add dob_year and edit antimalarial #189

ekamau · 2023-09-30T23:15:02Z

Added dob_year and
edited antimalarial attributes in visit table - moved from experimental agents to antimalarial treatment,
as in Miscellaneous bugs/inconsistencies #178

github-actions · 2023-09-30T23:15:27Z

Summary of the missing optional fields for the ccp-ghana parser:

table	missing	total_fields	percentage_coverage
subject	12	53	77.358491%
visit	16	56	71.428571%
observation	23	69	66.666667%

SUBJECT                                         
dataset_id                                      False
sex                                             False
preterm_infant                                  False
has_asplenia                                    False
has_tuberculosis                                False
has_chronic_respiratory_disease                 False
diabetes_type                                   False
has_apnoea                                      False
has_inflammatory_bowel_disease                  False
has_rare_disease_inborn_metabolism_error        False
has_tuberculosis_past                           False
has_comorbidity_other                           False
VISIT                                           
dataset_id                                      False
phase                                           False
treatment_oxygen_mask_prongs                    False
treatment_antifungal_agent_type                 False
treatment_anticoagulation                       False
treatment_steroids                              False
treatment_immunosuppressant                     False
treatment_cpr                                   False
treatment_offlabel                              False
treatment_respiratory_support                   False
treatment_colchicine                            False
treatment_immunoglobulins                       False
treatment_delirium                              False
treatment_delirium_type                         False
treatment_monoclonal_antibody                   False
treatment_pacing                                False
OBSERVATION                                     
acvpu                                           False
clinical_classification_critical_illness_scale  False
total_fluid_output_ml                           False
oxygen_o2hb                                     False
clinical_frailty_score                          False
inability_to_walk_scale                         False
blantyre_coma_score                             False
mid_upper_arm_circumference_cm                  False
richmond_agitation-sedation_scale               False
riker_sedation-agitation_scale                  False
mean_arterial_blood_pressure_mmHg               False
anorexia                                        False
bleeding                                        False
confusion                                       False
cyanosis                                        False
feeding_intolerance_pediatrics                  False
hepatomegaly                                    False
irritability_pediatrics                         False
lung_sounds                                     False
lymphadenopathy                                 False
musculoskeletal_pain                            False
severe_dehydration                              False
heart_sounds                                    False

github-actions · 2023-10-04T11:22:38Z

Summary of the missing optional fields for the ccp-ghana parser:

table	missing	total_fields	percentage_coverage
subject	12	53	77.358491%
visit	16	56	71.428571%
observation	23	69	66.666667%

SUBJECT                                         
dataset_id                                      False
sex                                             False
preterm_infant                                  False
has_asplenia                                    False
has_tuberculosis                                False
has_chronic_respiratory_disease                 False
diabetes_type                                   False
has_apnoea                                      False
has_inflammatory_bowel_disease                  False
has_rare_disease_inborn_metabolism_error        False
has_tuberculosis_past                           False
has_comorbidity_other                           False
VISIT                                           
dataset_id                                      False
phase                                           False
treatment_oxygen_mask_prongs                    False
treatment_antifungal_agent_type                 False
treatment_anticoagulation                       False
treatment_steroids                              False
treatment_immunosuppressant                     False
treatment_cpr                                   False
treatment_offlabel                              False
treatment_respiratory_support                   False
treatment_colchicine                            False
treatment_immunoglobulins                       False
treatment_delirium                              False
treatment_delirium_type                         False
treatment_monoclonal_antibody                   False
treatment_pacing                                False
OBSERVATION                                     
acvpu                                           False
clinical_classification_critical_illness_scale  False
total_fluid_output_ml                           False
oxygen_o2hb                                     False
clinical_frailty_score                          False
inability_to_walk_scale                         False
blantyre_coma_score                             False
mid_upper_arm_circumference_cm                  False
richmond_agitation-sedation_scale               False
riker_sedation-agitation_scale                  False
mean_arterial_blood_pressure_mmHg               False
anorexia                                        False
bleeding                                        False
confusion                                       False
cyanosis                                        False
feeding_intolerance_pediatrics                  False
hepatomegaly                                    False
irritability_pediatrics                         False
lung_sounds                                     False
lymphadenopathy                                 False
musculoskeletal_pain                            False
severe_dehydration                              False
heart_sounds                                    False

pipliggins · 2023-10-04T11:24:56Z

Thanks @ekamau! I've made a couple of minor edits (mostly just adding excludeWhen = "none" where required), but this all looks good to me now.

pipliggins · 2023-10-04T16:03:20Z

Left open until we decide how to deal with Washington (with age ranges rather than a single value).

sadiekelly · 2023-10-06T15:22:59Z

isaric/parsers/isaric-rapid.toml

+  ]
+
+[visit.treatment_antimalarial_type]
+  combinedType = "set"


@ekamau I don't think other antimalarial treatments as indicated in antimal_cmtype, daily_antimal_cmtype and overall_antimal_cmtype have all been included - I couldn't see these in the parser in the main branch and the edits here only include chloroquine and hydroxychloroquine. So these additional ones could be mapped also (primaquine, quinine/mefloquine etc.)

