diff --git a/mechanisticModel.tar.gz b/mechanisticModel.tar.gz
deleted file mode 100644
index a1a31b21f4475784e39e292129d77a33c48ca39a..0000000000000000000000000000000000000000
Binary files a/mechanisticModel.tar.gz and /dev/null differ
diff --git a/mechanisticModel_1.5.6.tar.gz b/mechanisticModel_1.5.6.tar.gz
new file mode 100644
index 0000000000000000000000000000000000000000..b06dd8920ab68c8e2637721c2fc7b17056333ec4
Binary files /dev/null and b/mechanisticModel_1.5.6.tar.gz differ
diff --git a/output/identif_alpha_mu_0.05.Rdata b/output/identif_alpha_mu_0.05.Rdata
deleted file mode 100644
index 8428c4573dcca3cc89e5735e9a8032f8a9a41a7b..0000000000000000000000000000000000000000
Binary files a/output/identif_alpha_mu_0.05.Rdata and /dev/null differ
diff --git a/output/identif_alpha_mu_0.542.Rdata b/output/identif_alpha_mu_0.542.Rdata
deleted file mode 100644
index c46dbac3aa5be6c367833ea3b834aad3c6911821..0000000000000000000000000000000000000000
Binary files a/output/identif_alpha_mu_0.542.Rdata and /dev/null differ
diff --git a/output/identif_alpha_mu_1.Rdata b/output/identif_alpha_mu_1.Rdata
deleted file mode 100644
index 8dc256519a61130296dea233769588c83ecffd2a..0000000000000000000000000000000000000000
Binary files a/output/identif_alpha_mu_1.Rdata and /dev/null differ
diff --git a/output/identifi_alpha_0.05.Rdata b/output/identifi_alpha_0.05.Rdata
deleted file mode 100644
index 70e5e818af6741072615daa7636c8d97dcac5011..0000000000000000000000000000000000000000
Binary files a/output/identifi_alpha_0.05.Rdata and /dev/null differ
diff --git a/output/identifi_alpha_0.542.Rdata b/output/identifi_alpha_0.542.Rdata
deleted file mode 100644
index c3a4e762a444ed7c678ec369a46e049c48591b32..0000000000000000000000000000000000000000
Binary files a/output/identifi_alpha_0.542.Rdata and /dev/null differ
diff --git a/output/identifi_alpha_1.Rdata b/output/identifi_alpha_1.Rdata
deleted file mode 100644
index 779100d7acbe9ba4784fe42cc7bd323e081d0135..0000000000000000000000000000000000000000
Binary files a/output/identifi_alpha_1.Rdata and /dev/null differ
diff --git a/output/identifi_mu_0.05.Rdata b/output/identifi_mu_0.05.Rdata
deleted file mode 100644
index 4d861d5a9f2d70c9a0403e98363a7d605255de72..0000000000000000000000000000000000000000
Binary files a/output/identifi_mu_0.05.Rdata and /dev/null differ
diff --git a/output/identifi_mu_0.542.Rdata b/output/identifi_mu_0.542.Rdata
deleted file mode 100644
index 631d6f48dcc6f584d5fc36d61adceca536ca27a1..0000000000000000000000000000000000000000
Binary files a/output/identifi_mu_0.542.Rdata and /dev/null differ
diff --git a/output/identifi_mu_1.Rdata b/output/identifi_mu_1.Rdata
deleted file mode 100644
index c38e461e174c04b69c3bcd96d4050bd645bec1dc..0000000000000000000000000000000000000000
Binary files a/output/identifi_mu_1.Rdata and /dev/null differ
diff --git a/settings.json b/settings.json
index 104c7a65294219782d2c76a5a6dd014fadaf20b1..fd702c23cbf84c009b215338d6caeae0fc2a9ac8 100644
--- a/settings.json
+++ b/settings.json
@@ -1,6 +1,6 @@
{
"analysis_name": "Identifi",
