---
title: "Creating an Findings SDTM domain"
output: 
  rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Creating an Findings SDTM domain}
  %\VignetteEncoding{UTF-8}
  %\VignetteEngine{knitr::rmarkdown}
---

```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(sdtm.oak)
library(admiraldev)
library(rlang)
library(dplyr, warn.conflicts = FALSE)
```

# Introduction

This article describes how to create a Findings SDTM domain using the {sdtm.oak} package. Examples are currently presented and tested in the context of the VS domain.

Before reading this article, it is recommended that users review the "Creating an Interventions Domain" article, which provides a detailed explanation of various concepts in {sdtm.oak}, such as `oak_id_vars`, `condition_add`, etc. It also offers guidance on which mapping algorithms or functions to use for different mappings and provides a more detailed explanation of how these mapping algorithms or functions work.

In this article, we will dive directly into programming and provide further explanation only where it is required.

# Programming workflow

In {sdtm.oak} we process one raw dataset at a time. Similar raw datasets (example Vital Signs - Screening (OID - vs_raw), Vital Signs - Treatment (OID - vs_t_raw)) can be stacked together before processing.

* [Read in data](#readdata)
* [Create oak_id_vars](#oakidvars)
* [Read in CT](#readct)
* [Map Topic Variable](#maptopic)
* [Map Rest of the Variables](#maprest)
* [Repeat Map Topic and Map Rest](#repeatsteps)

Repeat the above steps for different raw datasets before proceeding with the below steps.

* [Create SDTM derived variables](#derivedvars)
* [Add Labels and Attributes](#attributes)

## Read in data {#readdata}

Read all the raw datasets into the environment. In this example, the raw dataset name is `vs_raw`. Users can read it from the package using the below code:

```{r eval=TRUE}
vs_raw <- read.csv(system.file("raw_data/vitals_raw_data.csv",
  package = "sdtm.oak"
))
```


```{r, eval=TRUE, echo=FALSE}
sdtm.oak:::dataset_oak_vignette(
  vs_raw,
  display_vars = exprs(
    PATNUM, FORML, ASMNTDN, TMPTC, VTLD, VTLTM, SUBPOS, SYS_BP, DIA_BP,
    PULSE, RESPRT, TEMP, TEMPLOC, OXY_SAT, LAT, LOC
  )
)
```

## Create oak_id_vars {#oakidvars}

```{r eval=TRUE}
vs_raw <- vs_raw %>%
  generate_oak_id_vars(
    pat_var = "PATNUM",
    raw_src = "vitals"
  )
```

```{r, eval=TRUE, echo=FALSE}
sdtm.oak:::dataset_oak_vignette(
  vs_raw,
  display_vars = exprs(
    oak_id, raw_source, patient_number, PATNUM, FORML, SYS_BP, DIA_BP
  )
)
```

Read in the DM domain

```{r eval=TRUE, echo=FALSE}
dm <- read.csv(system.file("raw_data/dm.csv",
  package = "sdtm.oak"
))
```


## Read in CT {#readct}

Controlled Terminology is part of the SDTM specification and it is prepared by the user.  In this example, the study controlled terminology name is `sdtm_ct.csv`. Users can read it from the package using the below code:

```{r eval=TRUE}
study_ct <- read.csv(system.file("raw_data/sdtm_ct.csv",
  package = "sdtm.oak"
))
```

```{r, eval=TRUE, echo=FALSE}
sdtm.oak:::dataset_oak_vignette(
  study_ct,
  display_vars = exprs(
    codelist_code, term_code, term_value, collected_value, term_preferred_term,
    term_synonyms
  )
)
```

