From be583aa6d6c82d08792fbf1d4d90e87ac9ae2d35 Mon Sep 17 00:00:00 2001 From: hillalex Date: Thu, 24 Oct 2024 14:40:22 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20seroanal?= =?UTF-8?q?ytics/epikinetics@265ac4ac02004c0bb7db47f39abd2de993527fe7=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- 404.html | 2 +- LICENSE.html | 2 +- articles/biokinetics.html | 162 +++++------ articles/data.html | 2 +- articles/index.html | 4 +- articles/model.html | 325 +++++++++++++++++++++- authors.html | 2 +- index.html | 2 +- pkgdown.yml | 2 +- reference/add_exposure_data.html | 2 +- reference/biokinetics.html | 2 +- reference/biokinetics_priors.html | 2 +- reference/convert_log2_scale_inverse.html | 2 +- reference/epikinetics-package.html | 2 +- reference/index.html | 2 +- 15 files changed, 414 insertions(+), 101 deletions(-) diff --git a/404.html b/404.html index b3a82ec..a30b39f 100644 --- a/404.html +++ b/404.html @@ -55,7 +55,7 @@ A guide to model input and output data
  • - Model + Summary of the Stan Model
    • diff --git a/LICENSE.html b/LICENSE.html index ad501d8..493973e 100644 --- a/LICENSE.html +++ b/LICENSE.html @@ -38,7 +38,7 @@ A guide to model input and output data
  • - Model + Summary of the Stan Model
    • diff --git a/articles/biokinetics.html b/articles/biokinetics.html index 52d4113..c44c5d7 100644 --- a/articles/biokinetics.html +++ b/articles/biokinetics.html @@ -55,7 +55,7 @@ A guide to model input and output data
  • - Model + Summary of the Stan Model
    • @@ -120,9 +120,9 @@

    Figure 2 
     res <- mod$simulate_population_trajectories()
-#> INFO [2024-10-23 12:39:32] Summarising fits
-#> INFO [2024-10-23 12:39:35] Adjusting by regression coefficients
-#> INFO [2024-10-23 12:39:38] Summarising into quantiles
+#> INFO [2024-10-24 14:38:25] Summarising fits
+#> INFO [2024-10-24 14:38:29] Adjusting by regression coefficients
+#> INFO [2024-10-24 14:38:31] Summarising into quantiles
 head(res)
 #>    time_since_last_exp       me        lo       hi titre_type infection_history
 #>                  <int>    <num>     <num>    <num>     <char>            <char>
@@ -191,11 +191,11 @@ 
    Figure 4
 
     res <- mod$population_stationary_points(n_draws = 2000)
-#> INFO [2024-10-23 12:39:39] Extracting parameters
-#> INFO [2024-10-23 12:39:39] Adjusting by covariates
-#> INFO [2024-10-23 12:39:39] Calculating peak and switch titre values
-#> INFO [2024-10-23 12:39:39] Recovering covariate names
-#> INFO [2024-10-23 12:39:39] Calculating medians
+#> INFO [2024-10-24 14:38:32] Extracting parameters
+#> INFO [2024-10-24 14:38:33] Adjusting by covariates
+#> INFO [2024-10-24 14:38:33] Calculating peak and switch titre values
+#> INFO [2024-10-24 14:38:33] Recovering covariate names
+#> INFO [2024-10-24 14:38:33] Calculating medians
 head(res)
 #>    infection_history titre_type     mu_p     mu_s rel_drop_me  mu_p_me  mu_s_me
 #>               <char>     <char>    <num>    <num>       <num>    <num>    <num>
@@ -261,15 +261,15 @@ 
    Figure 5
 