- "r_script": "identif_mu.R",
+ "r_script": "identifiabilite.R",
"py_env": "base",
"reticulate_env": "",
"logfile": "install.log",
@@ -18,7 +18,7 @@
"lib": ""
},
"dependencies": {
- "R-local": ["mechanisticModel.tar.gz"],
+ "R-local": ["mechanisticModel_1.5.6.tar.gz"],
"R": ["glue","doParallel"],
"reticulate": [],
"python": []
diff --git a/src/identif_alpha.R b/src/identif_alpha.R
index 413deb92a807c13ec0b3eba08606bc40e3b2974d..a8b2d8d60c15557b2286616c3762e5a761890d3d 100644
--- a/src/identif_alpha.R
+++ b/src/identif_alpha.R
@@ -5,22 +5,18 @@ library(doParallel)
-control <- saemix::saemixControl(map = FALSE,fix.seed = T, fim = FALSE, ll.is = FALSE, nbiter.saemix = c(300, 50), nb.chains = 1, nbiter.burn = 5, nbiter.mcmc = c(2, 2, 2, 0), displayProgress = FALSE, print= FALSE, save = FALSE, nbdisplay = 50)
+control <- saemix::saemixControl(map = FALSE,fix.seed = T, fim = FALSE, ll.is = FALSE, nbiter.saemix = c(300, 50), nb.chains = 1, nbiter.burn = 5, nbiter.mcmc = c(2, 2, 2, 0), displayProgress = FALSE, print= FALSE, save = FALSE, nbdisplay = 50, save.graphs = F)
alpha_pop = exp(-6.34)
mu_pop = exp(-26.8)
sigma = 1
-omega_alpha = 1
-omega_mu = 0
+omega_alpha = 3.37
+omega_mu = 3.78
-true_v = c(alpha_pop,mu_pop,sigma,omega_alpha,omega_mu)
+true_v = c(alpha_pop,mu_pop,sigma,omega_alpha,omega_mu)
-alpha <- c()
-mu <- c()
-omega_alpha <- c()
-omega_mu <- c()
Ncpus <- parallel::detectCores() - 1
cl <- parallel::makeCluster(Ncpus)
@@ -40,17 +36,23 @@ res <- foreach::foreach(i=1:100 , .packages = c("tidyverse","mechanisticModel"))
Surv(tps, event) ~ TTR(vdiag),
log(alpha) ~ 1, log(mu) ~ 1,
data = JD1,
- alpha_0 = 0.001, mu_0 = 2e-12, sigma_0 = 1, omega_0 = c(1, 0),
+ alpha_0 = 0.001, mu_0 = 2e-12, sigma_0 = sigma, omega_0 = c(3.37, 1),
beta_0 = list(alpha = numeric(), mu = numeric()),
options = control
)
- m = fit(m, silent = T, N_sim_surv = 0)
+ m = fit(m, silent = T, N_sim_surv = 0, omega.estim = c(1, 0), fixed.estim = c(1, 0, 0))
}
parallel::stopCluster(cl)
+alpha <- c()
+mu <- c()
+omega_alpha <- c()
+omega_mu <- c()
+
+
for(i in 1:100){
alpha <- append(alpha,unlist(res[[i]]$coefs[1])[1])
mu <- append(mu,unlist(res[[i]]$coefs[1])[2])
diff --git a/src/identif_mu.R b/src/identif_mu.R
index 3e1494cec0c61b6ed098c3f336c678a92b73e031..d8f0b7349d7dd0b584db9199c13a8f9a786b9e0f 100644
--- a/src/identif_mu.R
+++ b/src/identif_mu.R
@@ -5,34 +5,27 @@ library(doParallel)
-control <- saemix::saemixControl(map = FALSE,fix.seed = T, fim = FALSE, ll.is = FALSE, nbiter.saemix = c(300, 50), nb.chains = 1, nbiter.burn = 5, nbiter.mcmc = c(2, 2, 2, 0), displayProgress = FALSE, print= FALSE, save = FALSE, nbdisplay = 50)
+control <- saemix::saemixControl(map = FALSE,fix.seed = T, fim = FALSE, ll.is = FALSE, nbiter.saemix = c(300, 50), nb.chains = 1, nbiter.burn = 5, nbiter.mcmc = c(2, 2, 2, 0), displayProgress = FALSE, print= FALSE, save = FALSE, nbdisplay = 50, save.graphs = F)
alpha_pop = exp(-6.34)
mu_pop = exp(-26.8)
sigma = 1
-omega_alpha = 0
-omega_mu = 1
+omega_alpha = 3.37
+omega_mu = 3.78
