Merge pull request #1308 from cmu-delphi/release/indicators_v0.1.24_utils_v0.1.16

Release covidcast-indicators 0.1.24

Author: krivard

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.1.23
+current_version = 0.1.24
 commit = True
 message = chore: bump covidcast-indicators to {new_version}
 tag = False

.github/workflows/r-ci.yml

@@ -48,17 +48,12 @@ jobs:
             ${{ runner.os }}-r-facebook-survey-
       - name: Install R dependencies
         run: |
-          if ( !require("readr") || packageVersion("readr") != "1.4.0" ) {
-            install.packages("devtools")
-            devtools::install_version("readr", version = "1.4.0")
-          }
-
           if ( !require("remotes") ) {
             install.packages("remotes")
           }
           remotes::update_packages(c("rcmdcheck", "mockr", "remotes"), upgrade="always")
           dependency_list <- remotes::dev_package_deps(dependencies=TRUE)
-          remotes::update_packages(dependency_list$package[dependency_list$package != "readr"], upgrade="always")
+          remotes::update_packages(dependency_list$package, upgrade="always")
         shell: Rscript {0}
       - name: Check
         run: |

ansible/templates/facebook-params-prod.json.j2

@@ -11,6 +11,8 @@
   "end_date": "2021-08-16",
   "export_dir": "./receiving",
   "individual_dir": "./individual",
+  "individual_raceeth_dir": "./individual_raceeth",
+  "produce_individual_raceeth": false,
   "input": [
     "2021-08-17.2021-08-10.2021-08-17.Survey_of_COVID-Like_Illness_-_TODEPLOY_......_-_US_Expansion.csv",
     "2021-08-17.2021-08-10.2021-08-17.Survey_of_COVID-Like_Illness_-_Wave_10.csv",

facebook/Dockerfile

@@ -10,9 +10,9 @@ RUN install2.r --error \
     data.table \
     roxygen2 \
     Rcpp \
-    BH
+    BH \
+    readr
 
-RUN R --no-restore --no-save -e 'devtools::install_version("readr", version="1.4.0")'
 RUN apt-get update && apt-get install -qq -y \
     python3-venv \
     sshpass \

facebook/delphiFacebook/DESCRIPTION

@@ -13,7 +13,7 @@ Depends:
 Imports:
     stats,
     rlang,
-    readr (<= 1.4.0),
+    readr,
     dplyr,
     stringi,
     jsonlite,

facebook/delphiFacebook/R/aggregate.R

@@ -181,7 +181,10 @@ summarize_indicators_day <- function(day_df, indicators, target_day, geo_level,
 
       # Copy only columns we're using.
       select_cols <- c(metric, var_weight, "weight_in_location")
-      ind_df <- sub_df[, select_cols, with=FALSE][!is.na(sub_df[[var_weight]]) & !is.na(sub_df[[metric]]), ]
+      # This filter uses `x[, cols, with=FALSE]` rather than the newer
+      # recommended `x[, ..cols]` format to take advantage of better
+      # performance. Switch to using `..` if `with` is deprecated in the future.
+      ind_df <- sub_df[!is.na(sub_df[[var_weight]]) & !is.na(sub_df[[metric]]), select_cols, with=FALSE]
 
       if (nrow(ind_df) > 0)
       {

facebook/delphiFacebook/R/contingency_aggregate.R

@@ -336,7 +336,10 @@ summarize_aggregations_group <- function(group_df, aggregations, target_group, g
 
     # Copy only columns we're using.
     select_cols <- c(metric, var_weight, "weight_in_location")
-    agg_df <- group_df[, select_cols, with=FALSE][!is.na(eval(as.name(metric))), ]
+    # This filter uses `x[, cols, with=FALSE]` rather than the newer recommended
+    # `x[, ..cols]` format to take advantage of better performance. Switch to
+    # using `..` if `with` is deprecated in the future.
+    agg_df <- group_df[!is.na(eval(as.name(metric))), select_cols, with=FALSE]
 
     if (nrow(agg_df) > 0) {
       s_mix_coef <- params$s_mix_coef

facebook/delphiFacebook/R/contingency_indicators.R

@@ -63,7 +63,8 @@ get_aggs <- function() {
     c("gender", "edulevel"),
     c("occupation"),
     c("pregnant", "raceethnicity"),
-    c("race", "hispanic", "pregnant")
+    c("race", "hispanic", "pregnant"),
+    c("vaccinationstatus")
   )
 
   indicators <- tribble(

facebook/delphiFacebook/R/contingency_variables.R

@@ -227,6 +227,40 @@ code_health <- function(input_data, wave) {
   return(input_data)
 }
 
+#' Vaccinated summary variable for making table cuts
+#'
+#' @param input_data input data frame of raw survey data
+#' @param wave integer indicating survey version
+#' 
+#' @return augmented data frame
+code_vaccinated_breakdown <- function(input_data, wave) {
+  # grouping variable - vaccination status
+  if (all(c("V1", "V3a", "V11a") %in% names(input_data))) {
+    input_data$vaccinationstatus <- case_when(
+      input_data$V1 == 1 ~ "Vaccinated",
+      input_data$V3a == 1 ~ "Accept/Appointment",
+      input_data$V3a == 2 ~ "Accept/Appointment",
+      input_data$V11a == 1 ~ "Accept/Appointment",
+      input_data$V3a == 3 ~ "Hesitant",
+      input_data$V3a == 4 ~ "Hesitant",
+      TRUE ~ NA_character_
+    )
+  } else if (all(c("V1", "V3") %in% names(input_data))) {
+    input_data$vaccinationstatus <- case_when(
+      input_data$V1 == 1 ~ "Vaccinated",
+      input_data$V3 == 1 ~ "Accept/Appointment",
+      input_data$V3 == 2 ~ "Accept/Appointment",
+      input_data$V3 == 3 ~ "Hesitant",
+      input_data$V3 == 4 ~ "Hesitant",
+      TRUE ~ NA_character_
+    )
+  } else {
+    input_data$vaccinationstatus <- NA
+  }
+
+  return(input_data)
+}
+
 #' COVID vaccination variables with modifications for contingency tables
 #'
 #' @param input_data input data frame of raw survey data

facebook/delphiFacebook/R/responses.R

@@ -220,6 +220,7 @@ load_response_one <- function(input_filename, params, contingency_run) {
     input_data <- code_race_ethnicity(input_data, wave)
     input_data <- code_occupation(input_data, wave)
     input_data <- code_education(input_data, wave)
+    input_data <- code_vaccinated_breakdown(input_data, wave)
 
     # Indicators
     input_data <- code_addl_vaccines(input_data, wave)