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Add survey integration tests to CI #1365

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22a999d
remove all survey indicators using weight_unif
nmdefries Oct 25, 2021
c35cdd7
suppress all unweighted survey indicators in sirCAL
nmdefries Oct 25, 2021
a8c0212
run tests on subset of indicators
nmdefries Oct 26, 2021
b8a5570
recombine unit and integration tests
nmdefries Nov 16, 2021
880dc38
survey workflow can use make target now
nmdefries Nov 16, 2021
08504cd
Merge branch 'main' into add-integration-tests-to-ci
nmdefries Nov 16, 2021
205dfb8
change working dir to facebook
nmdefries Nov 16, 2021
c74e63b
turn off manual check
nmdefries Nov 16, 2021
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4 changes: 2 additions & 2 deletions .github/workflows/r-ci.yml
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Expand Up @@ -57,5 +57,5 @@ jobs:
shell: Rscript {0}
- name: Check
run: |
rcmdcheck::rcmdcheck(args = c("--no-manual", "--test-dir=unit-tests"), error_on = "error")
shell: Rscript {0}
make test
working-directory: facebook
155 changes: 154 additions & 1 deletion ansible/templates/sir_complainsalot-params-prod.json.j2
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Expand Up @@ -85,7 +85,160 @@
["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_precautions", "hrr"], ["smoothed_wdontneed_reason_precautions", "hrr"],
"raw_cli",
"raw_ili",
"smoothed_cli",
"smoothed_ili",
"raw_hh_cmnty_cli",
"raw_nohh_cmnty_cli",
"smoothed_hh_cmnty_cli",
"smoothed_nohh_cmnty_cli",
"smoothed_wearing_mask",
"smoothed_wearing_mask_7d",
"smoothed_others_masked",
"smoothed_others_masked_public",
"smoothed_others_distanced_public",
"smoothed_worried_become_ill",
"smoothed_worried_finances",
"smoothed_anxious_5d",
"smoothed_depressed_5d",
"smoothed_felt_isolated_5d",
"smoothed_anxious_7d",
"smoothed_depressed_7d",
"smoothed_felt_isolated_7d",
"smoothed_worried_catch_covid",
"smoothed_travel_outside_state_5d",
"smoothed_travel_outside_state_7d",
"wip_smoothed_work_outside_home_5d",
"smoothed_work_outside_home_1d",
"smoothed_work_outside_home_indoors_1d",
"smoothed_shop_1d",
"smoothed_restaurant_1d",
"smoothed_spent_time_1d",
"smoothed_large_event_1d",
"smoothed_public_transit_1d",
"smoothed_shop_indoors_1d",
"smoothed_restaurant_indoors_1d",
"smoothed_spent_time_indoors_1d",
"smoothed_large_event_indoors_1d",
"smoothed_tested_14d",
"smoothed_tested_positive_14d",
"smoothed_screening_tested_positive_14d",
"smoothed_wanted_test_14d",
"smoothed_had_covid_ever",
"smoothed_accept_covid_vaccine",
"smoothed_accept_covid_vaccine_no_appointment",
"smoothed_appointment_or_accept_covid_vaccine",
"smoothed_covid_vaccinated_or_accept",
"smoothed_covid_vaccinated_appointment_or_accept",
"smoothed_appointment_not_vaccinated",
"smoothed_covid_vaccinated",
"smoothed_worried_vaccine_side_effects",
"smoothed_received_2_vaccine_doses",
"smoothed_covid_vaccinated_friends",
"smoothed_vaccinate_children",
"smoothed_try_vaccinate_1m",
"smoothed_vaccine_likely_friends",
"smoothed_vaccine_likely_local_health",
"smoothed_vaccine_likely_who",
"smoothed_vaccine_likely_govt_health",
"smoothed_vaccine_likely_politicians",
"smoothed_vaccine_likely_doctors",
"smoothed_trust_covid_info_doctors",
"smoothed_trust_covid_info_experts",
"smoothed_trust_covid_info_cdc",
"smoothed_trust_covid_info_govt_health",
"smoothed_trust_covid_info_politicians",
"smoothed_trust_covid_info_journalists",
"smoothed_trust_covid_info_friends",
"smoothed_trust_covid_info_religious",
"smoothed_hesitancy_reason_sideeffects",
"smoothed_hesitancy_reason_allergic",
"smoothed_hesitancy_reason_ineffective",
"smoothed_hesitancy_reason_unnecessary",
"smoothed_hesitancy_reason_dislike_vaccines",
"smoothed_hesitancy_reason_not_recommended",
