Merge pull request #19 from vimc/vimc-6488

vimc-6488: Split stoner stochastic process into units
vimc · Jun 22, 2022 · 37ae630 · 37ae630
2 parents ff339a5 + b414883
commit 37ae630
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Showing 8 changed files with 533 additions and 456 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: stoner
 Title: Support for Building VIMC Montagu Touchstones, using Dettl
-Version: 0.1.5
+Version: 0.1.6
 Authors@R:
     c(person("Wes", "Hinsley",role = c("aut", "cre", "cst", "dnc", "elg", "itr", "sng"),
            email = "w.hinsley@imperial.ac.uk"),
@@ -19,6 +19,8 @@ Imports:
     RPostgres,
     utils,
     data.table,
+    dplyr,
+    magrittr,
     readr,
     withr,
     jsonlite

diff --git a/NAMESPACE b/NAMESPACE
@@ -13,5 +13,6 @@ export(stoner_calculate_dalys)
 export(stoner_dalys_for_db)
 import(data.table)
 import(readr)
+importFrom(magrittr,"%>%")
 importFrom(utils,read.csv)
 importFrom(utils,write.csv)
diff --git a/R/dalys.R b/R/dalys.R
@@ -101,13 +101,13 @@ test_args <- function(con, dalys_params, life_table) {
     c("average_duration", "disability_weight","outcome", "proportion"),
       paste("dalys_params needs columns outcome, proportion,",
             "average_duration and disablility_weight"))
-  
+
 
   if (!is.null(life_table)) {
-    if (class(life_table) != "data.frame") {
+    if (!is.data.frame(life_table)) {
       stop("life_table (if specified) must be data.frame")
     }
-    assert_set_equal(names(life_table), c("code", "value"),
+    assert_set_equal(names(life_table), c(".code", "value"),
       "life_table (if specified) must have columns .code and value")
   }
 }