Logistic Regression Analysis module

robalexclark · Mar 27, 2020 · bc7c3ef · bc7c3ef
1 parent 4a04b14
commit bc7c3ef
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Showing 41 changed files with 4,120 additions and 104 deletions.
diff --git a/SilveR.IntegrationTests/xunit.runner.json b/SilveR.IntegrationTests/xunit.runner.json
@@ -1,3 +1,3 @@
 {
-  "parallelizeTestCollections": true
+  "parallelizeTestCollections": false
 }
diff --git a/SilveR/Controllers/AnalysesController.cs b/SilveR/Controllers/AnalysesController.cs
@@ -181,6 +181,12 @@ public async Task<IActionResult> LinearRegressionAnalysis(LinearRegressionAnalys
             return await RunAnalysis(model, ignoreWarnings);
         }
 
+        [HttpPost]
+        public async Task<IActionResult> LogisticRegressionAnalysis(LogisticRegressionAnalysisModel model, bool ignoreWarnings)
+        {
+            return await RunAnalysis(model, ignoreWarnings);
+        }
+
         [HttpPost]
         public async Task<IActionResult> DoseResponseAndNonLinearRegressionAnalysis(DoseResponseAndNonLinearRegressionAnalysisModel model, bool ignoreWarnings)
         {

diff --git a/SilveR/Scripts/ChiSquaredAndFishersExactTest.R b/SilveR/Scripts/ChiSquaredAndFishersExactTest.R
@@ -437,15 +437,27 @@ if (BarnardsExactTest == "Y") {
 #===================================================================================================================
 Ref_list<-R_refs()
 
-HTML.title("Statistical references", HR=2, align="left")
+if (UpdateIVS == "N") {
+	HTML.title("Statistical references", HR=2, align="left")
+}
+if (UpdateIVS == "Y") {
+	HTML.title("References", HR=2, align="left")
+	HTML(Ref_list$IVS_ref, align="left")
+}
 HTML(Ref_list$BateClark_ref, align="left")
 
 if(BarnardsExactTest == "Y" && row == 2 && col == 2)
 {
 	HTML("Lydersen, S., Fagerland, M.W. and Laake, P. (2009). Recommended tests for association in 2 x 2 tables. Statistics in Medicine, 28, 1159-1175.", align="left")
 }
 
-HTML.title("R references", HR=2, align="left")
+if (UpdateIVS == "N") {
+	HTML.title("R references", HR=2, align="left")
+}
+if (UpdateIVS == "Y") {
+	HTML.title("R references", HR=4, align="left")
+}
+
 HTML(Ref_list$R_ref  ,  align="left")
 HTML(Ref_list$R2HTML_ref, align="left")
 

diff --git a/SilveR/Scripts/Common_Functions.R b/SilveR/Scripts/Common_Functions.R
@@ -2,6 +2,9 @@
 #branding <- "InVivoStat (beta version)"
 branding <- "InVivoStat"
 
+#Software update
+UpdateIVS <- "N"
+
 #Beta warning
 Betawarn <- "N"
 BetaMessage <- "This output has been generated using the beta test version of InVivoStat. Care should be taken when making decisions based on the output."
@@ -947,7 +950,6 @@ NONCAT_CPP <- function() {
 	g <- ggplot(graphdata, aes(Time_IVS, yvarrr_IVS)) +
 		theme_map +
 		mytheme +
-		theme(legend.position = "none") +
 		ylab(YAxisTitle) +
 		xlab(XAxisTitle) +
 		ggtitle(MainTitle2) +
@@ -956,6 +958,14 @@ NONCAT_CPP <- function() {
 		geom_point(aes(colour = Animal_IVS), size = 3, shape = 16) +
 		geom_line(aes(group = Animal_IVS, color = Animal_IVS), size = Line_size)
 
+	if (UpdateIVS == "N") {
+		 g <- g + theme(legend.position = "none") 
+	}
+	if (UpdateIVS == "Y") {
+		 g <- g + 	theme(legend.position = "Gr_legend_pos") + 
+				labs(fill = "Animal_IVS")
+	}
+
 	if (ReferenceLine != "NULL") {
 		g1 <- g + geom_hline(yintercept = Gr_intercept, lty = Gr_line_typeint, size = Line_size, colour = Gr_line)
 	} else {
@@ -969,7 +979,6 @@ ONECATSEP_CPP <- function() {
 	g <- ggplot(graphdata, aes(Time_IVS, yvarrr_IVS)) +
 		theme_map +
 		mytheme +
-		theme(legend.position = "none") +
 		ylab(YAxisTitle) +
 		xlab(XAxisTitle) +
 		ggtitle(MainTitle2) +
@@ -978,6 +987,14 @@ ONECATSEP_CPP <- function() {
 		geom_point(aes(colour = Animal_IVS), size = 3, shape = 16) +
 		facet_wrap(~l_l)
 