"smoothed_hesitancy_reason_wait_safety",
"smoothed_hesitancy_reason_low_priority",
"smoothed_hesitancy_reason_cost",
"smoothed_hesitancy_reason_distrust_vaccines",
"smoothed_hesitancy_reason_distrust_gov",
"smoothed_hesitancy_reason_health_condition",
"smoothed_hesitancy_reason_other",
"smoothed_hesitancy_reason_pregnant",
"smoothed_hesitancy_reason_religious",
"smoothed_vaccine_barrier_eligible",
"smoothed_vaccine_barrier_no_appointments",
"smoothed_vaccine_barrier_appointment_time",
"smoothed_vaccine_barrier_technical_difficulties",
"smoothed_vaccine_barrier_document",
"smoothed_vaccine_barrier_technology_access",
"smoothed_vaccine_barrier_travel",
"smoothed_vaccine_barrier_language",
"smoothed_vaccine_barrier_childcare",
"smoothed_vaccine_barrier_time",
"smoothed_vaccine_barrier_type",
"smoothed_vaccine_barrier_none",
"smoothed_vaccine_barrier_eligible_has",
"smoothed_vaccine_barrier_no_appointments_has",
"smoothed_vaccine_barrier_appointment_time_has",
"smoothed_vaccine_barrier_technical_difficulties_has",
"smoothed_vaccine_barrier_document_has",
"smoothed_vaccine_barrier_technology_access_has",
"smoothed_vaccine_barrier_travel_has",
"smoothed_vaccine_barrier_language_has",
"smoothed_vaccine_barrier_childcare_has",
"smoothed_vaccine_barrier_time_has",
"smoothed_vaccine_barrier_type_has",
"smoothed_vaccine_barrier_none_has",
"smoothed_vaccine_barrier_eligible_tried",
"smoothed_vaccine_barrier_no_appointments_tried",
"smoothed_vaccine_barrier_appointment_time_tried",
"smoothed_vaccine_barrier_technical_difficulties_tried",
"smoothed_vaccine_barrier_document_tried",
"smoothed_vaccine_barrier_technology_access_tried",
"smoothed_vaccine_barrier_travel_tried",
"smoothed_vaccine_barrier_language_tried",
"smoothed_vaccine_barrier_childcare_tried",
"smoothed_vaccine_barrier_time_tried",
"smoothed_vaccine_barrier_type_tried",
"smoothed_vaccine_barrier_none_tried",
"smoothed_dontneed_reason_had_covid",
"smoothed_dontneed_reason_dont_spend_time",
"smoothed_dontneed_reason_not_high_risk",
"smoothed_dontneed_reason_precautions",
"smoothed_dontneed_reason_not_serious",
"smoothed_dontneed_reason_not_beneficial",
"smoothed_dontneed_reason_other",
"smoothed_inperson_school_fulltime",
"smoothed_inperson_school_parttime",
"smoothed_belief_masking_effective",
"smoothed_belief_distancing_effective",
"smoothed_belief_vaccinated_mask_unnecessary",
"smoothed_belief_children_immune",
"smoothed_belief_created_small_group",
"smoothed_belief_govt_exploitation",
"smoothed_race_treated_fairly_healthcare",
"smoothed_delayed_care_cost",
"smoothed_received_news_local_health",
"smoothed_received_news_experts",
"smoothed_received_news_cdc",
"smoothed_received_news_govt_health",
"smoothed_received_news_politicians",
"smoothed_received_news_journalists",
"smoothed_received_news_friends",
"smoothed_received_news_religious",
"smoothed_received_news_none",
"smoothed_want_info_covid_treatment",
"smoothed_want_info_vaccine_access",
"smoothed_want_info_vaccine_types",
"smoothed_want_info_covid_variants",
"smoothed_want_info_children_education",
"smoothed_want_info_mental_health",
"smoothed_want_info_relationships",
"smoothed_want_info_employment",
"smoothed_want_info_none"
]
},
"indicator-combination": {
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3 changes: 1 addition & 2 deletions facebook/Makefile
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Expand Up @@ -156,8 +156,7 @@ lint: coverage
test: delphiFacebook_1.0.tar.gz
if [ ! -f params.json ]; then cp params.json.template params.json; fi
grep testthat params.json
R CMD check --test-dir=unit-tests $<
R CMD check --test-dir=integration-tests $<
R CMD check --no-manual $<

delphiFacebook_1.0.tar.gz: $(wildcard delphiFacebook/R/*.R)
R CMD build delphiFacebook
Expand Down
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