Merge pull request #1433 from cmu-delphi/release/indicators_v0.2.17_utils_v0.2.7

Release covidcast-indicators 0.2.17

Author: korlaxxalrok

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.2.16
+current_version = 0.2.17
 commit = True
 message = chore: bump covidcast-indicators to {new_version}
 tag = False

README.md

@@ -39,7 +39,7 @@ Each indicator pipeline includes its own documentation.
 
 The release process consists of multiple steps which can all be done via the GitHub website:
 
-1. Got to [create_release GitHub Action](https://github.com/cmu-delphi/covidcast-indicators/actions/workflows/create-release.yml) and click the `Run workflow` dropdown button. Leave branch as `main` unless you know what you're doing. Enter the type of release (patch: bugfixes, params file changes, new signals for existing indicators; minor: new indicators, new utilities; major: backwards-incompatible changes requiring substantial refactoring) and GitHub will automatically compute the next version number for you; alternately, specify the version number by hand. Hit the green `Run workflow` button.
+1. Go to [create_release GitHub Action](https://github.com/cmu-delphi/covidcast-indicators/actions/workflows/create-release.yml) and click the `Run workflow` dropdown button. Leave branch as `main` unless you know what you're doing. Enter the type of release (patch: bugfixes, params file changes, new signals for existing indicators; minor: new indicators, new utilities; major: backwards-incompatible changes requiring substantial refactoring) and GitHub will automatically compute the next version number for you; alternately, specify the version number by hand. Hit the green `Run workflow` button.
 2. The action will prepare a new release and generate an associated [Pull Request](https://github.com/cmu-delphi/covidcast-indicators/pulls).
 3. Edit the PR description and **list all pull requests included in this release**. This is a manual step to make sure you are aware of 100% of the changes that will be deployed. You can use `#xxx` notation and GitHub will automatically render the title of each PR in Preview mode and when the edit is saved.
 4. Verify that CI passes for the PR as a whole and for the most-recent/bottom-most commit in the PR. We're currently having problems where [python-ci does not run on release PRs](https://github.com/cmu-delphi/covidcast-indicators/issues/1310), but if you see a green check next to the most-recent commit you should be fine.

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

@@ -37,6 +37,7 @@
         "Survey of COVID-Like Illness - Wave 10": "fb-survey",
         "Survey of COVID-Like Illness - Wave 11": "fb-survey",
         "Survey of COVID-Like Illness - Wave 12": "fb-survey",
+        "Survey of COVID-Like Illness - Wave 12 - Full Launch": "fb-survey",
         "Survey of COVID-Like Illness - Wave 4": "fb-survey",
         "Survey of COVID-Like Illness - Wave 5": "fb-survey",
         "Survey of COVID-Like Illness - Wave 6": "fb-survey",

facebook/delphiFacebook/R/binary.R

@@ -129,6 +129,9 @@ get_binary_indicators <- function() {
 
     "smoothed_vaccinate_children", "weight_unif", "v_vaccinate_children", 6, compute_binary_response, jeffreys_binary,
     "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_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,
 