+	if (UpdateIVS == "N") {
+		 g <- g + theme(legend.position = "none") 
+	}
+	if (UpdateIVS == "Y") {
+		 g <- g + 	theme(legend.position = "Gr_legend_pos") + 
+				labs(fill = "Animal_IVS")
+	}
+
 	if (ReferenceLine != "NULL") {
 		g1 <- g + geom_hline(yintercept = Gr_intercept, lty = Gr_line_typeint, size = Line_size, colour = Gr_line)
 	} else {
@@ -991,7 +1008,6 @@ TWOCATSEP_CPP <- function() {
 	g <- ggplot(graphdata, aes(Time_IVS, yvarrr_IVS)) +
 		theme_map +
 		mytheme +
-		theme(legend.position = "none") +
 		ylab(YAxisTitle) +
 		xlab(XAxisTitle) +
 		ggtitle(MainTitle2) +
@@ -1000,6 +1016,13 @@ TWOCATSEP_CPP <- function() {
 		geom_point(aes(colour = Animal_IVS), size = 3, shape = 16) +
 		facet_grid(firstcatvarrr_IVS ~ secondcatvarrr_IVS)
 
+	if (UpdateIVS == "N") {
+		 g <- g + theme(legend.position = "none") 
+	}
+	if (UpdateIVS == "Y") {
+		 g <- g + 	theme(legend.position = "Gr_legend_pos") + 
+				labs(fill = "Animal_IVS")
+	}
 	if (ReferenceLine != "NULL") {
 		g1 <- g + geom_hline(yintercept = Gr_intercept, lty = Gr_line_typeint, size = Line_size, colour = Gr_line)
 	} else {
@@ -1657,9 +1680,10 @@ R_refs <- function() {
 	Barnard_ref <- "Peter Calhoun (2013). Exact: Unconditional Exact Test. R package version 1.4. http://CRAN.R-project.org/package=Exact."
 
 	power_ref <- "Stephane Champely (2018). pwr: Basic Functions for Power Analysis. R package version 1.2-2. https://CRAN.R-project.org/package=pwr"
-
+	IVS_ref <- "When referring to InVivoStat, please cite 'InVivoStat, version 4.1'."
 
 	Refs <- list(
+		IVS_ref = IVS_ref,
 		R_ref = R_ref,
 		mtvnorm_ref = mtvnorm_ref,
 		GridExtra_ref = GridExtra_ref,

diff --git a/SilveR/Scripts/ComparisonOfMeansPowerAnalysisDatasetBasedInputs.R b/SilveR/Scripts/ComparisonOfMeansPowerAnalysisDatasetBasedInputs.R
@@ -542,11 +542,22 @@ HTML("Biologically relevant effect: The size of effect that is of scientific int
 #===================================================================================================================
 Ref_list <- R_refs()
 
-HTML.title("Statistical references", HR = 2, align = "left")
+if (UpdateIVS == "N") {
+	HTML.title("Statistical references", HR=2, align="left")
+}
+if (UpdateIVS == "Y") {
+	HTML.title("References", HR=2, align="left")
+	HTML(Ref_list$IVS_ref, align="left")
+}
 HTML(Ref_list$BateClark_ref, align = "left")
 #HTML("Harrison, D.A. and Brady, A.R. (2004). Sample size and power calculations using the noncentral t-distribution. The Stata Journal, 4(2), 142-153.", align = "left")
 
-HTML.title("R references", HR = 2, align = "left")
+if (UpdateIVS == "N") {
+	HTML.title("R references", HR=2, align="left")
+}
+if (UpdateIVS == "Y") {
+	HTML.title("R references", HR=4, align="left")
+}
 HTML(Ref_list$R_ref,  align = "left")
 HTML(Ref_list$GGally_ref,  align = "left")
 HTML(Ref_list$RColorBrewers_ref,  align = "left")

diff --git a/SilveR/Scripts/ComparisonOfMeansPowerAnalysisUserBasedInputs.R b/SilveR/Scripts/ComparisonOfMeansPowerAnalysisUserBasedInputs.R
@@ -542,11 +542,22 @@ HTML("Biologically relevant effect: The size of effect that is of scientific int
 #===================================================================================================================
 Ref_list <- R_refs()
 
