Calculate MMD with kernlab #42

src/naomi-simple_mmd/mmd.Rmd

@@ -11,7 +11,7 @@ output:
     code_folding: show
     theme: lumen
 abstract: |
-  **Background**  We have run the simplified Naomi model using a range of inference methods: `TMB`, `aghq`, `adam` and `tmbstan`.
+  **Background**  We have run the simplified Naomi model using a range of inference methods: `TMB`, `aghq` and `tmbstan`.
   
   **Task** In this report, we compare the accuracy of the posterior distributions obtained from these inference methods using maximum mean discrepancy.
 ---
@@ -24,9 +24,6 @@ Import these inference results as follows:
 ```{r}
 tmb <- readRDS("depends/tmb.rds")
 aghq <- readRDS("depends/aghq.rds")
-adam <- readRDS("depends/adam.rds")
-adam_time <- adam$time
-adam <- adam$adam
 tmbstan <- readRDS("depends/tmbstan.rds")
 
 depends <- yaml::read_yaml("orderly.yml")$depends
@@ -36,49 +33,15 @@ Check that the parameters (latent field, hyperparameters, model outputs) sampled
 
 ```{r}
 stopifnot(names(tmb$fit$sample) == names(aghq$quad$sample))
-stopifnot(names(tmb$fit$sample) == names(adam$adam$sample))
 stopifnot(names(tmb$fit$sample) == names(tmbstan$mcmc$sample))
 ```
 
-## Run details {.tabset}
-
-For more information about the conditions under which these results were generated, see:
-
-### `TMB`
-
-```{r}
-dependency_details <- function(i) {
-  report_name <- names(depends[[i]])
-  print(paste0("Inference results obtained from ", report_name, " with the query ", depends[[i]][[report_name]]$id))
-  report_id <- orderly::orderly_search(query = depends[[i]][[report_name]]$id, report_name)
-  print(paste0("Obtained report had ID ", report_id, " and was run with the following parameters:"))
-  print(orderly::orderly_info(report_id, report_name)$parameters)
-}
-
-dependency_details(1)
-```
-
-### `aghq`
-
-```{r}
-dependency_details(2)
-```
-
-### `adam`
-
-```{r}
-dependency_details(3)
-```
-
-### `tmbstan`
-
-```{r}
-tmbstan_details <- dependency_details(4)
-tmbstan_details
-```
-
 # Maximum mean discrepancy
 
 ```{r}
-#' To write!
+mmd1 <- kernlab::kmmd(matrix(tmb$fit$sample$beta_rho), matrix(tmbstan$mcmc$sample$beta_rho))
+mmd2 <- kernlab::kmmd(matrix(aghq$quad$sample$beta_rho), matrix(tmbstan$mcmc$sample$beta_rho))
+
+mmd1
+mmd2
 ```

src/naomi-simple_mmd/orderly.yml

@@ -25,6 +25,7 @@ packages:
   - bayesplot
   - patchwork
   - gt
+  - kernlab
 
 depends:
   - naomi-simple_fit:
@@ -35,11 +36,8 @@ depends:
       id: latest(parameter:aghq == TRUE && parameter:k == 3 && parameter:s == 8)
       use:
         depends/aghq.rds: out.rds
-  - naomi-simple_fit:
-      id: latest(parameter:adam == TRUE)
-      use:
-        depends/adam.rds: out.rds
   - naomi-simple_fit:
       id: latest(parameter:tmbstan == TRUE && parameter:niter > 50000)
       use:
         depends/tmbstan.rds: out.rds
+