@@ -193,7 +196,9 @@ get_binary_indicators <- function() {
     "smoothed_whesitancy_reason_pregnant", "weight", "v_hesitancy_reason_pregnant", 6, compute_binary_response, jeffreys_binary,
     "smoothed_hesitancy_reason_religious", "weight_unif", "v_hesitancy_reason_religious", 6, compute_binary_response, jeffreys_binary,
     "smoothed_whesitancy_reason_religious", "weight", "v_hesitancy_reason_religious", 6, compute_binary_response, jeffreys_binary,
-    
+    "smoothed_hesitancy_reason_dislike_vaccines_generally", "weight_unif", "v_hesitancy_reason_dislike_vaccines_generally", 6, compute_binary_response, jeffreys_binary,
+    "smoothed_whesitancy_reason_dislike_vaccines_generally", "weight", "v_hesitancy_reason_dislike_vaccines_generally", 6, compute_binary_response, jeffreys_binary,
+
     # vaccine barriers
     "smoothed_vaccine_barrier_eligible", "weight_unif", "v_vaccine_barrier_eligible", 6, compute_binary_response, jeffreys_binary,
     "smoothed_wvaccine_barrier_eligible", "weight", "v_vaccine_barrier_eligible", 6, compute_binary_response, jeffreys_binary,
@@ -219,6 +224,10 @@ get_binary_indicators <- function() {
     "smoothed_wvaccine_barrier_type", "weight", "v_vaccine_barrier_type", 6, compute_binary_response, jeffreys_binary,
     "smoothed_vaccine_barrier_none", "weight_unif", "v_vaccine_barrier_none", 6, compute_binary_response, jeffreys_binary,
     "smoothed_wvaccine_barrier_none", "weight", "v_vaccine_barrier_none", 6, compute_binary_response, jeffreys_binary,
+    "smoothed_vaccine_barrier_appointment_location", "weight_unif", "v_vaccine_barrier_appointment_location", 6, compute_binary_response, jeffreys_binary,
+    "smoothed_wvaccine_barrier_appointment_location", "weight", "v_vaccine_barrier_appointment_location", 6, compute_binary_response, jeffreys_binary,
+    "smoothed_vaccine_barrier_other", "weight_unif", "v_vaccine_barrier_other", 6, compute_binary_response, jeffreys_binary,
+    "smoothed_wvaccine_barrier_other", "weight", "v_vaccine_barrier_other", 6, compute_binary_response, jeffreys_binary,
 
     # vaccine barriers for vaccinated
     "smoothed_vaccine_barrier_eligible_has", "weight_unif", "v_vaccine_barrier_eligible_has", 6, compute_binary_response, jeffreys_binary,
@@ -245,6 +254,10 @@ get_binary_indicators <- function() {
     "smoothed_wvaccine_barrier_type_has", "weight", "v_vaccine_barrier_type_has", 6, compute_binary_response, jeffreys_binary,
     "smoothed_vaccine_barrier_none_has", "weight_unif", "v_vaccine_barrier_none_has", 6, compute_binary_response, jeffreys_binary,
     "smoothed_wvaccine_barrier_none_has", "weight", "v_vaccine_barrier_none_has", 6, compute_binary_response, jeffreys_binary,
+    "smoothed_vaccine_barrier_appointment_location_has", "weight_unif", "v_vaccine_barrier_appointment_location_has", 6, compute_binary_response, jeffreys_binary,
+    "smoothed_wvaccine_barrier_appointment_location_has", "weight", "v_vaccine_barrier_appointment_location_has", 6, compute_binary_response, jeffreys_binary,
+    "smoothed_vaccine_barrier_other_has", "weight_unif", "v_vaccine_barrier_other_has", 6, compute_binary_response, jeffreys_binary,
+    "smoothed_wvaccine_barrier_other_has", "weight", "v_vaccine_barrier_other_has", 6, compute_binary_response, jeffreys_binary,
 
     # vaccine barriers for attempted vaccinated
     "smoothed_vaccine_barrier_eligible_tried", "weight_unif", "v_vaccine_barrier_eligible_tried", 6, compute_binary_response, jeffreys_binary,
@@ -271,6 +284,11 @@ get_binary_indicators <- function() {
     "smoothed_wvaccine_barrier_type_tried", "weight", "v_vaccine_barrier_type_tried", 6, compute_binary_response, jeffreys_binary,
     "smoothed_vaccine_barrier_none_tried", "weight_unif", "v_vaccine_barrier_none_tried", 6, compute_binary_response, jeffreys_binary,
     "smoothed_wvaccine_barrier_none_tried", "weight", "v_vaccine_barrier_none_tried", 6, compute_binary_response, jeffreys_binary,
+    "smoothed_vaccine_barrier_appointment_location_tried", "weight_unif", "v_vaccine_barrier_appointment_location_tried", 6, compute_binary_response, jeffreys_binary,
+    "smoothed_wvaccine_barrier_appointment_location_tried", "weight", "v_vaccine_barrier_appointment_location_tried", 6, compute_binary_response, jeffreys_binary,
+    "smoothed_vaccine_barrier_other_tried", "weight_unif", "v_vaccine_barrier_other_tried", 6, compute_binary_response, jeffreys_binary,
+    "smoothed_wvaccine_barrier_other_tried", "weight", "v_vaccine_barrier_other_tried", 6, compute_binary_response, jeffreys_binary,
+    
 
