.runner.visualstudio" Version="2.4.3">
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48 changes: 40 additions & 8 deletions SilveR.IntegrationTests/StatsTests/EquivalenceTOSTTestTests.cs
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Expand Up @@ -31,6 +31,9 @@ public async Task ETT1()
model.DatasetID = _factory.SheetNames.Single(x => x.Value == "Equivalence TOST").Key;
model.Response = "Resp 1";
model.Treatments = new string[] { "Resp 1" };
model.EquivalenceBoundsType = EquivalenceTOSTTestModel.EquivalenceBoundsOption.Percentage;
model.LowerBoundPercentageChange = 10;
model.UpperBoundPercentageChange = 20;

//Act
HttpResponseMessage response = await client.PostAsync("Analyses/EquivalenceTOSTTest", new FormUrlEncodedContent(model.ToKeyValue()));
Expand All @@ -53,6 +56,9 @@ public async Task ETT2()
model.DatasetID = _factory.SheetNames.Single(x => x.Value == "Equivalence TOST").Key;
model.Response = "Resp6";
model.Treatments = new string[] { "Treat1" };
model.EquivalenceBoundsType = EquivalenceTOSTTestModel.EquivalenceBoundsOption.Percentage;
model.LowerBoundPercentageChange = 10;
model.UpperBoundPercentageChange = 20;

//Act
HttpResponseMessage response = await client.PostAsync("Analyses/EquivalenceTOSTTest", new FormUrlEncodedContent(model.ToKeyValue()));
Expand All @@ -75,6 +81,9 @@ public async Task ETT3()
model.DatasetID = _factory.SheetNames.Single(x => x.Value == "Equivalence TOST").Key;
model.Response = "Resp 1";
model.Treatments = new string[] { "Treat7" };
model.EquivalenceBoundsType = EquivalenceTOSTTestModel.EquivalenceBoundsOption.Percentage;
model.LowerBoundPercentageChange = 10;
model.UpperBoundPercentageChange = 20;

//Act
HttpResponseMessage response = await client.PostAsync("Analyses/EquivalenceTOSTTest", new FormUrlEncodedContent(model.ToKeyValue()));
Expand All @@ -98,6 +107,9 @@ public async Task ETT4()
model.DatasetID = _factory.SheetNames.Single(x => x.Value == "Equivalence TOST").Key;
model.Response = "Resp 1";
model.Treatments = new string[] { "Tre at4" };
model.EquivalenceBoundsType = EquivalenceTOSTTestModel.EquivalenceBoundsOption.Percentage;
model.LowerBoundPercentageChange = 10;
model.UpperBoundPercentageChange = 20;

//Act
HttpResponseMessage response = await client.PostAsync("Analyses/EquivalenceTOSTTest", new FormUrlEncodedContent(model.ToKeyValue()));
Expand All @@ -120,6 +132,9 @@ public async Task ETT5()
model.DatasetID = _factory.SheetNames.Single(x => x.Value == "Equivalence TOST").Key;
model.Response = "Resp4";
model.Treatments = new string[] { "Treat1" };
model.EquivalenceBoundsType = EquivalenceTOSTTestModel.EquivalenceBoundsOption.Percentage;
model.LowerBoundPercentageChange = 10;
model.UpperBoundPercentageChange = 20;

//Act
HttpResponseMessage response = await client.PostAsync("Analyses/EquivalenceTOSTTest", new FormUrlEncodedContent(model.ToKeyValue()));
Expand All @@ -143,6 +158,9 @@ public async Task ETT6()
model.Response = "Resp 1";
model.Treatments = new string[] { "Treat1" };
model.Covariates = new string[] { "Cov4" };
model.EquivalenceBoundsType = EquivalenceTOSTTestModel.EquivalenceBoundsOption.Percentage;
model.LowerBoundPercentageChange = 10;
model.UpperBoundPercentageChange = 20;

//Act
HttpResponseMessage response = await client.PostAsync("Analyses/EquivalenceTOSTTest", new FormUrlEncodedContent(model.ToKeyValue()));
Expand All @@ -165,6 +183,9 @@ public async Task ETT7()
model.DatasetID = _factory.SheetNames.Single(x => x.Value == "Equivalence TOST").Key;
model.Response = "Resp5";
model.Treatments = new string[] { "Treat1" };
model.EquivalenceBoundsType = EquivalenceTOSTTestModel.EquivalenceBoundsOption.Percentage;
model.LowerBoundPercentageChange = 10;
model.UpperBoundPercentageChange = 20;

