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Merged
merged 22 commits into from
Apr 4, 2022
Merged

Release covidcast-indicators 0.3.9 #1569

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5a5584a
type of schooling
nmdefries Feb 28, 2022
00ac1ce
remote/inperson/mix school
nmdefries Feb 28, 2022
c796acc
school safety measures
nmdefries Feb 28, 2022
6c2b328
will vaccinate child breakdown
nmdefries Feb 28, 2022
bbff812
children ages
nmdefries Feb 28, 2022
1143b25
Merge branch 'main' into ndefries/wave12-new-indicators
nmdefries Mar 7, 2022
6adb7d3
add new tool to print matrix items + refactoring
nmdefries Mar 15, 2022
d39921a
print num matrix items
nmdefries Mar 16, 2022
eeff479
correctly handle fixed display logic
nmdefries Mar 17, 2022
95fb526
Merge pull request #1561 from cmu-delphi/bot/sync-prod-main
krivard Mar 21, 2022
4528f6c
Merge pull request #1559 from cmu-delphi/ndefries/if-false-displaylogic
krivard Mar 29, 2022
ff229b8
suppress sircal warnings for vax_varrier*_tried, dontneed_reason_*
nmdefries Mar 29, 2022
32496d2
Merge pull request #1563 from cmu-delphi/ndefries/sircal-dontneedreas…
krivard Mar 30, 2022
96e8d2f
Merge branch 'main' into ndefries/output-qsf-matrix-items
nmdefries Mar 30, 2022
83c8b67
missing close parens
nmdefries Mar 30, 2022
1ce3434
diff to export affected subqs columns for matrix items
nmdefries Mar 30, 2022
651f9c5
subq export list uses recoded and carried-forward values
nmdefries Mar 30, 2022
11047b7
report oldest child age and type of schooling less frequently
nmdefries Apr 1, 2022
e5196eb
Merge pull request #1541 from cmu-delphi/ndefries/wave12-new-indicators
krivard Apr 4, 2022
18a2ce8
Merge pull request #1564 from cmu-delphi/ndefries/qsf-differ-export-m…
krivard Apr 4, 2022
7bf632a
Merge pull request #1557 from cmu-delphi/ndefries/output-qsf-matrix-i…
krivard Apr 4, 2022
06954ad
chore: bump covidcast-indicators to 0.3.9
Apr 4, 2022
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2 changes: 1 addition & 1 deletion .bumpversion.cfg
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@@ -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
38 changes: 19 additions & 19 deletions ansible/templates/sir_complainsalot-params-prod.json.j2
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Expand Up @@ -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",
Expand Down
37 changes: 28 additions & 9 deletions facebook/delphiFacebook/R/binary.R
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Expand Up @@ -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,

Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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
)


Expand Down
40 changes: 37 additions & 3 deletions facebook/delphiFacebook/R/contingency_indicators.R
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Expand Up @@ -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),
Expand Down Expand Up @@ -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")
Expand Down Expand Up @@ -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))
}
Expand Down
1 change: 1 addition & 0 deletions facebook/delphiFacebook/R/responses.R
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Expand Up @@ -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)
Expand Down
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