     # reasons for belief that vaccine is unnecessary
     "smoothed_dontneed_reason_had_covid", "weight_unif", "v_dontneed_reason_had_covid", 6, compute_binary_response, jeffreys_binary,
@@ -294,6 +312,11 @@ 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,
+    
     # 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,

facebook/delphiFacebook/R/contingency_indicators.R

@@ -135,6 +135,7 @@ get_aggs <- function() {
     "pct_covid_vaccinated_friends", "v_covid_vaccinated_friends", compute_binary, jeffreys_binary,
 
     "pct_vaccinate_children", "v_vaccinate_children", compute_binary, jeffreys_binary,
+    "pct_vaccinate_child_oldest", "v_vaccinate_child_oldest", compute_binary, jeffreys_binary,
 
     "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),
@@ -203,6 +204,7 @@ get_aggs <- function() {
     "pct_hesitant_barrier_health_condition", "v_hesitant_barrier_health_condition", compute_binary, jeffreys_binary,
     "pct_hesitant_barrier_pregnant", "v_hesitant_barrier_pregnant", compute_binary, jeffreys_binary,
     "pct_hesitant_barrier_other", "v_hesitant_barrier_other", compute_binary, jeffreys_binary,
+    "pct_hesitant_barrier_dislike_vaccines_generally", "v_hesitant_barrier_dislike_vaccines_generally", compute_binary, jeffreys_binary,
 
     "pct_hesitant_dontneed_reason_had_covid", "v_hesitant_dontneed_reason_had_covid", compute_binary, jeffreys_binary,
     "pct_hesitant_dontneed_reason_dont_spend_time", "v_hesitant_dontneed_reason_dont_spend_time", compute_binary, jeffreys_binary,
@@ -227,6 +229,7 @@ get_aggs <- function() {
     "pct_barrier_health_condition", "v_hesitancy_reason_health_condition", compute_binary, jeffreys_binary,
     "pct_barrier_pregnant", "v_hesitancy_reason_pregnant", compute_binary, jeffreys_binary,
     "pct_barrier_other", "v_hesitancy_reason_other", compute_binary, jeffreys_binary,
+    "pct_barrier_dislike_vaccines_generally", "v_hesitancy_reason_dislike_vaccines_generally", compute_binary, jeffreys_binary,
 
     # vaccine "don't need" reasons
     "pct_dontneed_reason_had_covid", "v_dontneed_reason_had_covid_5abc_6", compute_binary, jeffreys_binary,
@@ -252,6 +255,7 @@ get_aggs <- function() {
     "pct_defno_barrier_health_condition", "v_defno_barrier_health_condition", compute_binary, jeffreys_binary,
     "pct_defno_barrier_pregnant", "v_defno_barrier_pregnant", compute_binary, jeffreys_binary,
     "pct_defno_barrier_other", "v_defno_barrier_other", compute_binary, jeffreys_binary,
+    "pct_defno_barrier_dislike_vaccines_generally", "v_defno_barrier_dislike_vaccines_generally", compute_binary, jeffreys_binary,
 
     "pct_defno_dontneed_reason_had_covid", "v_defno_dontneed_reason_had_covid", compute_binary, jeffreys_binary,
     "pct_defno_dontneed_reason_dont_spend_time", "v_defno_dontneed_reason_dont_spend_time", compute_binary, jeffreys_binary,
@@ -284,6 +288,8 @@ get_aggs <- function() {
     "pct_vaccine_barrier_time", "v_vaccine_barrier_time", compute_binary, jeffreys_binary,
     "pct_vaccine_barrier_type", "v_vaccine_barrier_type", compute_binary, jeffreys_binary,
     "pct_vaccine_barrier_none", "v_vaccine_barrier_none", compute_binary, jeffreys_binary,
+    "pct_vaccine_barrier_appointment_location", "v_vaccine_barrier_appointment_location", compute_binary, jeffreys_binary,
+    "pct_vaccine_barrier_other", "v_vaccine_barrier_other", compute_binary, jeffreys_binary,
 