     res <- mod$simulate_individual_trajectories(n_draws = 250)
-#> INFO [2024-10-23 12:39:40] Extracting parameters
-#> INFO [2024-10-23 12:39:44] Simulating individual trajectories
-#> INFO [2024-10-23 12:39:48] Recovering covariate names
-#> INFO [2024-10-23 12:39:49] Calculating exposure days. Adjusting exposures by 0 days
-#> INFO [2024-10-23 12:39:52] Resampling
+#> INFO [2024-10-24 14:38:34] Extracting parameters
+#> INFO [2024-10-24 14:38:38] Simulating individual trajectories
+#> INFO [2024-10-24 14:38:42] Recovering covariate names
+#> INFO [2024-10-24 14:38:42] Calculating exposure days. Adjusting exposures by 0 days
+#> INFO [2024-10-24 14:38:45] Resampling
 #> Registered S3 method overwritten by 'mosaic':
 #>   method                           from   
 #>   fortify.SpatialPolygonsDataFrame ggplot2
-#> INFO [2024-10-23 12:40:02] Summarising into population quantiles
+#> INFO [2024-10-24 14:38:55] Summarising into population quantiles
 head(res)
 #>    calendar_day titre_type       me       lo       hi time_shift
 #>          <IDat>     <char>    <num>    <num>    <num>      <num>
@@ -348,72 +348,72 @@ 
    Figure 5  shift <- time_shift_values[index]
   mod$simulate_individual_trajectories(n_draws = 50, time_shift = shift)
 })
-#> INFO [2024-10-23 12:40:03] Extracting parameters
-#> INFO [2024-10-23 12:40:06] Simulating individual trajectories
-#> INFO [2024-10-23 12:40:07] Recovering covariate names
-#> INFO [2024-10-23 12:40:07] Calculating exposure days. Adjusting exposures by -75 days
-#> INFO [2024-10-23 12:40:08] Resampling
-#> INFO [2024-10-23 12:40:10] Summarising into population quantiles
-#> INFO [2024-10-23 12:40:10] Extracting parameters
-#> INFO [2024-10-23 12:40:14] Simulating individual trajectories
-#> INFO [2024-10-23 12:40:14] Recovering covariate names
-#> INFO [2024-10-23 12:40:14] Calculating exposure days. Adjusting exposures by -60 days
-#> INFO [2024-10-23 12:40:15] Resampling
-#> INFO [2024-10-23 12:40:17] Summarising into population quantiles
-#> INFO [2024-10-23 12:40:17] Extracting parameters
-#> INFO [2024-10-23 12:40:21] Simulating individual trajectories
-#> INFO [2024-10-23 12:40:21] Recovering covariate names
-#> INFO [2024-10-23 12:40:21] Calculating exposure days. Adjusting exposures by -45 days
-#> INFO [2024-10-23 12:40:22] Resampling
-#> INFO [2024-10-23 12:40:23] Summarising into population quantiles
-#> INFO [2024-10-23 12:40:24] Extracting parameters
-#> INFO [2024-10-23 12:40:27] Simulating individual trajectories
-#> INFO [2024-10-23 12:40:28] Recovering covariate names
-#> INFO [2024-10-23 12:40:28] Calculating exposure days. Adjusting exposures by -30 days
-#> INFO [2024-10-23 12:40:28] Resampling
-#> INFO [2024-10-23 12:40:30] Summarising into population quantiles
-#> INFO [2024-10-23 12:40:31] Extracting parameters
-#> INFO [2024-10-23 12:40:34] Simulating individual trajectories
-#> INFO [2024-10-23 12:40:35] Recovering covariate names
-#> INFO [2024-10-23 12:40:35] Calculating exposure days. Adjusting exposures by -15 days
-#> INFO [2024-10-23 12:40:35] Resampling
-#> INFO [2024-10-23 12:40:37] Summarising into population quantiles
-#> INFO [2024-10-23 12:40:38] Extracting parameters
-#> INFO [2024-10-23 12:40:41] Simulating individual trajectories
-#> INFO [2024-10-23 12:40:42] Recovering covariate names
-#> INFO [2024-10-23 12:40:42] Calculating exposure days. Adjusting exposures by 0 days
-#> INFO [2024-10-23 12:40:43] Resampling
-#> INFO [2024-10-23 12:40:45] Summarising into population quantiles
-#> INFO [2024-10-23 12:40:45] Extracting parameters
-#> INFO [2024-10-23 12:40:49] Simulating individual trajectories
-#> INFO [2024-10-23 12:40:49] Recovering covariate names
-#> INFO [2024-10-23 12:40:49] Calculating exposure days. Adjusting exposures by 15 days
-#> INFO [2024-10-23 12:40:50] Resampling
-#> INFO [2024-10-23 12:40:52] Summarising into population quantiles
-#> INFO [2024-10-23 12:40:53] Extracting parameters
-#> INFO [2024-10-23 12:40:56] Simulating individual trajectories
-#> INFO [2024-10-23 12:40:57] Recovering covariate names
-#> INFO [2024-10-23 12:40:57] Calculating exposure days. Adjusting exposures by 30 days
-#> INFO [2024-10-23 12:40:57] Resampling
-#> INFO [2024-10-23 12:40:59] Summarising into population quantiles
-#> INFO [2024-10-23 12:41:00] Extracting parameters
-#> INFO [2024-10-23 12:41:03] Simulating individual trajectories
-#> INFO [2024-10-23 12:41:04] Recovering covariate names
-#> INFO [2024-10-23 12:41:04] Calculating exposure days. Adjusting exposures by 45 days
-#> INFO [2024-10-23 12:41:04] Resampling
-#> INFO [2024-10-23 12:41:06] Summarising into population quantiles
-#> INFO [2024-10-23 12:41:07] Extracting parameters
-#> INFO [2024-10-23 12:41:10] Simulating individual trajectories
