Merge pull request #1569 from cmu-delphi/release/indicators_v0.3.9_utils_v0.3.3

Release covidcast-indicators 0.3.9

Author: krivard

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.3.8
+current_version = 0.3.9
 commit = True
 message = chore: bump covidcast-indicators to {new_version}
 tag = False

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

@@ -79,27 +79,27 @@
         "smoothed_inperson_school_fulltime", "smoothed_winperson_school_fulltime",
         "smoothed_inperson_school_parttime", "smoothed_winperson_school_parttime",
         "smoothed_vaccinate_children", "smoothed_wvaccinate_children",
-        ["smoothed_vaccine_barrier_appointment_time_tried", "msa"], ["smoothed_wvaccine_barrier_appointment_time_tried", "msa"],
-        ["smoothed_vaccine_barrier_childcare_tried", "msa"], ["smoothed_wvaccine_barrier_childcare_tried", "msa"],
-        ["smoothed_vaccine_barrier_document_tried", "msa"], ["smoothed_wvaccine_barrier_document_tried", "msa"],
-        ["smoothed_vaccine_barrier_eligible_tried", "msa"], ["smoothed_wvaccine_barrier_eligible_tried", "msa"],
-        ["smoothed_vaccine_barrier_language_tried", "msa"], ["smoothed_wvaccine_barrier_language_tried", "msa"],
-        ["smoothed_vaccine_barrier_no_appointments_tried", "msa"], ["smoothed_wvaccine_barrier_no_appointments_tried", "msa"],
-        ["smoothed_vaccine_barrier_none_tried", "msa"], ["smoothed_wvaccine_barrier_none_tried", "msa"],
-        ["smoothed_vaccine_barrier_technical_difficulties_tried", "msa"], ["smoothed_wvaccine_barrier_technical_difficulties_tried", "msa"],
-        ["smoothed_vaccine_barrier_technology_access_tried", "msa"], ["smoothed_wvaccine_barrier_technology_access_tried", "msa"],
-        ["smoothed_vaccine_barrier_time_tried", "msa"], ["smoothed_wvaccine_barrier_time_tried", "msa"],
-        ["smoothed_vaccine_barrier_travel_tried", "msa"], ["smoothed_wvaccine_barrier_travel_tried", "msa"],
-        ["smoothed_vaccine_barrier_type_tried", "msa"], ["smoothed_wvaccine_barrier_type_tried", "msa"],
+        ["smoothed_vaccine_barrier_appointment_time_tried", "msa", "county", "state"], ["smoothed_wvaccine_barrier_appointment_time_tried", "msa", "county", "state"],
+        ["smoothed_vaccine_barrier_childcare_tried", "msa", "county", "state"], ["smoothed_wvaccine_barrier_childcare_tried", "msa", "county", "state"],
+        ["smoothed_vaccine_barrier_document_tried", "msa", "county", "state"], ["smoothed_wvaccine_barrier_document_tried", "msa", "county", "state"],
+        ["smoothed_vaccine_barrier_eligible_tried", "msa", "county", "state"], ["smoothed_wvaccine_barrier_eligible_tried", "msa", "county", "state"],
+        ["smoothed_vaccine_barrier_language_tried", "msa", "county", "state"], ["smoothed_wvaccine_barrier_language_tried", "msa", "county", "state"],
+        ["smoothed_vaccine_barrier_no_appointments_tried", "msa", "county", "state"], ["smoothed_wvaccine_barrier_no_appointments_tried", "msa", "county", "state"],