     # beliefs
     "pct_belief_masking_effective", "b_belief_masking_effective", compute_binary, jeffreys_binary,
@@ -397,6 +403,8 @@ get_aggs <- function() {
     "pct_vaccine_barrier_time_has", "v_vaccine_barrier_time_has", compute_binary, jeffreys_binary,
     "pct_vaccine_barrier_type_has", "v_vaccine_barrier_type_has", compute_binary, jeffreys_binary,
     "pct_vaccine_barrier_none_has", "v_vaccine_barrier_none_has", compute_binary, jeffreys_binary,
+    "pct_vaccine_barrier_appointment_location_has", "v_vaccine_barrier_appointment_location_has", compute_binary, jeffreys_binary,
+    "pct_vaccine_barrier_other_has", "v_vaccine_barrier_other_has", compute_binary, jeffreys_binary,
 
     # vaccine barriers for tried vaccinated
     "pct_vaccine_barrier_eligible_tried", "v_vaccine_barrier_eligible_tried", compute_binary, jeffreys_binary,
@@ -410,7 +418,9 @@ get_aggs <- function() {
     "pct_vaccine_barrier_childcare_tried", "v_vaccine_barrier_childcare_tried", compute_binary, jeffreys_binary,
     "pct_vaccine_barrier_time_tried", "v_vaccine_barrier_time_tried", compute_binary, jeffreys_binary,
     "pct_vaccine_barrier_type_tried", "v_vaccine_barrier_type_tried", compute_binary, jeffreys_binary,
-    "pct_vaccine_barrier_none_tried", "v_vaccine_barrier_none_tried", compute_binary, jeffreys_binary
+    "pct_vaccine_barrier_none_tried", "v_vaccine_barrier_none_tried", compute_binary, jeffreys_binary,
+    "pct_vaccine_barrier_appointment_location_tried", "v_vaccine_barrier_appointment_location_tried", compute_binary, jeffreys_binary,
+    "pct_vaccine_barrier_other_tried", "v_vaccine_barrier_other_tried", compute_binary, jeffreys_binary
   )
 
   aggs <- create_aggs_product(regions, groups, indicators)

facebook/delphiFacebook/R/contingency_variables.R

@@ -503,16 +503,27 @@ code_vaccine_barriers <- function(input_data, wave) {
     input_data$v_hesitant_barrier_other <- is_selected(hesitancy_reasons, "13")
     input_data$v_hesitant_barrier_pregnant <- is_selected(hesitancy_reasons, "14")
     input_data$v_hesitant_barrier_religious <- is_selected(hesitancy_reasons, "15")
+    input_data$v_hesitant_barrier_dislike_vaccines_generally <- is_selected(hesitancy_reasons, "16") # replacing choice 5 as of Wave 12
 
-    # These response choices were removed starting in Wave 11. They are explicitly set to missing
-    # for waves 11 and later since `is_selected` will return FALSE (meaning "not selected") for
-    # them if the respondent selected at least once answer choice.
-    input_data$v_hesitant_barrier_allergic[input_data$wave >= 11] <- NA
-    input_data$v_hesitant_barrier_not_recommended[input_data$wave >= 11] <- NA
-    input_data$v_hesitant_barrier_distrust_vaccines[input_data$wave >= 11] <- NA
-    input_data$v_hesitant_barrier_health_condition[input_data$wave >= 11] <- NA
-    input_data$v_hesitant_barrier_pregnant[input_data$wave >= 11] <- NA
-    
+    # For waves before a given response choice existed, explicitly set the
+    # derived field to missing since `is_selected` will return FALSE (meaning
+    # "not selected") for them if the respondent selected at least once answer
+    # choice.
+    if (wave >= 11) {
+      input_data$v_hesitant_barrier_allergic <- NA
+      input_data$v_hesitant_barrier_not_recommended <- NA
+      input_data$v_hesitant_barrier_health_condition <- NA
+      input_data$v_hesitant_barrier_pregnant <- NA
+    }
+    if (wave == 11) {
+      input_data$v_hesitant_barrier_distrust_vaccines <- NA
+    }
+    if (wave < 12) {
+      input_data$v_hesitant_barrier_dislike_vaccines_generally <- NA
+    }
+    if (wave >= 12) {
+      input_data$v_hesitant_barrier_dislike_vaccines <- NA
+    }
   } else {
     input_data$v_hesitant_barrier_sideeffects <- NA
     input_data$v_hesitant_barrier_allergic <- NA
@@ -529,6 +540,7 @@ code_vaccine_barriers <- function(input_data, wave) {
     input_data$v_hesitant_barrier_other <- NA
     input_data$v_hesitant_barrier_pregnant <- NA
     input_data$v_hesitant_barrier_religious <- NA
+    input_data$v_hesitant_barrier_dislike_vaccines_generally <- NA
   }
 