-#> INFO [2024-10-23 12:41:11] Recovering covariate names
-#> INFO [2024-10-23 12:41:11] Calculating exposure days. Adjusting exposures by 60 days
-#> INFO [2024-10-23 12:41:11] Resampling
-#> INFO [2024-10-23 12:41:13] Summarising into population quantiles
-#> INFO [2024-10-23 12:41:14] Extracting parameters
-#> INFO [2024-10-23 12:41:17] Simulating individual trajectories
-#> INFO [2024-10-23 12:41:18] Recovering covariate names
-#> INFO [2024-10-23 12:41:18] Calculating exposure days. Adjusting exposures by 75 days
-#> INFO [2024-10-23 12:41:18] Resampling
-#> INFO [2024-10-23 12:41:20] Summarising into population quantiles
+#> INFO [2024-10-24 14:38:56] Extracting parameters
+#> INFO [2024-10-24 14:39:00] Simulating individual trajectories
+#> INFO [2024-10-24 14:39:01] Recovering covariate names
+#> INFO [2024-10-24 14:39:01] Calculating exposure days. Adjusting exposures by -75 days
+#> INFO [2024-10-24 14:39:01] Resampling
+#> INFO [2024-10-24 14:39:03] Summarising into population quantiles
+#> INFO [2024-10-24 14:39:04] Extracting parameters
+#> INFO [2024-10-24 14:39:07] Simulating individual trajectories
+#> INFO [2024-10-24 14:39:08] Recovering covariate names
+#> INFO [2024-10-24 14:39:08] Calculating exposure days. Adjusting exposures by -60 days
+#> INFO [2024-10-24 14:39:08] Resampling
+#> INFO [2024-10-24 14:39:10] Summarising into population quantiles
+#> INFO [2024-10-24 14:39:11] Extracting parameters
+#> INFO [2024-10-24 14:39:14] Simulating individual trajectories
+#> INFO [2024-10-24 14:39:15] Recovering covariate names
+#> INFO [2024-10-24 14:39:15] Calculating exposure days. Adjusting exposures by -45 days
+#> INFO [2024-10-24 14:39:15] Resampling
+#> INFO [2024-10-24 14:39:17] Summarising into population quantiles
+#> INFO [2024-10-24 14:39:18] Extracting parameters
+#> INFO [2024-10-24 14:39:21] Simulating individual trajectories
+#> INFO [2024-10-24 14:39:22] Recovering covariate names
+#> INFO [2024-10-24 14:39:22] Calculating exposure days. Adjusting exposures by -30 days
+#> INFO [2024-10-24 14:39:22] Resampling
+#> INFO [2024-10-24 14:39:24] Summarising into population quantiles
+#> INFO [2024-10-24 14:39:24] Extracting parameters
+#> INFO [2024-10-24 14:39:28] Simulating individual trajectories
+#> INFO [2024-10-24 14:39:28] Recovering covariate names
+#> INFO [2024-10-24 14:39:29] Calculating exposure days. Adjusting exposures by -15 days
+#> INFO [2024-10-24 14:39:29] Resampling
+#> INFO [2024-10-24 14:39:31] Summarising into population quantiles
+#> INFO [2024-10-24 14:39:32] Extracting parameters
+#> INFO [2024-10-24 14:39:35] Simulating individual trajectories
+#> INFO [2024-10-24 14:39:36] Recovering covariate names
+#> INFO [2024-10-24 14:39:36] Calculating exposure days. Adjusting exposures by 0 days
+#> INFO [2024-10-24 14:39:36] Resampling
+#> INFO [2024-10-24 14:39:38] Summarising into population quantiles
+#> INFO [2024-10-24 14:39:39] Extracting parameters
+#> INFO [2024-10-24 14:39:42] Simulating individual trajectories
+#> INFO [2024-10-24 14:39:43] Recovering covariate names
+#> INFO [2024-10-24 14:39:43] Calculating exposure days. Adjusting exposures by 15 days
+#> INFO [2024-10-24 14:39:43] Resampling
+#> INFO [2024-10-24 14:39:45] Summarising into population quantiles
+#> INFO [2024-10-24 14:39:46] Extracting parameters
+#> INFO [2024-10-24 14:39:50] Simulating individual trajectories
+#> INFO [2024-10-24 14:39:50] Recovering covariate names
+#> INFO [2024-10-24 14:39:50] Calculating exposure days. Adjusting exposures by 30 days
+#> INFO [2024-10-24 14:39:51] Resampling
+#> INFO [2024-10-24 14:39:53] Summarising into population quantiles
+#> INFO [2024-10-24 14:39:53] Extracting parameters
+#> INFO [2024-10-24 14:39:57] Simulating individual trajectories
+#> INFO [2024-10-24 14:39:57] Recovering covariate names
+#> INFO [2024-10-24 14:39:57] Calculating exposure days. Adjusting exposures by 45 days
+#> INFO [2024-10-24 14:39:58] Resampling
+#> INFO [2024-10-24 14:40:00] Summarising into population quantiles
+#> INFO [2024-10-24 14:40:00] Extracting parameters
+#> INFO [2024-10-24 14:40:03] Simulating individual trajectories
+#> INFO [2024-10-24 14:40:04] Recovering covariate names
+#> INFO [2024-10-24 14:40:04] Calculating exposure days. Adjusting exposures by 60 days
+#> INFO [2024-10-24 14:40:05] Resampling
+#> INFO [2024-10-24 14:40:07] Summarising into population quantiles
+#> INFO [2024-10-24 14:40:07] Extracting parameters
+#> INFO [2024-10-24 14:40:10] Simulating individual trajectories
+#> INFO [2024-10-24 14:40:11] Recovering covariate names
+#> INFO [2024-10-24 14:40:11] Calculating exposure days. Adjusting exposures by 75 days
+#> INFO [2024-10-24 14:40:12] Resampling
+#> INFO [2024-10-24 14:40:13] Summarising into population quantiles
 