+        ["smoothed_vaccine_barrier_none_tried", "msa", "county", "state"], ["smoothed_wvaccine_barrier_none_tried", "msa", "county", "state"],
+        ["smoothed_vaccine_barrier_technical_difficulties_tried", "msa", "county", "state"], ["smoothed_wvaccine_barrier_technical_difficulties_tried", "msa", "county", "state"],
+        ["smoothed_vaccine_barrier_technology_access_tried", "msa", "county", "state"], ["smoothed_wvaccine_barrier_technology_access_tried", "msa", "county", "state"],
+        ["smoothed_vaccine_barrier_time_tried", "msa", "county", "state"], ["smoothed_wvaccine_barrier_time_tried", "msa", "county", "state"],
+        ["smoothed_vaccine_barrier_travel_tried", "msa", "county", "state"], ["smoothed_wvaccine_barrier_travel_tried", "msa", "county", "state"],
+        ["smoothed_vaccine_barrier_type_tried", "msa", "county", "state"], ["smoothed_wvaccine_barrier_type_tried", "msa", "county", "state"],
         ["smoothed_try_vaccinate_1m", "hrr"], ["smoothed_wtry_vaccinate_1m", "hrr"],
         ["smoothed_try_vaccinate_1m", "msa"], ["smoothed_wtry_vaccinate_1m", "msa"],
-        ["smoothed_dontneed_reason_dont_spend_time", "hrr"], ["smoothed_wdontneed_reason_dont_spend_time", "hrr"],
-        ["smoothed_dontneed_reason_had_covid", "hrr"], ["smoothed_wdontneed_reason_had_covid", "hrr"],
-        ["smoothed_dontneed_reason_not_beneficial", "hrr"], ["smoothed_wdontneed_reason_not_beneficial", "hrr"],
-        ["smoothed_dontneed_reason_not_high_risk", "hrr"], ["smoothed_wdontneed_reason_not_high_risk", "hrr"],
-        ["smoothed_dontneed_reason_not_serious", "hrr"], ["smoothed_wdontneed_reason_not_serious", "hrr"],
-        ["smoothed_dontneed_reason_other", "hrr"], ["smoothed_wdontneed_reason_other", "hrr"],
-        ["smoothed_dontneed_reason_precautions", "hrr"], ["smoothed_wdontneed_reason_precautions", "hrr"],
+        ["smoothed_dontneed_reason_dont_spend_time", "hrr"], ["smoothed_wdontneed_reason_dont_spend_time", "hrr", "msa"],
+        ["smoothed_dontneed_reason_had_covid", "hrr"], ["smoothed_wdontneed_reason_had_covid", "hrr", "msa"],
+        ["smoothed_dontneed_reason_not_beneficial", "hrr"], ["smoothed_wdontneed_reason_not_beneficial", "hrr", "msa"],
+        ["smoothed_dontneed_reason_not_high_risk", "hrr"], ["smoothed_wdontneed_reason_not_high_risk", "hrr", "msa"],
+        ["smoothed_dontneed_reason_not_serious", "hrr"], ["smoothed_wdontneed_reason_not_serious", "hrr", "msa"],
+        ["smoothed_dontneed_reason_other", "hrr"], ["smoothed_wdontneed_reason_other", "hrr", "msa"],
+        ["smoothed_dontneed_reason_precautions", "hrr"], ["smoothed_wdontneed_reason_precautions", "hrr", "msa"],
         "smoothed_screening_tested_positive_14d", "smoothed_wscreening_tested_positive_14d",
         "smoothed_travel_outside_state_7d", "smoothed_wtravel_outside_state_7d",
         "smoothed_belief_vaccinated_mask_unnecessary", "smoothed_wbelief_vaccinated_mask_unnecessary",

