From 29efa02528337314d5f1afe851f14f2371c6958a Mon Sep 17 00:00:00 2001
From: Paul-Corbalan <58653590+Paul-Corbalan@users.noreply.github.com>
Date: Tue, 10 May 2022 11:30:40 +0200
Subject: [PATCH 1/2] Add tau_scan, tau_H1 in CompareMethods

---
 Comparaison_of_methods.rmd | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/Comparaison_of_methods.rmd b/Comparaison_of_methods.rmd
index 92e04d0..9eb4225 100644
--- a/Comparaison_of_methods.rmd
+++ b/Comparaison_of_methods.rmd
@@ -380,7 +380,7 @@ LocalScoreMC <- function(lambda0, lambda1, NbSeq, T, X_seq, P_X, tbe0){
 
 ## 4. Experience plan for comparaison
 ```{r}
-CompareMethods <- function(lambda0, lambda1, NbSeq, T, tau){
+CompareMethods <- function(lambda0, lambda1, NbSeq, T, tau_scan, tau_H1){
     if (lambda0 < lambda1){
         
         cat("For T = ", T, ", Nb = ", NbSeq, ", lambda0 = ", lambda0, " and lambda1 = ", lambda1, ":\n", sep = "")
@@ -398,7 +398,7 @@ CompareMethods <- function(lambda0, lambda1, NbSeq, T, tau){
             tbe0[[i]] = tbei
             
             #Simulation for sequences under H1
-            ppj1 = SimulationH1(lambda0, lambda1, T, 3)
+            ppj1 = SimulationH1(lambda0, lambda1, T, tau_H1)
             nj = length(ppj1)
             pp1[[i]] = ppj1
             tbej = ppj1[2:nj]-ppj1[1:nj-1]
@@ -412,9 +412,9 @@ CompareMethods <- function(lambda0, lambda1, NbSeq, T, tau){
         LS_obtained = c(LS_H0$class, LS_H1$class)
         options(warn = -1) 
           
-        Emp = EmpDistrib(lambda0,10**4,T,tau)
-        SS_H0 = ScanStatMC(NbSeq, T, tau, Emp, pp0)
-        SS_H1 = ScanStatMC(NbSeq, T, tau, Emp, pp1)
+        # Emp = EmpDistrib(lambda0, 10**4, T, tau_scan)
+        SS_H0 = ScanStatMC(NbSeq, T, tau_scan, Emp, pp0)
+        SS_H1 = ScanStatMC(NbSeq, T, tau_scan, Emp, pp1)
         SS_obtained = c(SS_H0$class, SS_H1$class)
           
                     

From 0054d077be4d9c6752e6e8f9800da8bacf0f4f85 Mon Sep 17 00:00:00 2001
From: Paul-Corbalan <58653590+Paul-Corbalan@users.noreply.github.com>
Date: Tue, 10 May 2022 18:45:12 +0200
Subject: [PATCH 2/2] Add NbSeq.NonNulles to LocalScoreMC

---
 Comparaison_of_methods.rmd | 40 +++++++++++++++++++++-----------------
 1 file changed, 22 insertions(+), 18 deletions(-)

diff --git a/Comparaison_of_methods.rmd b/Comparaison_of_methods.rmd
index 9eb4225..0aaf67c 100644
--- a/Comparaison_of_methods.rmd
+++ b/Comparaison_of_methods.rmd
@@ -356,24 +356,28 @@ plot_graph_distrib_score(distrib_score_theo, distrib_score_mc)
 ### 3.2. Local score calculation
 ```{r}
 LocalScoreMC <- function(lambda0, lambda1, NbSeq, T, X_seq, P_X, tbe0){
-  E = ComputeE(lambda0, lambda1)
-  
-  pvalue = c()
-  X = c()
-  
-  min_X = min(X_seq)
-  max_X = max(X_seq)
-  
-  for (i in 1:NbSeq){
-      x = floor(E*log(dexp(tbe0[[i]], rate = lambda1)/dexp(tbe0[[i]], rate = lambda0)))
-      LS = localScoreC(x)$localScore[1]
-      
-      daudin_result = daudin(localScore = LS, score_probabilities = P_X, sequence_length = length(x), sequence_min = min_X, sequence_max = max_X)
-      options(warn = -1) # Disable warnings print
-      
-      pvalue = c(pvalue, daudin_result)
+    E = ComputeE(lambda0, lambda1)
+
+    pvalue = c()
+
+    min_X = min(X_seq)
+    max_X = max(X_seq)
+
+    NbSeq.NonNulles = 0
+
+    for (i in 1:NbSeq){
+        x = floor(E*log(dexp(tbe0[[i]], rate = lambda1)/dexp(tbe0[[i]], rate = lambda0)))
+        if (length(x)!=0){
+            LS = localScoreC(x)$localScore[1]
+
+            daudin_result = daudin(localScore = LS, score_probabilities = P_X, sequence_length = length(x), sequence_min = min_X, sequence_max = max_X)
+            options(warn = -1) # Disable warnings print
+
+            pvalue = c(pvalue, daudin_result)
+            NbSeq.NonNulles = NbSeq.NonNulles + 1
+        }
   }
-  LS_H0=data.frame(num=1:NbSeq, pvalue_scan=pvalue, class=as.numeric(pvalue<0.05))
+  LS_H0=data.frame(num=1:NbSeq.NonNulles, pvalue_scan=pvalue, class=as.numeric(pvalue<0.05))
   return(LS_H0)
 }
 ```
@@ -451,7 +455,7 @@ CompareMethods <- function(lambda0, lambda1, NbSeq, T, tau_scan, tau_H1){
 ```
 
 ```{r}
-NbSeq = 10**2
+NbSeq = 10**4
 T = 10
 tau = 2