   # defno_barrier_<reason>
@@ -554,16 +566,27 @@ code_vaccine_barriers <- function(input_data, wave) {
     input_data$v_defno_barrier_other <- is_selected(defno_reasons, "13")
     input_data$v_defno_barrier_pregnant <- is_selected(defno_reasons, "14")
     input_data$v_defno_barrier_religious <- is_selected(defno_reasons, "15")
-
-    # These response choices were removed starting in Wave 11. They are explicitly set to missing
-    # for waves 11 and later since `is_selected` will return FALSE (meaning "not selected") for
-    # them if the respondent selected at least once answer choice.
-    input_data$v_defno_barrier_allergic[input_data$wave >= 11] <- NA
-    input_data$v_defno_barrier_not_recommended[input_data$wave >= 11] <- NA
-    input_data$v_defno_barrier_distrust_vaccines[input_data$wave >= 11] <- NA
-    input_data$v_defno_barrier_health_condition[input_data$wave >= 11] <- NA
-    input_data$v_defno_barrier_pregnant[input_data$wave >= 11] <- NA
-
+    input_data$v_defno_barrier_dislike_vaccines_generally <- is_selected(defno_reasons, "16") # replacing choice 5 as of Wave 12
+    
+    # For waves before a given response choice existed, explicitly set the
+    # derived field to missing since `is_selected` will return FALSE (meaning
+    # "not selected") for them if the respondent selected at least once answer
+    # choice.
+    if (wave >= 11) {
+      input_data$v_defno_barrier_allergic <- NA
+      input_data$v_defno_barrier_not_recommended <- NA
+      input_data$v_defno_barrier_health_condition <- NA
+      input_data$v_defno_barrier_pregnant <- NA
+    }
+    if (wave == 11) {
+      input_data$v_defno_barrier_distrust_vaccines <- NA
+    }
+    if (wave < 12) {
+      input_data$v_defno_barrier_dislike_vaccines_generally <- NA
+    }
+    if (wave >= 12) {
+      input_data$v_defno_barrier_dislike_vaccines <- NA
+    }
   } else {
     input_data$v_defno_barrier_sideeffects <- NA
     input_data$v_defno_barrier_allergic <- NA
@@ -580,6 +603,7 @@ code_vaccine_barriers <- function(input_data, wave) {
     input_data$v_defno_barrier_other <- NA
     input_data$v_defno_barrier_pregnant <- NA
     input_data$v_defno_barrier_religious <- NA
+    input_data$v_defno_barrier_dislike_vaccines_generally <- NA
   }
 
 # dontneed_reason_<reason>

facebook/delphiFacebook/R/responses.R

@@ -694,7 +694,7 @@ surveyID_to_wave <- Vectorize(function(surveyID) {
                 "SV_6PADB8DyF9SIyXk" = 10,
                 "SV_4VEaeffqQtDo33M" = 11,
                 "SV_3TL0r243mLkDzCK" = 12.5, # experimental version of Wave 12
-                "TBD finalized version" = 12 # finalized version of Wave 12
+                "SV_eDISRi5wQcNU70G" = 12 # finalized version of Wave 12
   )
 
   if ( any(names(waves) == surveyID) ) {