//Act
HttpResponseMessage response = await client.PostAsync("Analyses/EquivalenceTOSTTest", new FormUrlEncodedContent(model.ToKeyValue()));
Expand All @@ -189,6 +210,9 @@ public async Task ETT8()
model.Treatments = new string[] { "Treat1" };
model.Covariates = new string[] { "Cov5" };
model.PrimaryFactor = "Treat1";
model.EquivalenceBoundsType = EquivalenceTOSTTestModel.EquivalenceBoundsOption.Percentage;
model.LowerBoundPercentageChange = 10;
model.UpperBoundPercentageChange = 20;

//Act
HttpResponseMessage response = await client.PostAsync("Analyses/EquivalenceTOSTTest", new FormUrlEncodedContent(model.ToKeyValue()));
Expand All @@ -211,6 +235,9 @@ public async Task ETT9()
model.DatasetID = _factory.SheetNames.Single(x => x.Value == "Equivalence TOST").Key;
model.Response = "Resp 1";
model.Treatments = new string[] { "T reat5" };
model.EquivalenceBoundsType = EquivalenceTOSTTestModel.EquivalenceBoundsOption.Percentage;
model.LowerBoundPercentageChange = 10;
model.UpperBoundPercentageChange = 20;

//Act
HttpResponseMessage response = await client.PostAsync("Analyses/EquivalenceTOSTTest", new FormUrlEncodedContent(model.ToKeyValue()));
Expand All @@ -233,6 +260,9 @@ public async Task ETT10()
model.DatasetID = _factory.SheetNames.Single(x => x.Value == "Equivalence TOST").Key;
model.Response = "Resp 1";
model.Treatments = new string[] { "Treat6" };
model.EquivalenceBoundsType = EquivalenceTOSTTestModel.EquivalenceBoundsOption.Percentage;
model.LowerBoundPercentageChange = 10;
model.UpperBoundPercentageChange = 20;

//Act
HttpResponseMessage response = await client.PostAsync("Analyses/EquivalenceTOSTTest", new FormUrlEncodedContent(model.ToKeyValue()));
Expand Down Expand Up @@ -336,7 +366,7 @@ public async Task ETT14()
model.Covariates = new string[] { "Cov2" };
model.CovariateTransformation = "Log10";
model.PrimaryFactor = "Treat1";
model.EquivalenceBoundsType = EquivalenceTOSTTestModel.EquivalenceBoundsOption.Percentage;
model.EquivalenceBoundsType = EquivalenceTOSTTestModel.EquivalenceBoundsOption.Absolute;
model.LowerBoundAbsolute = 10;
model.UpperBoundAbsolute = 20;

Expand Down Expand Up @@ -364,7 +394,7 @@ public async Task ETT15()
model.Covariates = new string[] { "Cov3" };
model.CovariateTransformation = "Loge";
model.PrimaryFactor = "Treat1";
model.EquivalenceBoundsType = EquivalenceTOSTTestModel.EquivalenceBoundsOption.Percentage;
model.EquivalenceBoundsType = EquivalenceTOSTTestModel.EquivalenceBoundsOption.Absolute;
model.LowerBoundAbsolute = 10;
model.UpperBoundAbsolute = 20;

Expand Down Expand Up @@ -528,6 +558,7 @@ public async Task ETT21()
model.DatasetID = _factory.SheetNames.Single(x => x.Value == "Equivalence TOST").Key;
model.Response = "Resp8";
model.Treatments = new string[] { "Treat12", "Treat13" };
model.SelectedEffect = "Treat12";
model.EquivalenceBoundsType = EquivalenceTOSTTestModel.EquivalenceBoundsOption.Absolute;
model.LowerBoundAbsolute = 10;
model.UpperBoundAbsolute = 20;
Expand All @@ -553,6 +584,7 @@ public async Task ETT22()
model.DatasetID = _factory.SheetNames.Single(x => x.Value == "Equivalence TOST").Key;
model.Response = "Resp11";
model.Treatments = new string[] { "Treat14" };
model.SelectedEffect = "Treat14";
model.EquivalenceBoundsType = EquivalenceTOSTTestModel.EquivalenceBoundsOption.Absolute;
model.LowerBoundAbsolute = 10;
model.UpperBoundAbsolute = 20;
Expand Down Expand Up @@ -612,7 +644,7 @@ public async Task ETT25()
IEnumerable<string> errors = await Helpers.ExtractErrors(response);

//Assert
Assert.Contains("The field Lower bound percentage must be between 0 and 100.", errors);
Assert.Contains("User cannot select a negative Percentage change.", errors);
Helpers.SaveOutput("EquivalenceTOSTTest", testName, errors);
}

Expand All @@ -637,7 +669,7 @@ public async Task ETT26()
IEnumerable<string> errors = await Helpers.ExtractErrors(response);

//Assert
Assert.Contains("The field Lower bound percentage must be between 0 and 100.", errors);
Assert.Contains("User cannot select a negative Percentage change.", errors);
Helpers.SaveOutput("EquivalenceTOSTTest", testName, errors);
}

