update before more serious tests

snaketron · Mar 25, 2024 · 936fed9 · 936fed9
1 parent 451f61a
commit 936fed9
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Showing 3 changed files with 25 additions and 7 deletions.
diff --git a/data/d_zibb_4.RData b/data/d_zibb_4.RData
diff --git a/inst/scripts/d_zibb_4.R b/inst/scripts/d_zibb_4.R
@@ -21,7 +21,6 @@ data {
   array [N_sample] int N;                  // repertoire size
   array [N_individual] int condition_id;   // id of conditions
   array [N_sample] int individual_id;      // id of replicate
-  vector [N_gene] alpha;
   real <lower=0> phi;
   real <lower=0, upper=1> kappa;
   array [N_condition] vector [N_gene] beta_condition;
@@ -31,13 +30,17 @@ data {
 }
 
 generated quantities {
+  vector [N_gene] alpha;
   array [N_sample] vector <lower=0, upper=1> [N_gene] theta;
   array [N_sample] vector [N_gene] beta_sample;
   array [N_individual] vector [N_gene] beta_individual;
-  
   // generate usage
   array [N_gene, N_sample] int Y;
   
+  for(i in 1:N_gene) {
+    alpha[i] = normal_rng(-3, 3);
+  }
+  
   for(i in 1:N_individual) {
     for(j in 1:N_gene) {
       beta_individual[i][j] = normal_rng(beta_condition[condition_id[i]][j], sigma_individual[condition_id[i]]);
@@ -88,8 +91,6 @@ N <- rep(x = 1000, times = N_sample)
 
 individual_id <- rep(x = 1:N_individual, each = N_replicates)
 
-alpha <- rnorm(n = N_gene, mean = -5, sd = 3)
-
 phi <- 200
 
 kappa <- 0.02
@@ -118,7 +119,6 @@ l <- list(N_sample = N_sample,
           N = N,
           condition_id = condition_id,
           individual_id = individual_id,
-          alpha = alpha,
           phi = phi,
           kappa = kappa,
           beta_condition = beta_condition,
@@ -168,7 +168,11 @@ d_zibb_4 <- ysim_df
 save(d_zibb_4, file = "data/d_zibb_4.RData", compress = T)
 
 
+# save(sim, file = "mytests/sim_d_zibb_4.RData", compress = T)
 # ggplot(data = d_zibb_4)+
 #   geom_sina(aes(x = gene_name, y = gene_usage_count, col = condition))+
 #   theme_bw(base_size = 10)+
 #   theme(legend.position = "none")
+
+s <- data.frame(summary(sim)$summary)
+s$par <- rownames(s)
diff --git a/vignettes/User_Manual.Rmd b/vignettes/User_Manual.Rmd
@@ -548,8 +548,22 @@ g2 <- ggplot(data = stats)+
 ```
 
 
-# Case Study C: analyzing paired-IRRs
-Stub, to be continued ...
+<!-- # Case Study C: analyzing paired-IRRs -->
+<!-- Stub, to be continued ... -->
+
+<!-- ```{r} -->
+<!-- M <- DGU(ud = d_zibb_2, # input data -->
+<!--          mcmc_warmup = 500, # how many MCMC warm-ups per chain (default: 500) -->
+<!--          mcmc_steps = 1500, # how many MCMC steps per chain (default: 1,500) -->
+<!--          mcmc_chains = 3, # how many MCMC chain to run (default: 4) -->
+<!--          mcmc_cores = 1, # how many PC cores to use? (e.g. parallel chains) -->
+<!--          hdi_lvl = 0.95, # highest density interval level (de fault: 0.95) -->
+<!--          adapt_delta = 0.8, # MCMC target acceptance rate (default: 0.95) -->
+<!--          max_treedepth = 10, # tree depth evaluated at each step (default: 12) -->
+<!--          paired = TRUE)  -->
+<!-- ``` -->
+
+
 
 # Session