Merge pull request #239 from cmu-delphi/release/6.0.0

Release 6.0.0

Author: nmdefries

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 5.0.1
+current_version = 6.0.0
 commit = False
 tag = False
 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: forecasteval
 Title: Forecast Evaluation Dashboard
-Version: 5.0.1
+Version: 6.0.0
 Authors@R: c(person("Kate", "Harwood", email = "[email protected]", role = "cre"),
 	   person("Chris", "Scott", role = "ctb"),
 	   person("Jed", "Grabman", role = "ctb"))

app/R/data.R

@@ -84,16 +84,13 @@ getAllData <- function(loadFile) {
     covCols
   )
 
-  dfStateCases <- dfStateCases %>% select(all_of(expectedCols))
-  dfStateDeaths <- dfStateDeaths %>% select(all_of(expectedCols))
-  dfStateHospitalizations <- dfStateHospitalizations %>% select(all_of(expectedCols))
-  dfNationCases <- dfNationCases %>% select(all_of(expectedCols))
-  dfNationDeaths <- dfNationDeaths %>% select(all_of(expectedCols))
-  dfNationHospitalizations <- dfNationHospitalizations %>% select(all_of(expectedCols))
-
-  df <- rbind(
-    dfStateCases, dfStateDeaths, dfStateHospitalizations,
-    dfNationCases, dfNationDeaths, dfNationHospitalizations
+  df <- bind_rows(
+    dfStateCases %>% select(all_of(expectedCols)),
+    dfStateDeaths %>% select(all_of(expectedCols)),
+    dfStateHospitalizations %>% select(all_of(expectedCols)),
+    dfNationCases %>% select(all_of(expectedCols)),
+    dfNationDeaths %>% select(all_of(expectedCols)),
+    dfNationHospitalizations %>% select(all_of(expectedCols))
   )
   df <- df %>% rename(
     "10" = cov_10, "20" = cov_20, "30" = cov_30,

app/R/data_manipulation.R

@@ -66,24 +66,31 @@ filterHospitalizationsAheads <- function(scoreDf) {
     group_by(target_end_date, forecaster) %>%
     filter(ahead == min(ahead)) %>%
     mutate(ahead = HOSPITALIZATIONS_AHEAD_OPTIONS[1])
-  twoAheadDf <- scoreDf %>%
-    filter(ahead >= 7 + HOSPITALIZATIONS_OFFSET) %>%
-    filter(ahead < 14 + HOSPITALIZATIONS_OFFSET) %>%
-    group_by(target_end_date, forecaster) %>%
-    filter(ahead == min(ahead)) %>%
-    mutate(ahead = HOSPITALIZATIONS_AHEAD_OPTIONS[2])
-  threeAheadDf <- scoreDf %>%
-    filter(ahead >= 14 + HOSPITALIZATIONS_OFFSET) %>%
-    filter(ahead < 21 + HOSPITALIZATIONS_OFFSET) %>%
-    group_by(target_end_date, forecaster) %>%
-    filter(ahead == min(ahead)) %>%
-    mutate(ahead = HOSPITALIZATIONS_AHEAD_OPTIONS[3])
-  fourAheadDf <- scoreDf %>%
-    filter(ahead >= 21 + HOSPITALIZATIONS_OFFSET) %>%
-    filter(ahead < 28 + HOSPITALIZATIONS_OFFSET) %>%
-    group_by(target_end_date, forecaster) %>%
-    filter(ahead == min(ahead)) %>%
-    mutate(ahead = HOSPITALIZATIONS_AHEAD_OPTIONS[4])
 
-  return(rbind(oneAheadDf, twoAheadDf, threeAheadDf, fourAheadDf))
+  return(bind_rows(
+    scoreDf %>%
+      filter(ahead >= HOSPITALIZATIONS_OFFSET) %>%
+      filter(ahead < 7 + HOSPITALIZATIONS_OFFSET) %>%
+      group_by(target_end_date, forecaster) %>%
+      filter(ahead == min(ahead)) %>%
+      mutate(ahead = HOSPITALIZATIONS_AHEAD_OPTIONS[1]),
+    scoreDf %>%
+      filter(ahead >= 7 + HOSPITALIZATIONS_OFFSET) %>%
+      filter(ahead < 14 + HOSPITALIZATIONS_OFFSET) %>%
+      group_by(target_end_date, forecaster) %>%
+      filter(ahead == min(ahead)) %>%
+      mutate(ahead = HOSPITALIZATIONS_AHEAD_OPTIONS[2]),
+    scoreDf %>%
+      filter(ahead >= 14 + HOSPITALIZATIONS_OFFSET) %>%
+      filter(ahead < 21 + HOSPITALIZATIONS_OFFSET) %>%
+      group_by(target_end_date, forecaster) %>%
+      filter(ahead == min(ahead)) %>%
+      mutate(ahead = HOSPITALIZATIONS_AHEAD_OPTIONS[3]),
+    scoreDf %>%
+      filter(ahead >= 21 + HOSPITALIZATIONS_OFFSET) %>%
+      filter(ahead < 28 + HOSPITALIZATIONS_OFFSET) %>%
+      group_by(target_end_date, forecaster) %>%
+      filter(ahead == min(ahead)) %>%
+      mutate(ahead = HOSPITALIZATIONS_AHEAD_OPTIONS[4])
+  ))
 }

app/global.R

@@ -8,7 +8,7 @@ library(viridis)
 library(tsibble)
 library(covidcast)
 
-appVersion <- "5.0.1"
+appVersion <- "6.0.0"
 
 COVERAGE_INTERVALS <- c("10", "20", "30", "40", "50", "60", "70", "80", "90", "95", "98")
 DEATH_FILTER <- "deaths_incidence_num"
@@ -29,6 +29,16 @@ HOSPITALIZATIONS_AHEAD_OPTIONS <- c(
   HOSPITALIZATIONS_OFFSET + 14, HOSPITALIZATIONS_OFFSET + 21
 )
 
+# Sets the previous target to be the same as the first one, Deaths
+PREV_TARGET <- "Deaths"
+
+# When RE_RENDER_TRUTH = TRUE
+# summaryPlot will be called only to update TruthPlot
+RE_RENDER_TRUTH <- FALSE
+
+# USE_CURR_TRUTH indicates when we can use the previous TruthPlot
+USE_CURR_TRUTH <- FALSE
+
 # Earliest 'as of' date available from covidcast API
 MIN_AVAIL_NATION_AS_OF_DATE <- as.Date("2020-04-02")
 MIN_AVAIL_HOSP_AS_OF_DATE <- as.Date("2020-11-16")