-HTML.title("Statistical references", HR = 2, align = "left")
+if (UpdateIVS == "N") {
+	HTML.title("Statistical references", HR=2, align="left")
+}
+if (UpdateIVS == "Y") {
+	HTML.title("References", HR=2, align="left")
+	HTML(Ref_list$IVS_ref, align="left")
+}
 HTML(Ref_list$BateClark_ref, align = "left")
 #HTML("Harrison, D.A. and Brady, A.R. (2004). Sample size and power calculations using the noncentral t-distribution. The Stata Journal, 4(2), 142-153.", align = "left")
 
-HTML.title("R references", HR = 2, align = "left")
+if (UpdateIVS == "N") {
+	HTML.title("R references", HR=2, align="left")
+}
+if (UpdateIVS == "Y") {
+	HTML.title("R references", HR=4, align="left")
+}
 HTML(Ref_list$R_ref,  align = "left")
 HTML(Ref_list$GGally_ref,  align = "left")
 HTML(Ref_list$RColorBrewers_ref,  align = "left")

diff --git a/SilveR/Scripts/CorrelationAnalysis.R b/SilveR/Scripts/CorrelationAnalysis.R
@@ -894,8 +894,15 @@ Ref_list<-R_refs()
 #Bate and Clark comment
 HTML(refxx, align="left")	
 
-HTML.title("Statistical references", HR=2, align="left")
+if (UpdateIVS == "N") {
+	HTML.title("Statistical references", HR=2, align="left")
+}
+if (UpdateIVS == "Y") {
+	HTML.title("References", HR=2, align="left")
+	HTML(Ref_list$IVS_ref, align="left")
+}
 HTML(Ref_list$BateClark_ref, align="left")
+
 if (method == "Pearson") {
 	HTML("Snedecor, G.W. and Cochran, W.G. (1989). Statistical Methods. 8th edition; Iowa State University Press, Iowa, USA.", align="left") 
 }
@@ -905,7 +912,14 @@ if (method == "Spearman") {
 if (method == "Spearman" || method == "Kendall") {
 	HTML("Hollander, M. and Wolfe, D.A. (1973). Nonparametric Statistical Methods. New York: John Wiley & Sons. P185-194. ", align="left")
 }
-HTML.title("R references", HR=2, align="left")
+
+if (UpdateIVS == "N") {
+	HTML.title("R references", HR=2, align="left")
+}
+if (UpdateIVS == "Y") {
+	HTML.title("R references", HR=4, align="left")
+}
+
 HTML(Ref_list$R_ref , align="left")
 HTML(Ref_list$GGally_ref, align="left")
 HTML(Ref_list$RColorBrewers_ref, align="left")

diff --git a/SilveR/Scripts/DoseResponseAndNonLinearRegressionAnalysis.R b/SilveR/Scripts/DoseResponseAndNonLinearRegressionAnalysis.R
@@ -1024,10 +1024,21 @@ if (DoseResponseType == "FourParameter") {
 #===================================================================================================================
 Ref_list <- R_refs()
 
-HTML.title("Statistical references", HR = 2, align = "left")
+if (UpdateIVS == "N") {
+	HTML.title("Statistical references", HR=2, align="left")
+}
+if (UpdateIVS == "Y") {
+	HTML.title("References", HR=2, align="left")
+	HTML(Ref_list$IVS_ref, align="left")
+}
 HTML(Ref_list$BateClark_ref, align = "left")
 
-HTML.title("R references", HR = 2, align = "left")
+if (UpdateIVS == "N") {
+	HTML.title("R references", HR=2, align="left")
+}
+if (UpdateIVS == "Y") {
+	HTML.title("R references", HR=4, align="left")
+}
 HTML(Ref_list$R_ref, align = "left")
 HTML(Ref_list$mtvnorm_ref, align = "left")
 HTML(Ref_list$GGally_ref, align = "left")

diff --git a/SilveR/Scripts/GraphicalAnalysis.R b/SilveR/Scripts/GraphicalAnalysis.R
@@ -926,7 +926,13 @@ if(CaseProfilesPlot == "Y" && FirstCatFactor == "NULL" && SecondCatFactor == "NU
 	graphdata$Animal_IVS<-as.factor(eval(parse(text = paste("graphdata$", CaseIDFactor))))
 	graphdata<-graphdata[order(graphdata$Animal_IVS, graphdata$Time_IVS), ]
 } else	{
-	graphdata$Animal_IVS<-paste(graphdata$l_l  , "=" , as.factor(eval(parse(text = paste("graphdata$", CaseIDFactor)))), sep = "")
+
+	if (UpdateIVS =="N") {
+		graphdata$Animal_IVS<-paste(graphdata$l_l  , "=" , as.factor(eval(parse(text = paste("graphdata$", CaseIDFactor)))), sep = "")
+	}
+	if (UpdateIVS =="Y") {
+		graphdata$Animal_IVS<-paste(as.factor(eval(parse(text = paste("graphdata$", CaseIDFactor)))), " (", graphdata$l_l , ")", sep = "")
+	}
 	graphdata<-graphdata[order(graphdata$Animal_IVS, graphdata$Time_IVS), ]
 }
 