facebook/delphiFacebook/R/binary.R

@@ -131,7 +131,13 @@ get_binary_indicators <- function() {
     "smoothed_wvaccinate_children", "weight", "v_vaccinate_children", 6, compute_binary_response, jeffreys_binary,
     "smoothed_vaccinate_child_oldest", "weight_unif", "v_vaccinate_child_oldest", 6, compute_binary_response, jeffreys_binary,
     "smoothed_wvaccinate_child_oldest", "weight", "v_vaccinate_child_oldest", 6, compute_binary_response, jeffreys_binary,
-    
+
+    "smoothed_wchild_vaccine_already", "weight", "v_child_vaccine_already", 6, compute_binary_response, jeffreys_multinomial_factory(5),
+    "smoothed_wchild_vaccine_yes_def", "weight", "v_child_vaccine_yes_def", 6, compute_binary_response, jeffreys_multinomial_factory(5),
+    "smoothed_wchild_vaccine_yes_prob", "weight", "v_child_vaccine_yes_prob", 6, compute_binary_response, jeffreys_multinomial_factory(5),
+    "smoothed_wchild_vaccine_no_prob", "weight", "v_child_vaccine_no_prob", 6, compute_binary_response, jeffreys_multinomial_factory(5),
+    "smoothed_wchild_vaccine_no_def", "weight", "v_child_vaccine_no_def", 6, compute_binary_response, jeffreys_multinomial_factory(5),
+
     "smoothed_try_vaccinate_1m", "weight_unif", "v_try_vaccinate_1m", 6, compute_binary_response, jeffreys_binary,
     "smoothed_wtry_vaccinate_1m", "weight", "v_try_vaccinate_1m", 6, compute_binary_response, jeffreys_binary,
 
@@ -332,11 +338,26 @@ get_binary_indicators <- function() {
     "smoothed_inperson_school_parttime", "weight_unif", "s_inperson_school_parttime", 6, compute_binary_response, jeffreys_binary,
     "smoothed_winperson_school_parttime", "weight", "s_inperson_school_parttime", 6, compute_binary_response, jeffreys_binary,
 
-    "smoothed_inperson_school_fulltime_oldest", "weight_unif", "s_inperson_school_fulltime_oldest", 6, compute_binary_response, jeffreys_binary,
-    "smoothed_winperson_school_fulltime_oldest", "weight", "s_inperson_school_fulltime_oldest", 6, compute_binary_response, jeffreys_binary,
-    "smoothed_inperson_school_parttime_oldest", "weight_unif", "s_inperson_school_parttime_oldest", 6, compute_binary_response, jeffreys_binary,
-    "smoothed_winperson_school_parttime_oldest", "weight", "s_inperson_school_parttime_oldest", 6, compute_binary_response, jeffreys_binary,
-    
+    "smoothed_inperson_school_fulltime_oldest", "weight_unif", "s_inperson_school_fulltime_oldest", 6, compute_binary_response, jeffreys_multinomial_factory(3),
+    "smoothed_winperson_school_fulltime_oldest", "weight", "s_inperson_school_fulltime_oldest", 6, compute_binary_response, jeffreys_multinomial_factory(3),
+    "smoothed_inperson_school_parttime_oldest", "weight_unif", "s_inperson_school_parttime_oldest", 6, compute_binary_response, jeffreys_multinomial_factory(3),
+    "smoothed_winperson_school_parttime_oldest", "weight", "s_inperson_school_parttime_oldest", 6, compute_binary_response, jeffreys_multinomial_factory(3),
+    "smoothed_wremote_school_fulltime_oldest", "weight", "s_remote_school_fulltime_oldest", 6, compute_binary_response, jeffreys_multinomial_factory(3),
+
+    "smoothed_wschool_safety_measures_mask_students", "weight", "s_school_safety_measures_mask_students", 6, compute_binary_response, jeffreys_binary,
+    "smoothed_wschool_safety_measures_mask_teachers", "weight", "s_school_safety_measures_mask_teachers", 6, compute_binary_response, jeffreys_binary,
+    "smoothed_wschool_safety_measures_restricted_entry", "weight", "s_school_safety_measures_restricted_entry", 6, compute_binary_response, jeffreys_binary,
+    "smoothed_wschool_safety_measures_separators", "weight", "s_school_safety_measures_separators", 6, compute_binary_response, jeffreys_binary,
+    "smoothed_wschool_safety_measures_extracurricular", "weight", "s_school_safety_measures_extracurricular", 6, compute_binary_response, jeffreys_binary,
+    "smoothed_wschool_safety_measures_symptom_screen", "weight", "s_school_safety_measures_symptom_screen", 6, compute_binary_response, jeffreys_binary,
+    "smoothed_wschool_safety_measures_ventilation", "weight", "s_school_safety_measures_ventilation", 6, compute_binary_response, jeffreys_binary,
+    "smoothed_wschool_safety_measures_testing_staff", "weight", "s_school_safety_measures_testing_staff", 6, compute_binary_response, jeffreys_binary,
+    "smoothed_wschool_safety_measures_testing_students", "weight", "s_school_safety_measures_testing_students", 6, compute_binary_response, jeffreys_binary,
+    "smoothed_wschool_safety_measures_vaccine_staff", "weight", "s_school_safety_measures_vaccine_staff", 6, compute_binary_response, jeffreys_binary,
+    "smoothed_wschool_safety_measures_vaccine_students", "weight", "s_school_safety_measures_vaccine_students", 6, compute_binary_response, jeffreys_binary,
+    "smoothed_wschool_safety_measures_cafeteria", "weight", "s_school_safety_measures_cafeteria", 6, compute_binary_response, jeffreys_binary,
+    "smoothed_wschool_safety_measures_dont_know", "weight", "s_school_safety_measures_dont_know", 6, compute_binary_response, jeffreys_binary,
+
     # beliefs
     "smoothed_belief_masking_effective", "weight_unif", "b_belief_masking_effective", 6, compute_binary_response, jeffreys_binary,
     "smoothed_wbelief_masking_effective", "weight", "b_belief_masking_effective", 6, compute_binary_response, jeffreys_binary,
@@ -396,9 +417,7 @@ get_binary_indicators <- function() {
     "smoothed_want_info_employment", "weight_unif", "i_want_info_employment", 6, compute_binary_response, jeffreys_binary,
     "smoothed_wwant_info_employment", "weight", "i_want_info_employment", 6, compute_binary_response, jeffreys_binary,
     "smoothed_want_info_none", "weight_unif", "i_want_info_none", 6, compute_binary_response, jeffreys_binary,
-    "smoothed_wwant_info_none", "weight", "i_want_info_none", 6, compute_binary_response, jeffreys_binary,
-   
-    
+    "smoothed_wwant_info_none", "weight", "i_want_info_none", 6, compute_binary_response, jeffreys_binary
   )
 
