From acc05df8b177bd56f3b46052da49e57004116f50 Mon Sep 17 00:00:00 2001 From: hillalex Date: Thu, 24 Oct 2024 17:01:16 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20seroanal?= =?UTF-8?q?ytics/epikinetics@433388b6cd64f73bd826f0ef76568e564a05e366=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 | 56 ++++---- articles/index.html | 4 +- articles/model.html | 2 +- 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, 122 insertions(+), 124 deletions(-) diff --git a/404.html b/404.html index a30b39f..aa374e2 100644 --- a/404.html +++ b/404.html @@ -52,7 +52,7 @@ biokinetics case study
  • - A guide to model input and output data + A guide to biokinetics input and output data
  • Summary of the Stan Model diff --git a/LICENSE.html b/LICENSE.html index 493973e..05ceadb 100644 --- a/LICENSE.html +++ b/LICENSE.html @@ -35,7 +35,7 @@ biokinetics case study
  • - A guide to model input and output data + A guide to biokinetics input and output data
  • Summary of the Stan Model diff --git a/articles/biokinetics.html b/articles/biokinetics.html index c44c5d7..7992cc2 100644 --- a/articles/biokinetics.html +++ b/articles/biokinetics.html @@ -52,7 +52,7 @@ biokinetics case study
  • - A guide to model input and output data + A guide to biokinetics input and output data
  • Summary of the Stan Model @@ -120,9 +120,9 @@