Thanks @sadiekelly - I have added the extra variables

sadiekelly · 2023-10-06T15:39:23Z

isaric/parsers/western-australia.toml

+    { field = "daily_exper_cmtype___2", values = { 1 = true } },
+    { field = "exper_cmtype___1", values = { 1 = true } },
+    { field = "exper_cmtype___2", values = { 1 = true } },
+  ]


same comment as for RAPID re. the other antimalarials listed in *antimal_cmtype variables not yet mapped

Thanks @sadiekelly - I have added the extra variables

ekamau · 2023-10-08T02:09:32Z

Hi @pipliggins - kindly check the changes to experimental agent .. I moved or changed these to 'treatment_other'. I think we are also meant to move some experimental agent information to metadata.
Thanks!

github-actions · 2023-11-08T18:46:24Z

Summary of the missing optional fields for the ccp-cameroon parser:

table	missing	total_fields	percentage_coverage
subject	17	56	69.642857%
visit	26	53	50.943396%
observation	29	70	58.571429%

SUBJECT                                         
dataset_id                                      False
sex_at_birth                                    False
ethnicity                                       False
works_microbiology_lab                          False
pregnancy_date_of_delivery                      False
pregnancy_post_partum                           False
preterm_infant                                  False
has_asplenia                                    False
has_chronic_respiratory_disease                 False
diabetes_type                                   False
has_apnoea                                      False
has_inflammatory_bowel_disease                  False
has_rare_disease_inborn_metabolism_error        False
has_solid_organ_transplant                      False
has_tuberculosis_past                           False
has_hiv_art                                     False
has_immunosuppression                           False
VISIT                                           
dataset_id                                      False
phase                                           False
treatment_corticosteroid_type                   False
treatment_corticosteroid_type_other             False
treatment_oxygen_mask_prongs                    False
treatment_antifungal_agent_type                 False
treatment_antibiotics_type                      False
treatment_anticoagulation                       False
treatment_ace_inhibitors                        False
treatment_arb                                   False
treatment_antimalarial_type                     False
treatment_high_flow_nasal_cannula               False
treatment_steroids                              False
treatment_immunosuppressant                     False
treatment_intravenous_fluids                    False
treatment_nsaid                                 False
treatment_neuromuscular_blocking_agents         False
treatment_cpr                                   False
treatment_offlabel                              False
treatment_respiratory_support                   False
treatment_colchicine                            False
treatment_immunoglobulins                       False
treatment_delirium                              False
treatment_delirium_type                         False
treatment_monoclonal_antibody                   False
treatment_pacing                                False
OBSERVATION                                     
avpu                                            False
acvpu                                           False
oxygen_flow_volume_max                          False
oxygen_flow_volume_max                          False
clinical_classification_critical_illness_scale  False
total_fluid_output_ml                           False
base_excess                                     False
clinical_frailty_score                          False
inability_to_walk_scale                         False
glasgow_coma_score                              False
blantyre_coma_score                             False
mid_upper_arm_circumference_cm                  False
fio2_percent                                    False
pao2_mmHg                                       False
pco2_mmHg                                       False
pH                                              False
richmond_agitation-sedation_scale               False
riker_sedation-agitation_scale                  False
other_symptom                                   False
mean_arterial_blood_pressure_mmHg               False
anorexia                                        False
bleeding                                        False
confusion                                       False
cyanosis                                        False
feeding_intolerance_pediatrics                  False
hepatomegaly                                    False
inability_to_walk                               False
irritability_pediatrics                         False
lung_sounds                                     False
heart_sounds                                    False

github-actions · 2023-11-08T18:53:01Z

Summary of the missing optional fields for the ccp-cameroon parser:

table	missing	total_fields	percentage_coverage
subject	17	56	69.642857%
visit	26	53	50.943396%
observation	29	70	58.571429%