 

facebook/delphiFacebook/R/contingency_indicators.R

@@ -141,6 +141,12 @@ get_aggs <- function() {
     "pct_vaccinate_children", "v_vaccinate_children", compute_binary, jeffreys_binary,
     "pct_vaccinate_child_oldest", "v_vaccinate_child_oldest", compute_binary, jeffreys_binary,
 
+    "pct_child_vaccine_already", "v_child_vaccine_already", compute_binary, jeffreys_multinomial_factory(5),
+    "pct_child_vaccine_yes_def", "v_child_vaccine_yes_def", compute_binary, jeffreys_multinomial_factory(5),
+    "pct_child_vaccine_yes_prob", "v_child_vaccine_yes_prob", compute_binary, jeffreys_multinomial_factory(5),
+    "pct_child_vaccine_no_prob", "v_child_vaccine_no_prob", compute_binary, jeffreys_multinomial_factory(5),
+    "pct_child_vaccine_no_def", "v_child_vaccine_no_def", compute_binary, jeffreys_multinomial_factory(5),
+
     "pct_accept_vaccine_defyes", "v_accept_vaccine_defyes", compute_binary, jeffreys_multinomial_factory(4),
     "pct_accept_vaccine_probyes", "v_accept_vaccine_probyes", compute_binary, jeffreys_multinomial_factory(4),
     "pct_accept_vaccine_probno", "v_accept_vaccine_probno", compute_binary, jeffreys_multinomial_factory(4),
@@ -448,11 +454,39 @@ get_aggs <- function() {
 
