DHSC-Capstone/chapter3.qmd

# Methods

need brief description and IRB statement

## Population and Data

This study was designed using the Medical Information Mart for Intensive
Care (MIMIC) database [@johnsonalistair]. MIMIC (Medical Information
Mart for Intensive Care) is an extensive, freely-available database
comprising de-identified health-related data from patients who were
admitted to the critical care units of the Beth Israel Deaconess Medical
Center. The database contains many different types of information, but
only data from the patients and laboratory events table are used in this
study. The database contains many kinds of information, but only data
from the patients and laboratory events table are used in this study.
The study uses version IV of the database, comprising data from 2008 -
2019.

## Data Variables and Outcomes

```{r}
#| include: FALSE

source(here::here("ML","1-data-exploration.R"))

```

A total of 18 variables were chosen for this study. The age and gender
of the patient were pulled from the patient table in the MIMIC database.
While this database contains some additional demographic information, it
is incomplete and thus unusable for this study. 16 lab values were
selected for this study, this includes:

-   **BMP**: BUN, bicarbonate, calcium, chloride, creatinine, glucose,
    potassium, sodium

-   **CBC**: Hematocrit, hemoglobin, platelet count, red blood cell
    count, white blood cell count

-   TSH

-   Free T4

The unique patient id and chart time were also retained for identifying
each sample. Each sample contains one set of 16 lab values for each
patient. Patients may have several samples in the data set that were run
at different times. Rows were retained as long as they had less than
three missing results. These missing results can be filled in by
imputation later in the process. Samples were also filtered for those
with TSH above or below the reference range of 0.27 - 4.2 uIU/mL. These
represent samples that would have reflexed for Free T4 testing. After
filtering, the final data set contained `r nrow(ds1)` rows.

Once the final data set was collected, an additional column was created
for the outcome variable to determine if the Free T4 value was
diagnostic. After adding the outcome variable, the Free T4 value was
dropped from each row. @tbl-outcome_var shows how the outcomes were
added. @tbl-data_summary shows the summary statistics of each variable
selected for the study.

| TSH Value     | Free T4 Value | Outcome             |
|---------------|---------------|---------------------|
| \>4.2 uIU/ml  | \>0.93 ng/dL  | Non-Hypothyroidism  |
| \>4.2 uIU/ml  | \<0.93 ng/dL  | Hypothyroidism      |
| \<0.27 uIU/ml | \<1.7 ng/d    | Non-Hyperthyroidism |
| \<0.27 uIU/ml | \>1.7 ng/d    | Hyperthyroidism     |

: Outcome Variable {#tbl-outcome_var}

```{r}
#| label: tbl-data_summary
#| tbl-cap: Data Summary
#| echo: false

summary_tbl %>% gtsummary$as_kable()
```

## Data Inspection

![Distribution of
Variables](figures/distrubution_histo){#fig-distro_histo}

![Variable Correlation Plot](figures/corr_plot){#fig-corr_plot}

## Data Transformations

In progress

## Model Selection

In Progress