SUBJECT                                         
dataset_id                                      False
sex_at_birth                                    False
ethnicity                                       False
works_microbiology_lab                          False
pregnancy_date_of_delivery                      False
pregnancy_post_partum                           False
preterm_infant                                  False
has_asplenia                                    False
has_chronic_respiratory_disease                 False
diabetes_type                                   False
has_apnoea                                      False
has_inflammatory_bowel_disease                  False
has_rare_disease_inborn_metabolism_error        False
has_solid_organ_transplant                      False
has_tuberculosis_past                           False
has_hiv_art                                     False
has_immunosuppression                           False
VISIT                                           
dataset_id                                      False
phase                                           False
treatment_corticosteroid_type                   False
treatment_corticosteroid_type_other             False
treatment_oxygen_mask_prongs                    False
treatment_antifungal_agent_type                 False
treatment_antibiotics_type                      False
treatment_anticoagulation                       False
treatment_ace_inhibitors                        False
treatment_arb                                   False
treatment_antimalarial_type                     False
treatment_high_flow_nasal_cannula               False
treatment_steroids                              False
treatment_immunosuppressant                     False
treatment_intravenous_fluids                    False
treatment_nsaid                                 False
treatment_neuromuscular_blocking_agents         False
treatment_cpr                                   False
treatment_offlabel                              False
treatment_respiratory_support                   False
treatment_colchicine                            False
treatment_immunoglobulins                       False
treatment_delirium                              False
treatment_delirium_type                         False
treatment_monoclonal_antibody                   False
treatment_pacing                                False
OBSERVATION                                     
avpu                                            False
acvpu                                           False
oxygen_flow_volume_max                          False
oxygen_flow_volume_max                          False
clinical_classification_critical_illness_scale  False
total_fluid_output_ml                           False
base_excess                                     False
clinical_frailty_score                          False
inability_to_walk_scale                         False
glasgow_coma_score                              False
blantyre_coma_score                             False
mid_upper_arm_circumference_cm                  False
fio2_percent                                    False
pao2_mmHg                                       False
pco2_mmHg                                       False
pH                                              False
richmond_agitation-sedation_scale               False
riker_sedation-agitation_scale                  False
other_symptom                                   False
mean_arterial_blood_pressure_mmHg               False
anorexia                                        False
bleeding                                        False
confusion                                       False
cyanosis                                        False
feeding_intolerance_pediatrics                  False
hepatomegaly                                    False
inability_to_walk                               False
irritability_pediatrics                         False
lung_sounds                                     False
heart_sounds                                    False

add dob_year and edit antimalarial

04923c8

ekamau requested review from abhidg and pipliggins September 30, 2023 23:15

Minor edits

3ece599

pipliggins approved these changes Oct 4, 2023

View reviewed changes

ekamau added the needs-review label Oct 4, 2023

Merge branch 'main' into edits_misc_issues

d616b39

globaldothealth deleted a comment from github-actions bot Oct 5, 2023

sadiekelly reviewed Oct 6, 2023

View reviewed changes

ekamau added 2 commits October 7, 2023 17:45

merge experimental agents to others

9da4498

extra edits for antimalarials

8ed41cf

ekamau requested a review from pipliggins October 8, 2023 02:07

globaldothealth deleted a comment from github-actions bot Nov 8, 2023

pipliggins added 2 commits November 7, 2023 20:33

Fixes

80d22b4

Merge branch 'main' into edits_misc_issues

25fb240

globaldothealth deleted a comment from github-actions bot Nov 8, 2023

Add experimental agent metadata

c4b814a

Add dob_year for washington parser

2ab4a31

pipliggins merged commit 219a7d2 into main Nov 8, 2023
3 checks passed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

add dob_year and edit antimalarial #189

add dob_year and edit antimalarial #189

ekamau commented Sep 30, 2023

github-actions bot commented Sep 30, 2023

github-actions bot commented Oct 4, 2023

pipliggins commented Oct 4, 2023

pipliggins commented Oct 4, 2023

sadiekelly Oct 6, 2023

ekamau Oct 8, 2023

sadiekelly Oct 6, 2023

ekamau Oct 8, 2023

ekamau commented Oct 8, 2023

github-actions bot commented Nov 8, 2023

github-actions bot commented Nov 8, 2023

add dob_year and edit antimalarial #189

add dob_year and edit antimalarial #189

Conversation

ekamau commented Sep 30, 2023

github-actions bot commented Sep 30, 2023

github-actions bot commented Oct 4, 2023

pipliggins commented Oct 4, 2023

pipliggins commented Oct 4, 2023

sadiekelly Oct 6, 2023

Choose a reason for hiding this comment

ekamau Oct 8, 2023

Choose a reason for hiding this comment

sadiekelly Oct 6, 2023

Choose a reason for hiding this comment

ekamau Oct 8, 2023

Choose a reason for hiding this comment

ekamau commented Oct 8, 2023

github-actions bot commented Nov 8, 2023

github-actions bot commented Nov 8, 2023