Expand Down Expand Up @@ -1531,7 +1563,7 @@ public async Task ETT55()
model.Treatments = new string[] { "Treat1" };
model.EquivalenceBoundsType = EquivalenceTOSTTestModel.EquivalenceBoundsOption.Percentage;
//model.LowerBoundAbsolute = 0.2m;
model.UpperBoundAbsolute = 10m;
model.UpperBoundPercentageChange = 10m;
model.Significance = "0.05";
model.PRPlotSelected = true;
model.SelectedEffect = "Treat1";
Expand Down Expand Up @@ -1572,7 +1604,7 @@ public async Task ETT56()
model.Treatments = new string[] { "Treat1" };
model.EquivalenceBoundsType = EquivalenceTOSTTestModel.EquivalenceBoundsOption.Percentage;
//model.LowerBoundAbsolute = 0.2m;
model.UpperBoundAbsolute = 10m;
model.UpperBoundPercentageChange = 10m;
model.Significance = "0.05";
model.PRPlotSelected = true;
model.SelectedEffect = "Treat1";
Expand Down Expand Up @@ -1614,7 +1646,7 @@ public async Task ETT57()
model.Treatments = new string[] { "Treat1" };
model.EquivalenceBoundsType = EquivalenceTOSTTestModel.EquivalenceBoundsOption.Percentage;
//model.LowerBoundAbsolute = 0.2m;
model.UpperBoundAbsolute = 10m;
model.UpperBoundPercentageChange = 10m;
model.Significance = "0.05";
model.PRPlotSelected = true;
model.SelectedEffect = "Treat1";
Expand Down Expand Up @@ -1646,7 +1678,7 @@ public async Task ETT58()
model.Treatments = new string[] { "Treat1" };
model.EquivalenceBoundsType = EquivalenceTOSTTestModel.EquivalenceBoundsOption.Percentage;
//model.LowerBoundAbsolute = 0.2m;
model.UpperBoundAbsolute = 10m;
model.UpperBoundPercentageChange = 10m;
model.Significance = "0.05";
model.PRPlotSelected = true;
model.SelectedEffect = "Treat1";
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4 changes: 2 additions & 2 deletions SilveR/Scripts/EquivalenceTOSTTest.R
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Expand Up @@ -900,10 +900,10 @@ if(showLSMeans =="Y") {
HTML.title(CITitle2, HR=2, align="left")

if (GeomDisplay == "geometricmeansandpredictedmeansonlogscale") {
HTML("As the response was log transformed prior to analysis the least square (predicted) means are presented on the log scale. These results can be back transformed onto the original scale. These are known as the back-transformed geometric means.", align="left")
HTML("As the response was log transformed prior to analysis the means are presented back transformed onto the original scale. These are known as the back-transformed geometric means.", align="left")
}
if (GeomDisplay == "geometricmeansonly") {
HTML("As the response was log transformed prior to analysis the least square (predicted) means are presented back transformed onto the original scale. These are known as the back-transformed geometric means.", align="left")
HTML("As the response was log transformed prior to analysis the means are presented back transformed onto the original scale. These are known as the back-transformed geometric means.", align="left")
}

#Calculate LS Means Table
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6 changes: 3 additions & 3 deletions SilveR/SilveR.csproj
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Expand Up @@ -34,9 +34,9 @@
<PackageReference Include="ElectronNET.API" Version="13.5.1" />
<PackageReference Include="ExcelDataReader.DataSet" Version="3.6.0" />
<PackageReference Include="HtmlAgilityPack" Version="1.11.37" />
<PackageReference Include="Microsoft.AspNetCore.Mvc.NewtonsoftJson" Version="5.0.10" />
<PackageReference Include="Microsoft.EntityFrameworkCore.Sqlite" Version="5.0.10" />
<PackageReference Include="Microsoft.EntityFrameworkCore.Tools" Version="5.0.10">
<PackageReference Include="Microsoft.AspNetCore.Mvc.NewtonsoftJson" Version="5.0.11" />
<PackageReference Include="Microsoft.EntityFrameworkCore.Sqlite" Version="5.0.11" />
<PackageReference Include="Microsoft.EntityFrameworkCore.Tools" Version="5.0.11">
<PrivateAssets>all</PrivateAssets>
<IncludeAssets>runtime; build; native; contentfiles; analyzers; buildtransitive</IncludeAssets>
</PackageReference>
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7 changes: 1 addition & 6 deletions SilveR/StatsModels/AnalysisModelBase.cs
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Expand Up @@ -13,12 +13,7 @@ protected AnalysisModelBase(string scriptFileName)
this.ScriptFileName = scriptFileName;
}

public string CustomRCode { get; private set; }

public void SetCustomRCode(string rCode)
{
CustomRCode = rCode;
}
public string CustomRCode { get; set; }

public abstract ValidationInfo Validate();

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