@@ -1737,14 +1743,25 @@ Ref_list <- R_refs()
 #Bate and Clark comment
 HTML(refxx, align = "left")
 
-HTML.title("Statistical references", HR = 2, align = "left")
+if (UpdateIVS == "N") {
+	HTML.title("Statistical references", HR=2, align="left")
+}
+if (UpdateIVS == "Y") {
+	HTML.title("References", HR=2, align="left")
+	HTML(Ref_list$IVS_ref, align="left")
+}
 HTML(Ref_list$BateClark_ref, align = "left")
 
 if (BoxPlot == "Y" && is.numeric(graphdata$yvarrr_IVS) == TRUE) {
     HTML("Hyndman, R.J. and Fan, Y. (1996). Sample quantiles in statistical packages. American Statistician 50, 361-365. ", align = "left")
 }
 
-HTML.title("R references", HR = 2, align = "left")
+if (UpdateIVS == "N") {
+	HTML.title("R references", HR=2, align="left")
+}
+if (UpdateIVS == "Y") {
+	HTML.title("R references", HR=4, align="left")
+}
 HTML(Ref_list$R_ref, align = "left")
 HTML(Ref_list$GGally_ref, align = "left")
 HTML(Ref_list$RColorBrewers_ref,  align = "left")

diff --git a/SilveR/Scripts/IncompleteFactorialParametricAnalysis.R b/SilveR/Scripts/IncompleteFactorialParametricAnalysis.R
@@ -2038,7 +2038,13 @@ Ref_list<-R_refs()
 #Bate and Clark comment
 HTML(refxx,  align="left")	
 
-HTML.title("Statistical references", HR=2, align="left")
+if (UpdateIVS == "N") {
+	HTML.title("Statistical references", HR=2, align="left")
+}
+if (UpdateIVS == "Y") {
+	HTML.title("References", HR=2, align="left")
+	HTML(Ref_list$IVS_ref, align="left")
+}
 HTML(Ref_list$BateClark_ref,  align="left")
 
 if(showANOVA=="Y") {
@@ -2083,7 +2089,12 @@ if (allPairwiseTest != "NULL" | backToControlTest !="NULL") {
 	}
 }
 
-HTML.title("R references", HR=2, align="left")
+if (UpdateIVS == "N") {
+	HTML.title("R references", HR=2, align="left")
+}
+if (UpdateIVS == "Y") {
+	HTML.title("R references", HR=4, align="left")
+}
 HTML(Ref_list$R_ref ,  align="left")
 HTML(Ref_list$GGally_ref,  align="left")
 HTML(Ref_list$RColorBrewers_ref,  align="left")

diff --git a/SilveR/Scripts/LinearRegressionAnalysis.R b/SilveR/Scripts/LinearRegressionAnalysis.R
@@ -1146,7 +1146,13 @@ Ref_list<-R_refs()
 #Bate and Clark comment
 HTML(refxx, align="left")	
 
-HTML.title("Statistical references", HR=2, align="left")
+if (UpdateIVS == "N") {
+	HTML.title("Statistical references", HR=2, align="left")
+}
+if (UpdateIVS == "Y") {
+	HTML.title("References", HR=2, align="left")
+	HTML(Ref_list$IVS_ref, align="left")
+}
 HTML(Ref_list$BateClark_ref, align="left")
 
 if(showANOVA=="Y") {
@@ -1159,7 +1165,12 @@ if(covariatelist != "NULL") {
 	HTML("Morris, T.R. (1999). Experimental Design and Analysis in Animal Sciences. CABI publishing. Wallingford, Oxon (UK).", align="left")
 }
 
-HTML.title("R references", HR=2, align="left")
+if (UpdateIVS == "N") {
+	HTML.title("R references", HR=2, align="left")
+}
+if (UpdateIVS == "Y") {
+	HTML.title("R references", HR=4, align="left")
+}
 HTML(Ref_list$R_ref ,  align="left")
 HTML(Ref_list$GGally_ref,  align="left")
 HTML(Ref_list$RColorBrewers_ref,  align="left")