     # schooling
     "pct_inperson_school_fulltime", "s_inperson_school_fulltime", compute_binary, jeffreys_binary,
-    "pct_inperson_school_parttime", "s_inperson_school_parttime", compute_binary, jeffreys_binary
+    "pct_inperson_school_parttime", "s_inperson_school_parttime", compute_binary, jeffreys_binary,
+
+    "pct_remote_school_fulltime_oldest", "s_remote_school_fulltime_oldest", compute_binary, jeffreys_multinomial_factory(3),
+    "pct_inperson_school_fulltime_oldest", "s_inperson_school_fulltime_oldest", compute_binary, jeffreys_multinomial_factory(3),
+    "pct_inperson_school_parttime_oldest", "s_inperson_school_parttime_oldest", compute_binary, jeffreys_multinomial_factory(3),
+
+    "pct_school_safety_measures_mask_students", "s_school_safety_measures_mask_students", compute_binary, jeffreys_binary,
+    "pct_school_safety_measures_mask_teachers", "s_school_safety_measures_mask_teachers", compute_binary, jeffreys_binary,
+    "pct_school_safety_measures_restricted_entry", "s_school_safety_measures_restricted_entry", compute_binary, jeffreys_binary,
+    "pct_school_safety_measures_separators", "s_school_safety_measures_separators", compute_binary, jeffreys_binary,
+    "pct_school_safety_measures_extracurricular", "s_school_safety_measures_extracurricular", compute_binary, jeffreys_binary,
+    "pct_school_safety_measures_symptom_screen", "s_school_safety_measures_symptom_screen", compute_binary, jeffreys_binary,
+    "pct_school_safety_measures_ventilation", "s_school_safety_measures_ventilation", compute_binary, jeffreys_binary,
+    "pct_school_safety_measures_testing_staff", "s_school_safety_measures_testing_staff", compute_binary, jeffreys_binary,
+    "pct_school_safety_measures_testing_students", "s_school_safety_measures_testing_students", compute_binary, jeffreys_binary,
+    "pct_school_safety_measures_vaccine_staff", "s_school_safety_measures_vaccine_staff", compute_binary, jeffreys_binary,
+    "pct_school_safety_measures_vaccine_students", "s_school_safety_measures_vaccine_students", compute_binary, jeffreys_binary,
+    "pct_school_safety_measures_cafeteria", "s_school_safety_measures_cafeteria", compute_binary, jeffreys_binary,
+    "pct_school_safety_measures_dont_know", "s_school_safety_measures_dont_know", compute_binary, jeffreys_binary
   )
 
   aggs <- create_aggs_product(regions, groups, indicators)
-  
+
+
+  monthly_indicators <- tribble(
+    ~name, ~metric, ~compute_fn, ~post_fn,
+    "pct_child_school_public", "s_child_school_public", compute_binary, jeffreys_multinomial_factory(5),
+    "pct_child_school_private", "s_child_school_private", compute_binary, jeffreys_multinomial_factory(5),
+    "pct_child_school_homeschool", "s_child_school_homeschool", compute_binary, jeffreys_multinomial_factory(5),
+    "pct_child_school_not", "s_child_school_not", compute_binary, jeffreys_multinomial_factory(5),
+    "pct_child_school_other", "s_child_school_other", compute_binary, jeffreys_multinomial_factory(5)
+  )
+  monthly_aggs <- create_aggs_product(regions, groups, monthly_indicators)
 
   ### Include handful of original public tables not already covered by set above
   common_group <- c("agefull", "gender", "race", "hispanic")
@@ -509,7 +543,7 @@ get_aggs <- function() {
   aggs <- rbind(aggs, cut1_aggs, cut2_aggs, cut3_aggs, cut456_aggs, cut456_marginal_aggs)
 
   weekly_aggs <- aggs
-  monthly_aggs <- aggs
+  monthly_aggs <- rbind(aggs, monthly_aggs)
 
   return(list("week"=weekly_aggs, "month"=monthly_aggs))
 }

facebook/delphiFacebook/R/responses.R

@@ -193,6 +193,7 @@ load_response_one <- function(input_filename, params, contingency_run) {
   input_data <- code_activities(input_data, wave)
   input_data <- code_vaccines(input_data, wave)
   input_data <- code_schooling(input_data, wave)
+  input_data <- code_children(input_data, wave)
   input_data <- code_beliefs(input_data, wave)
   input_data <- code_news_and_info(input_data, wave)
   input_data <- code_gender(input_data, wave)