Merge pull request #94 from NSAPH-Software/paper_runs

Paper runs
NSAPH-Software · Jan 23, 2024 · 3530525 · 3530525
2 parents 6ecfd7f + 343b6b4
commit 3530525
Show file tree

Hide file tree

Showing 35 changed files with 659 additions and 649 deletions.
diff --git a/README.md b/README.md
@@ -73,12 +73,12 @@ Optimal hyper parameters(#trial: 300):
   alpha = 12.9154966501488   beta = 12.9154966501488   g_sigma = 0.1
 
 Optimal covariate balance: 
-  cf1 = 0.072 
+  cf1 = 0.069 
   cf2 = 0.082 
-  cf3 = 0.062 
-  cf4 = 0.068 
+  cf3 = 0.063 
+  cf4 = 0.066 
   cf5 = 0.056 
-  cf6 = 0.082
+  cf6 = 0.081
 
 Original covariate balance: 
   cf1 = 0.222 
@@ -87,7 +87,7 @@ Original covariate balance:
   cf4 = 0.318 
   cf5 = 0.198 
   cf6 = 0.257
-            ----***----       
+            ----***----      
 ```
 
 <p>
@@ -148,10 +148,10 @@ Optimal hyper parameters(#trial: 300):
   alpha = 0.0278255940220712   beta = 0.215443469003188   g_sigma = 0.1
 
 Optimal covariate balance: 
-  cf1 = 0.058 
-  cf2 = 0.071 
-  cf3 = 0.087 
-  cf4 = 0.066 
+  cf1 = 0.062 
+  cf2 = 0.070 
+  cf3 = 0.091 
+  cf4 = 0.062 
   cf5 = 0.076 
   cf6 = 0.088
 
@@ -162,7 +162,7 @@ Original covariate balance:
   cf4 = 0.296 
   cf5 = 0.208 
   cf6 = 0.225
-            ----***----                    
+            ----***----                       
 ```
 
 <p>

diff --git a/docker_singularity/Dockerfile b/docker_singularity/Dockerfile
@@ -30,9 +30,9 @@ RUN R -e "install.packages(c( \
     'rlang', \
     'Rfast', \
     'SuperLearner', \
+    'ranger', \
     'wCorr'), repos='https://cloud.r-project.org')"
 
-ENV RENV_VERSION 0.15.1
 RUN R -e "install.packages('remotes', repos = c(CRAN = 'https://cloud.r-project.org'))"
-RUN R -e "remotes::install_github('rstudio/renv@${RENV_VERSION}')"
+
 
diff --git a/docker_singularity/README.md b/docker_singularity/README.md
@@ -37,9 +37,9 @@ Run the following code to download and spin up the image.
 
 ```s
 docker run -it --rm \
-        -p 8230:8787 \
+        -p 8231:8787 \
         -e USER=rstudio \
         -e PASSWORD=pass \
-        -v "/path/to/your/folder/on/host:/home/rstudio/Project" nsaphsoftware/gpcerf_dev
+        -v $PWD:/home/rstudio/Project nsaphsoftware/gpcerf_dev
 
 ```
diff --git a/functional_tests/README.md b/functional_tests/README.md
diff --git a/functional_tests/ft_compute_deriv_nn.R b/functional_tests/ft_compute_deriv_nn.R
diff --git a/functional_tests/ft_compute_derive_weights_gp.R b/functional_tests/ft_compute_derive_weights_gp.R
diff --git a/functional_tests/ft_compute_inverse.R b/functional_tests/ft_compute_inverse.R
diff --git a/functional_tests/ft_compute_m_sigma.R b/functional_tests/ft_compute_m_sigma.R
diff --git a/functional_tests/ft_compute_posterior_m_nn.R b/functional_tests/ft_compute_posterior_m_nn.R
diff --git a/functional_tests/ft_compute_posterior_sd_nn.R b/functional_tests/ft_compute_posterior_sd_nn.R
diff --git a/functional_tests/ft_compute_sd_gp.R b/functional_tests/ft_compute_sd_gp.R
diff --git a/functional_tests/ft_compute_w_corr.R b/functional_tests/ft_compute_w_corr.R
diff --git a/functional_tests/ft_compute_weight_gp.R b/functional_tests/ft_compute_weight_gp.R
diff --git a/functional_tests/ft_estimate_mean_sd_nn.R b/functional_tests/ft_estimate_mean_sd_nn.R