Merge pull request #34 from sempwn/neg_bin_likelihood

Updated BC fit to run for more iter.
sempwn · Sep 5, 2021 · 178e5cb · 178e5cb
2 parents 1aad6a1 + ae22d0d
commit 178e5cb
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diff --git a/data/bc_fit.rda b/data/bc_fit.rda
diff --git a/data/bc_fit_zeta.rda b/data/bc_fit_zeta.rda
diff --git a/docs/articles/BC_outbreak_data_fitting.html b/docs/articles/BC_outbreak_data_fitting.html
diff --git a/...articles/BC_outbreak_data_fitting_files/figure-html/model diagnostic plot-1.png b/...articles/BC_outbreak_data_fitting_files/figure-html/model diagnostic plot-1.png
diff --git a/...articles/BC_outbreak_data_fitting_files/figure-html/model diagnostic plot-2.png b/...articles/BC_outbreak_data_fitting_files/figure-html/model diagnostic plot-2.png
diff --git a/...articles/BC_outbreak_data_fitting_files/figure-html/model diagnostic plot-3.png b/...articles/BC_outbreak_data_fitting_files/figure-html/model diagnostic plot-3.png
diff --git a/...articles/BC_outbreak_data_fitting_files/figure-html/model diagnostic plot-4.png b/...articles/BC_outbreak_data_fitting_files/figure-html/model diagnostic plot-4.png
diff --git a/docs/articles/BC_outbreak_data_fitting_files/figure-html/unnamed-chunk-1-1.png b/docs/articles/BC_outbreak_data_fitting_files/figure-html/unnamed-chunk-1-1.png
diff --git a/docs/articles/BC_outbreak_data_fitting_files/figure-html/unnamed-chunk-2-1.png b/docs/articles/BC_outbreak_data_fitting_files/figure-html/unnamed-chunk-2-1.png
diff --git a/docs/articles/BC_outbreak_data_fitting_files/figure-html/unnamed-chunk-3-1.png b/docs/articles/BC_outbreak_data_fitting_files/figure-html/unnamed-chunk-3-1.png
diff --git a/docs/articles/BC_outbreak_data_fitting_files/figure-html/unnamed-chunk-4-1.png b/docs/articles/BC_outbreak_data_fitting_files/figure-html/unnamed-chunk-4-1.png
diff --git a/docs/articles/BC_outbreak_data_fitting_files/figure-html/unnamed-chunk-5-1.png b/docs/articles/BC_outbreak_data_fitting_files/figure-html/unnamed-chunk-5-1.png
diff --git a/docs/articles/BC_outbreak_data_fitting_files/figure-html/unnamed-chunk-6-1.png b/docs/articles/BC_outbreak_data_fitting_files/figure-html/unnamed-chunk-6-1.png
diff --git a/docs/articles/BC_outbreak_data_fitting_files/figure-html/unnamed-chunk-7-1.png b/docs/articles/BC_outbreak_data_fitting_files/figure-html/unnamed-chunk-7-1.png
diff --git a/docs/articles/introduction_to_fitting.html b/docs/articles/introduction_to_fitting.html
diff --git a/docs/articles/introduction_to_fitting_files/figure-html/unnamed-chunk-6-1.png b/docs/articles/introduction_to_fitting_files/figure-html/unnamed-chunk-6-1.png
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -5,5 +5,5 @@ articles:
   BC_LTHC_additional_analysis: BC_LTHC_additional_analysis.html
   BC_outbreak_data_fitting: BC_outbreak_data_fitting.html
   introduction_to_fitting: introduction_to_fitting.html
-last_built: 2021-09-02T23:50Z
+last_built: 2021-09-03T19:36Z
 
diff --git a/docs/reference/seir_model_fit.html b/docs/reference/seir_model_fit.html
diff --git a/vignettes/BC_outbreak_data_fitting.Rmd b/vignettes/BC_outbreak_data_fitting.Rmd
@@ -70,7 +70,8 @@ bc_fit <- seir_model_fit(
                        stan_model = stan_mod,
                        tmax,n_outbreaks,outbreak_cases,outbreak_sizes,
                        intervention_switch = TRUE,
-                       multilevel_intervention = FALSE)
+                       multilevel_intervention = FALSE,
+                       iter = 2000)
 
 ```
 
@@ -155,7 +156,8 @@ bc_fit_zeta <- seir_model_fit(
   stan_model = stan_mod,
   tmax,n_outbreaks,outbreak_cases,outbreak_sizes,
   intervention_switch = TRUE,
-  multilevel_intervention = TRUE)
+  multilevel_intervention = TRUE,
+                       iter = 2000)