true_v = c(alpha_pop,mu_pop,sigma,omega_alpha,omega_mu)
-
-
-alpha <- c()
-mu <- c()
-omega_alpha <- c()
-omega_mu <- c()
-
Ncpus <- parallel::detectCores() - 1
cl <- parallel::makeCluster(Ncpus)
doParallel::registerDoParallel(cl)
-res <- foreach::foreach(i=1:100 , .packages = c("tidyverse","mechanisticModel"))%dopar%{
+res <- foreach::foreach(i=1:100, .packages = c("tidyverse","mechanisticModel"))%dopar%{
set.seed(i)
control$seed <- i
- JD1 <- GDC(1000,22.38,1.33,exp(-6.34),exp(-26.8),1,0,1,20*365)
+ JD1 <- GDC(1000,22.38,1.33,exp(-6.34),exp(-26.8),1,3.37,3.78,20*365)
JD1 <- JD1 %>% filter(tps > 0)
@@ -40,16 +33,20 @@ res <- foreach::foreach(i=1:100 , .packages = c("tidyverse","mechanisticModel"))
Surv(tps, event) ~ TTR(vdiag),
log(alpha) ~ 1, log(mu) ~ 1,
data = JD1,
- alpha_0 = 0.001, mu_0 = 2e-12, sigma_0 = 1, omega_0 = c(0, 1),
+ alpha_0 = 0.001, mu_0 = 2e-12, sigma_0 = sigma, omega_0 = c(1, 3.78),
beta_0 = list(alpha = numeric(), mu = numeric()),
options = control
)
- m = fit(m, silent = T, N_sim_surv = 0)
+ m = fit(m, silent = T, N_sim_surv = 0, omega.estim = c(0, 1), fixed.estim = c(0, 1, 0))
}
parallel::stopCluster(cl)
+alpha <- c()
+mu <- c()
+omega_alpha <- c()
+omega_mu <- c()
for(i in 1:100){
alpha <- append(alpha,unlist(res[[i]]$coefs[1])[1])
diff --git a/src/identifiabilite.R b/src/identifiabilite.R
index 4ea7939a327a09a6675f14b815b4f6f5e3e2c97e..072fa0b0e1a2aed913c07d976e04023e98f899e7 100644
--- a/src/identifiabilite.R
+++ b/src/identifiabilite.R
@@ -5,7 +5,7 @@ library(doParallel)
-control <- saemix::saemixControl(map = FALSE,fix.seed = T, fim = FALSE, ll.is = FALSE, nbiter.saemix = c(300, 50), nb.chains = 1, nbiter.burn = 5, nbiter.mcmc = c(2, 2, 2, 0), displayProgress = FALSE, print= FALSE, save = FALSE, nbdisplay = 50)
+control <- saemix::saemixControl(map = FALSE,fix.seed = T, fim = FALSE, ll.is = FALSE, nbiter.saemix = c(300, 50), nb.chains = 1, nbiter.burn = 5, nbiter.mcmc = c(2, 2, 2, 0), displayProgress = FALSE, print= FALSE, save = FALSE, nbdisplay = 50, save.graphs = F)
alpha_pop = exp(-6.34)
mu_pop = exp(-26.8)
@@ -15,13 +15,6 @@ omega_mu = 3.78
true_v = c(alpha_pop,mu_pop,sigma,omega_alpha,omega_mu)
-
-
-alpha <- c()
-mu <- c()
-omega_alpha <- c()
-omega_mu <- c()
-
Ncpus <- parallel::detectCores() - 1
cl <- parallel::makeCluster(Ncpus)
doParallel::registerDoParallel(cl)
@@ -40,17 +33,22 @@ res <- foreach::foreach(i=1:100 , .packages = c("tidyverse","mechanisticModel"))
Surv(tps, event) ~ TTR(vdiag),
log(alpha) ~ 1, log(mu) ~ 1,
data = JD1,
- alpha_0 = 0.001, mu_0 = 2e-12, sigma_0 = 1, omega_0 = c(3, 3),
+ alpha_0 = 0.001, mu_0 = 2e-12, sigma_0 = sigma, omega_0 = c(3, 3),
beta_0 = list(alpha = numeric(), mu = numeric()),
options = control
)
- m = fit(m, silent = T, N_sim_surv = 0)
+ m = fit(m, silent = T, N_sim_surv = 0, omega.estim = c(1, 1), fixed.estim = c(1, 1, 0))
}
parallel::stopCluster(cl)
+alpha <- c()
+mu <- c()
+omega_alpha <- c()
+omega_mu <- c()
+
for(i in 1:100){
alpha <- append(alpha,unlist(res[[i]]$coefs[1])[1])
mu <- append(mu,unlist(res[[i]]$coefs[1])[2])