## Map Topic Variable {#maptopic}

This raw dataset has multiple topic variables. Lets start with the first topic variable. Map topic variable SYSBP from the raw variable SYS_BP.

```{r eval=TRUE}
# Map topic variable SYSBP and its qualifiers.
vs_sysbp <-
  hardcode_ct(
    raw_dat = vs_raw,
    raw_var = "SYS_BP",
    tgt_var = "VSTESTCD",
    tgt_val = "SYSBP",
    ct_spec = study_ct,
    ct_clst = "C66741"
  ) %>%
  # Filter for records where VSTESTCD is not empty.
  # Only these records need qualifier mappings.
  dplyr::filter(!is.na(.data$VSTESTCD))
```

```{r, eval=TRUE, echo=FALSE}
sdtm.oak:::dataset_oak_vignette(
  vs_sysbp,
  display_vars = exprs(
    oak_id, raw_source, patient_number, VSTESTCD
  )
)
```

## Map Rest of the Variables {#maprest}

Map rest of the variables applicable to the topic variable SYSBP. This can include qualifiers, identifier and timing variables.

```{r eval=TRUE}
# Map topic variable SYSBP and its qualifiers.
vs_sysbp <- vs_sysbp %>%
  # Map VSTEST using hardcode_ct algorithm
  hardcode_ct(
    raw_dat = vs_raw,
    raw_var = "SYS_BP",
    tgt_var = "VSTEST",
    tgt_val = "Systolic Blood Pressure",
    ct_spec = study_ct,
    ct_clst = "C67153",
    id_vars = oak_id_vars()
  ) %>%
  # Map VSORRES using assign_no_ct algorithm
  assign_no_ct(
    raw_dat = vs_raw,
    raw_var = "SYS_BP",
    tgt_var = "VSORRES",
    id_vars = oak_id_vars()
  ) %>%
  # Map VSORRESU using hardcode_ct algorithm
  hardcode_ct(
    raw_dat = vs_raw,
    raw_var = "SYS_BP",
    tgt_var = "VSORRESU",
    tgt_val = "mmHg",
    ct_spec = study_ct,
    ct_clst = "C66770",
    id_vars = oak_id_vars()
  ) %>%
  # Map VSPOS using assign_ct algorithm
  assign_ct(
    raw_dat = vs_raw,
    raw_var = "SUBPOS",
    tgt_var = "VSPOS",
    ct_spec = study_ct,
    ct_clst = "C71148",
    id_vars = oak_id_vars()
  )
```

```{r, eval=TRUE, echo=FALSE}
sdtm.oak:::dataset_oak_vignette(
  vs_sysbp,
  display_vars = exprs(
    oak_id, raw_source, patient_number, VSTESTCD, VSTEST, VSORRES, VSORRESU, VSPOS
  )
)
```