 combined_data <- data.table::data.table(data.table::rbindlist(results_list))
    
 
    Plotting the median values:
    
diff --git a/articles/data.html b/articles/data.html
index fd8d3f2..4b49a31 100644
--- a/articles/data.html
+++ b/articles/data.html
@@ -55,7 +55,7 @@
       A guide to model input and output data
     
     
  • 
-      Model
+      Summary of the Stan Model
     
    • 
   
 
diff --git a/articles/index.html b/articles/index.html
index 442c1d4..6797c4c 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -38,7 +38,7 @@
       A guide to model input and output data
     
     
  • 
-      Model
+      Summary of the Stan Model
     
    • 
   
       
      
@@ -61,7 +61,7 @@ 
      All vignettes
      
         
      
         
      A guide to model input and output data
      
         
      
-        
      Model
      
+        
      Summary of the Stan Model
      diff --git a/articles/model.html b/articles/model.html index 5427383..64fbbf9 100644 --- a/articles/model.html +++ b/articles/model.html @@ -5,13 +5,13 @@ -Model • epikinetics +Summary of the Stan Model • epikinetics - + diff --git a/index.html b/index.html index bc1ea8d..a3f5342 100644 --- a/index.html +++ b/index.html @@ -56,7 +56,7 @@ A guide to model input and output data
    • - Model + Summary of the Stan Model
      • diff --git a/pkgdown.yml b/pkgdown.yml index d6d689b..727c43d 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -5,4 +5,4 @@ articles: biokinetics: biokinetics.html data: data.html model: model.html -last_built: 2024-10-23T12:35Z +last_built: 2024-10-24T14:34Z diff --git a/reference/add_exposure_data.html b/reference/add_exposure_data.html index 56afd23..0b915c7 100644 --- a/reference/add_exposure_data.html +++ b/reference/add_exposure_data.html @@ -40,7 +40,7 @@ A guide to model input and output data
    • - Model + Summary of the Stan Model
        • diff --git a/reference/biokinetics.html b/reference/biokinetics.html index af9d370..d932385 100644 --- a/reference/biokinetics.html +++ b/reference/biokinetics.html @@ -39,7 +39,7 @@ A guide to model input and output data
      • - Model + Summary of the Stan Model
          • diff --git a/reference/biokinetics_priors.html b/reference/biokinetics_priors.html index f36b70e..9c08e18 100644 --- a/reference/biokinetics_priors.html +++ b/reference/biokinetics_priors.html @@ -41,7 +41,7 @@ A guide to model input and output data
        • - Model + Summary of the Stan Model
            • diff --git a/reference/convert_log2_scale_inverse.html b/reference/convert_log2_scale_inverse.html index 3283540..1981f99 100644 --- a/reference/convert_log2_scale_inverse.html +++ b/reference/convert_log2_scale_inverse.html @@ -40,7 +40,7 @@ A guide to model input and output data
          • - Model + Summary of the Stan Model
              • diff --git a/reference/epikinetics-package.html b/reference/epikinetics-package.html index c5b7a3b..b0915c9 100644 --- a/reference/epikinetics-package.html +++ b/reference/epikinetics-package.html @@ -38,7 +38,7 @@ A guide to model input and output data
            • - Model + Summary of the Stan Model
                • diff --git a/reference/index.html b/reference/index.html index f47c8a1..4ebf3a2 100644 --- a/reference/index.html +++ b/reference/index.html @@ -38,7 +38,7 @@ A guide to model input and output data
              • - Model + Summary of the Stan Model