HiRID - Run discovery analysis

[dancoster]

1) Before running discovery analysis - review Ricu package and improve HIRID_MAPPING: https://cran.r-project.org/web/packages/ricu/ricu.pdf and map per each of the lab tests in MIMIC the same lab test in HiRid.

2) Run HiRiD discovery

3) Explore how can we match medications between HiRid and MIMIC (ATC5).

[dancoster]

• Run in a different job and estimate how much time is taken per 'part'.

[PavanReddy28]

Significant Medication<>Lab Pairs

hirid_sig_med_lab_pairs_pval_non_vital_signs.csv

• Hard threshold of 0.01: hirid_sig_med_lab_pairs_hard_non_vital_signs.csv
• FDR Analysis: hirid_sig_med_lab_pairs_fdr_non_vital_signs.csv
• Bonferroni Analysis - hirid_sig_med_lab_pairs_bonferroni_non_vital_signs.csv

[PavanReddy28]

1-Sampled T test on the ratios

hirid_sig_med_lab_pairs_pval_ratio_non_vital_signs.csv

• Hard threshold of 0.01: hirid_sig_med_lab_pairs_hard_ratio_non_vital_signs.csv
• FDR Analysis: hirid_sig_med_lab_pairs_fdr_ratio_non_vital_signs.csv
• Bonferroni Analysis: hirid_sig_med_lab_pairs_bonferroni_ratio_non_vital_signs.csv

[dancoster]

(1) Why there is only 12 measurements:

• Heart rate

• Respiratory rate

• Core body temperature

• Peripheral oxygen saturation

• Calcium.ionized [Moles/volume] in Blood

• Carboxyhemoglobin/Hemoglobin.total in Arterial blood

• Glucose [Moles/volume] in Serum or Plasma

• Hemoglobin [Mass/volume] in Arterial blood

• Methemoglobin/Hemoglobin.total in Arterial blood

• Potassium [Moles/volume] in Blood

• Sodium [Moles/volume] in Blood

• Hemoglobin [Mass/volume] in Blood

(2) Why ' Metronidazole tabl 200 mg' is consider a 'lab_name'? (It's a drug)

[PavanReddy28]

1. During generation of med lab pairs in HIRID, the lab mapping used included on the above 12 measurements. After working on HiRiD extract, there are more lab measurement labels.
2. In the HiRiD Variable reference table I found 300 variable id associated with both Respiratory rate and Metronidazole table 200 mg. I have temporarily removed 300 variable id.

[dancoster]

Please check how we can display (writing to a log file) the progress of the script.