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Fix RAPID temperature units #201

Merged
merged 4 commits into from
Nov 15, 2023
Merged

Fix RAPID temperature units #201

merged 4 commits into from
Nov 15, 2023

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pipliggins
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Update output file

Update output file
Script to convert temperature values
Update to use new file
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Summary of the missing optional fields for the isaric-rapid parser:

table missing total_fields percentage_coverage
subject 18 56 67.857143%
visit 15 53 71.698113%
observation 13 70 81.428571%
SUBJECT                                         
dataset_id                                      False
sex                                             False
works_microbiology_lab                          False
pregnancy_gestational_outcome                   False
pregnancy_whether_breastfed                     False
pregnancy_post_partum                           False
preterm_infant                                  False
has_chronic_hematologic_disease                 False
has_dementia                                    False
has_obesity                                     False
has_rheumatologic_disorder                      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_immunosuppression                           False
VISIT                                           
dataset_id                                      False
pathogen_test_date                              False
phase                                           False
treatment_antifungal_agent_type                 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
blantyre_coma_score                             False
other_symptom                                   False
anorexia                                        False
cyanosis                                        False
ear_pain                                        False
feeding_intolerance_pediatrics                  False
hepatomegaly                                    False
irritability_pediatrics                         False
lung_sounds                                     False
heart_sounds                                    False

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Summary of the missing optional fields for the isaric-rapid parser:

table missing total_fields percentage_coverage
subject 18 56 67.857143%
visit 15 53 71.698113%
observation 13 70 81.428571%
SUBJECT                                         
dataset_id                                      False
sex                                             False
works_microbiology_lab                          False
pregnancy_gestational_outcome                   False
pregnancy_whether_breastfed                     False
pregnancy_post_partum                           False
preterm_infant                                  False
has_chronic_hematologic_disease                 False
has_dementia                                    False
has_obesity                                     False
has_rheumatologic_disorder                      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_immunosuppression                           False
VISIT                                           
dataset_id                                      False
pathogen_test_date                              False
phase                                           False
treatment_antifungal_agent_type                 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
blantyre_coma_score                             False
other_symptom                                   False
anorexia                                        False
cyanosis                                        False
ear_pain                                        False
feeding_intolerance_pediatrics                  False
hepatomegaly                                    False
irritability_pediatrics                         False
lung_sounds                                     False
heart_sounds                                    False

@pipliggins
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pipliggins commented Nov 15, 2023

Fixes #169

@pipliggins pipliggins merged commit 44e9262 into main Nov 15, 2023
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