Added Parameter Uploading Script

SCRC/data_uploading/param_gen.R

@@ -0,0 +1,116 @@
+##############################################################################
+#                                                                            #
+#                        LSHTM Model Parameter Upload                        #
+#                                                                            #
+#   This script adds new entries into the data registry for the LSHTM model  #
+#   parameters and creates TOML files which should then be uploaded to the   #
+#   relevant storage platform (ScottishCovidResponse/DataRepository on       #
+#   GitHub at time of writing).                                              #
+#                                                                            #
+#   You will require an API token from the registry stored in:               #
+    token_file <- file.path(getwd(), "SCRC", "data_uploading", "token.txt")  #
+#                                                                            #
+#   This script is based on the upload scripts by Sonia Mitchell.            #
+#                                                                            #
+#   @author K. Zarebski                                                      #
+#   @date   last modified 2020-08-10                                         #
+    global_version <- "0.1.0"                                                #
+#                                                                            #
+##############################################################################
+
+library(SCRCdataAPI)    # Requires the latest SCRCdataAPI library
+library(progress)
+
+# Start constructing address locations:
+#   - LSHTM/fixed-parameters
+
+namespace <- "LSHTM"
+prefix <- list(fixed="fixed-parameters", dist="distributions")
+
+key <- read.table(token_file)
+
+# Assemble remote storage location objects
+data_github_url <- "[email protected]:ScottishCovidResponse/DataRepository.git"
+productStorageRoot <- "DataRepository"
+storage_rootId <- new_storage_root(
+  name = productStorageRoot,
+  root = "https://raw.githubusercontent.com/ScottishCovidResponse/DataRepository/",
+  key = key)
+
+namespaceId <- new_namespace(name = namespace,
+                             key = key)
+
+# List of fixed parameters and their values, if a single parameter is updated
+# without changing the others the version number should also be set
+params <- list(
+    list(name="tau",       value=1,      version=global_version),
+    list(name="rho",       value=1,      version=global_version)
+)
+
+# List of prior distributions and their parameters, if a single distribution is
+# updated without changing the others the version number should also be set
+distributions <- list(
+    list(name="R0", type="normal", params=list(mu=2.675739, sigma=0.5719293), version=global_version),
+    list(name="dE", type="gamma", params=list(k=4.0, theta=4.0), version=global_version),
+    list(name="dIa", type="gamma", params=list(k=5.0, theta=4.0), version=global_version),
+    list(name="dIp", type="gamma", params=list(k=1.5, theta=4.0), version=global_version),
+    list(name="dIs", type="gamma", params=list(k=3.5, theta=4.0), version=global_version),
+    list(name="to_icu", type="gamma", params=list(k=10, theta=10), version=global_version),
+    list(name="to_non_icu", type="gamma", params=list(k=8, theta=8), version=global_version),
+    list(name="ip_to_death", type="gamma", params=list(k=22, theta=22), version=global_version),
+    list(name="ip_to_hosp", type="gamma", params=list(k=7, theta=7), version=global_version)
+)
+
+# Iterate through fixed parameters creating TOML objects and adding them
+# as statements within the DataRegistry
+pb <- progress_bar$new(total = length(params))
+for(param in params)
+{
+    name <- file.path(prefix$fixed, param$name)
+    path <- paste("master", namespace, name, sep = "/")
+    filename <- paste0(param$version, ".toml")
+    component_name <- gsub("^.*/([^/]*)$", "\\1", name)
+
+    create_estimate(filename = filename,
+        path = file.path("data-raw", path),
+        parameters = as.list(setNames(param$value, component_name)))
+
+    upload_data_product(storage_root_id = storage_rootId,
+                    name = name,
+                   component_name = component_name,
+                   processed_path = file.path("data-raw", path, filename),
+                    product_path = file.path(path, filename),
+                   version = param$version,
+                    namespace_id = namespaceId,
+                    key = key)
+    pb$tick()
+}
+
+# Iterate through prior distibutions creating TOML objects and adding them
+# as statements within the DataRegistry
+pb <- progress_bar$new(total = length(distributions))
+for(dis in distributions)
+{
+    name <- file.path(prefix$dist, dis$name)
+    path <- paste("master", namespace, name, sep = "/")
+    filename <- paste0(dis$version, ".toml")
+    component_name <- gsub("^.*/([^/]*)$", "\\1", name)
+
+    create_distribution(
+        filename = filename,
+        file.path("data-raw", path),
+        name = dis$name,
+        distribution = dis$type,
+        parameters = dis$params
+    )
+
+    upload_data_product(storage_root_id = storage_rootId,
+                    name = name,
+                    component_name = component_name,
+                    processed_path = file.path("data-raw", path, filename),
+                    product_path = file.path(path, filename),
+                    version = dis$version,
+                    namespace_id = namespaceId,
+                    key = key)
+    pb$tick()
+}