    Figure 2 
     res <- mod$simulate_population_trajectories()
-#> 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
+#> INFO [2024-10-24 16:59:19] Summarising fits
+#> INFO [2024-10-24 16:59:22] Adjusting by regression coefficients
+#> INFO [2024-10-24 16:59:25] 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 [2024-10-24 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
+#> INFO [2024-10-24 16:59:26] Extracting parameters
+#> INFO [2024-10-24 16:59:27] Adjusting by covariates
+#> INFO [2024-10-24 16:59:27] Calculating peak and switch titre values
+#> INFO [2024-10-24 16:59:27] Recovering covariate names
+#> INFO [2024-10-24 16:59:27] 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$simulate_individual_trajectories(n_draws = 250)
-#> INFO [2024-10-24 14:38:34] Extracting parameters
-#> INFO [2024-10-24 14:38:38] Simulating individual trajectories
-#> INFO [2024-10-24 14:38:42] Recovering covariate names
-#> INFO [2024-10-24 14:38:42] Calculating exposure days. Adjusting exposures by 0 days
-#> INFO [2024-10-24 14:38:45] Resampling
+#> INFO [2024-10-24 16:59:28] Extracting parameters
+#> INFO [2024-10-24 16:59:31] Simulating individual trajectories
+#> INFO [2024-10-24 16:59:36] Recovering covariate names
+#> INFO [2024-10-24 16:59:36] Calculating exposure days. Adjusting exposures by 0 days
+#> INFO [2024-10-24 16:59:39] Resampling
 #> Registered S3 method overwritten by 'mosaic':
 #>   method                           from   
 #>   fortify.SpatialPolygonsDataFrame ggplot2
-#> INFO [2024-10-24 14:38:55] Summarising into population quantiles
+#> INFO [2024-10-24 16:59:49] Summarising into population quantiles
 head(res)
 #>    calendar_day titre_type       me       lo       hi time_shift
 #>          <IDat>     <char>    <num>    <num>    <num>      <num>
@@ -348,72 +348,72 @@ 
    Figure 5  shift <- time_shift_values[index]
   mod$simulate_individual_trajectories(n_draws = 50, time_shift = shift)
 })
-#> INFO [2024-10-24 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
+#> INFO [2024-10-24 16:59:50] Extracting parameters
+#> INFO [2024-10-24 16:59:53] Simulating individual trajectories
+#> INFO [2024-10-24 16:59:54] Recovering covariate names
+#> INFO [2024-10-24 16:59:54] Calculating exposure days. Adjusting exposures by -75 days
+#> INFO [2024-10-24 16:59:55] Resampling
+#> INFO [2024-10-24 16:59:57] Summarising into population quantiles
+#> INFO [2024-10-24 16:59:57] Extracting parameters
+#> INFO [2024-10-24 17:00:01] Simulating individual trajectories
+#> INFO [2024-10-24 17:00:01] Recovering covariate names
+#> INFO [2024-10-24 17:00:01] Calculating exposure days. Adjusting exposures by -60 days
+#> INFO [2024-10-24 17:00:02] Resampling
+#> INFO [2024-10-24 17:00:04] Summarising into population quantiles
+#> INFO [2024-10-24 17:00:04] Extracting parameters
+#> INFO [2024-10-24 17:00:08] Simulating individual trajectories
+#> INFO [2024-10-24 17:00:08] Recovering covariate names
+#> INFO [2024-10-24 17:00:08] Calculating exposure days. Adjusting exposures by -45 days
+#> INFO [2024-10-24 17:00:09] Resampling
+#> INFO [2024-10-24 17:00:10] Summarising into population quantiles
+#> INFO [2024-10-24 17:00:11] Extracting parameters
+#> INFO [2024-10-24 17:00:14] Simulating individual trajectories
+#> INFO [2024-10-24 17:00:15] Recovering covariate names
+#> INFO [2024-10-24 17:00:15] Calculating exposure days. Adjusting exposures by -30 days
+#> INFO [2024-10-24 17:00:15] Resampling
+#> INFO [2024-10-24 17:00:17] Summarising into population quantiles
+#> INFO [2024-10-24 17:00:18] Extracting parameters
+#> INFO [2024-10-24 17:00:21] Simulating individual trajectories
+#> INFO [2024-10-24 17:00:22] Recovering covariate names
+#> INFO [2024-10-24 17:00:22] Calculating exposure days. Adjusting exposures by -15 days
+#> INFO [2024-10-24 17:00:22] Resampling
+#> INFO [2024-10-24 17:00:24] Summarising into population quantiles
+#> INFO [2024-10-24 17:00:25] Extracting parameters
+#> INFO [2024-10-24 17:00:28] Simulating individual trajectories
+#> INFO [2024-10-24 17:00:29] Recovering covariate names
+#> INFO [2024-10-24 17:00:29] Calculating exposure days. Adjusting exposures by 0 days
+#> INFO [2024-10-24 17:00:29] Resampling
+#> INFO [2024-10-24 17:00:31] Summarising into population quantiles
+#> INFO [2024-10-24 17:00:32] Extracting parameters
+#> INFO [2024-10-24 17:00:35] Simulating individual trajectories
+#> INFO [2024-10-24 17:00:36] Recovering covariate names
+#> INFO [2024-10-24 17:00:36] Calculating exposure days. Adjusting exposures by 15 days
+#> INFO [2024-10-24 17:00:37] Resampling
+#> INFO [2024-10-24 17:00:39] Summarising into population quantiles
+#> INFO [2024-10-24 17:00:39] Extracting parameters
+#> INFO [2024-10-24 17:00:43] Simulating individual trajectories
+#> INFO [2024-10-24 17:00:43] Recovering covariate names
+#> INFO [2024-10-24 17:00:43] Calculating exposure days. Adjusting exposures by 30 days
+#> INFO [2024-10-24 17:00:44] Resampling
+#> INFO [2024-10-24 17:00:46] Summarising into population quantiles
+#> INFO [2024-10-24 17:00:46] Extracting parameters
+#> INFO [2024-10-24 17:00:50] Simulating individual trajectories
+#> INFO [2024-10-24 17:00:50] Recovering covariate names
+#> INFO [2024-10-24 17:00:50] Calculating exposure days. Adjusting exposures by 45 days
+#> INFO [2024-10-24 17:00:51] Resampling
+#> INFO [2024-10-24 17:00:53] Summarising into population quantiles
+#> INFO [2024-10-24 17:00:53] Extracting parameters
+#> INFO [2024-10-24 17:00:57] Simulating individual trajectories
+#> INFO [2024-10-24 17:00:57] Recovering covariate names
+#> INFO [2024-10-24 17:00:57] Calculating exposure days. Adjusting exposures by 60 days
+#> INFO [2024-10-24 17:00:58] Resampling
+#> INFO [2024-10-24 17:00:59] Summarising into population quantiles
+#> INFO [2024-10-24 17:01:00] Extracting parameters
+#> INFO [2024-10-24 17:01:03] Simulating individual trajectories
+#> INFO [2024-10-24 17:01:04] Recovering covariate names
+#> INFO [2024-10-24 17:01:04] Calculating exposure days. Adjusting exposures by 75 days
+#> INFO [2024-10-24 17:01:04] Resampling
+#> INFO [2024-10-24 17:01:06] 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 4b49a31..24d38a1 100644
--- a/articles/data.html
+++ b/articles/data.html
@@ -5,13 +5,13 @@
 
 
 
-A guide to model input and output data • epikinetics
+A guide to biokinetics input and output data • epikinetics
 
 
 
 
 
-
+