## Repeat Map Topic and Map Rest {#repeatsteps}

This raw data source has other topic variables DIABP, PULSE, RESP, TEMP, OXYSAT, VSALL and its corresponding qualifiers. Repeat mapping topic and qualifiers for each topic variable.

```{r eval=TRUE}
# Map topic variable DIABP and its qualifiers.
vs_diabp <-
  hardcode_ct(
    raw_dat = vs_raw,
    raw_var = "DIA_BP",
    tgt_var = "VSTESTCD",
    tgt_val = "DIABP",
    ct_spec = study_ct,
    ct_clst = "C66741"
  ) %>%
  dplyr::filter(!is.na(.data$VSTESTCD)) %>%
  # Map VSTEST using hardcode_ct algorithm
  hardcode_ct(
    raw_dat = vs_raw,
    raw_var = "DIA_BP",
    tgt_var = "VSTEST",
    tgt_val = "Diastolic Blood Pressure",
    ct_spec = study_ct,
    ct_clst = "C67153",
    id_vars = oak_id_vars()
  ) %>%
  # Map VSORRES using assign_no_ct algorithm
  assign_no_ct(
    raw_dat = vs_raw,
    raw_var = "DIA_BP",
    tgt_var = "VSORRES",
    id_vars = oak_id_vars()
  ) %>%
  # Map VSORRESU using hardcode_ct algorithm
  hardcode_ct(
    raw_dat = vs_raw,
    raw_var = "DIA_BP",
    tgt_var = "VSORRESU",
    tgt_val = "mmHg",
    ct_spec = study_ct,
    ct_clst = "C66770",
    id_vars = oak_id_vars()
  ) %>%
  # Map VSPOS using assign_ct algorithm
  assign_ct(
    raw_dat = vs_raw,
    raw_var = "SUBPOS",
    tgt_var = "VSPOS",
    ct_spec = study_ct,
    ct_clst = "C71148",
    id_vars = oak_id_vars()
  )

# Map topic variable PULSE and its qualifiers.
vs_pulse <-
  hardcode_ct(
    raw_dat = vs_raw,
    raw_var = "PULSE",
    tgt_var = "VSTESTCD",
    tgt_val = "PULSE",
    ct_spec = study_ct,
    ct_clst = "C66741"
  ) %>%
  dplyr::filter(!is.na(.data$VSTESTCD)) %>%
  # Map VSTEST using hardcode_ct algorithm
  hardcode_ct(
    raw_dat = vs_raw,
    raw_var = "PULSE",
    tgt_var = "VSTEST",
    tgt_val = "Pulse Rate",
    ct_spec = study_ct,
    ct_clst = "C67153",
    id_vars = oak_id_vars()
  ) %>%
  # Map VSORRES using assign_no_ct algorithm
  assign_no_ct(
    raw_dat = vs_raw,
    raw_var = "PULSE",
    tgt_var = "VSORRES",
    id_vars = oak_id_vars()
  ) %>%
  # Map VSORRESU using hardcode_ct algorithm
  hardcode_ct(
    raw_dat = vs_raw,
    raw_var = "PULSE",
    tgt_var = "VSORRESU",
    tgt_val = "beats/min",
    ct_spec = study_ct,
    ct_clst = "C66770",
    id_vars = oak_id_vars()
  )

# Map topic variable RESP from the raw variable RESPRT and its qualifiers.
vs_resp <-
  hardcode_ct(
    raw_dat = vs_raw,
    raw_var = "RESPRT",
    tgt_var = "VSTESTCD",
    tgt_val = "RESP",
    ct_spec = study_ct,
    ct_clst = "C66741"
  ) %>%
  dplyr::filter(!is.na(.data$VSTESTCD)) %>%
  # Map VSTEST using hardcode_ct algorithm
  hardcode_ct(
    raw_dat = vs_raw,
    raw_var = "RESPRT",
    tgt_var = "VSTEST",
    tgt_val = "Respiratory Rate",
    ct_spec = study_ct,
    ct_clst = "C67153",
    id_vars = oak_id_vars()
  ) %>%
  # Map VSORRES using assign_no_ct algorithm
  assign_no_ct(
    raw_dat = vs_raw,
    raw_var = "RESPRT",
    tgt_var = "VSORRES",
    id_vars = oak_id_vars()
  ) %>%
  # Map VSORRESU using hardcode_ct algorithm
  hardcode_ct(
    raw_dat = vs_raw,
    raw_var = "RESPRT",
    tgt_var = "VSORRESU",
    tgt_val = "breaths/min",
    ct_spec = study_ct,
    ct_clst = "C66770",
    id_vars = oak_id_vars()
  )

# Map topic variable TEMP from raw variable TEMP and its qualifiers.
vs_temp <-
  hardcode_ct(
    raw_dat = vs_raw,
    raw_var = "TEMP",
    tgt_var = "VSTESTCD",
    tgt_val = "TEMP",
    ct_spec = study_ct,
    ct_clst = "C66741"
  ) %>%
  dplyr::filter(!is.na(.data$VSTESTCD)) %>%
  # Map VSTEST using hardcode_ct algorithm
  hardcode_ct(
    raw_dat = vs_raw,
    raw_var = "TEMP",
    tgt_var = "VSTEST",
    tgt_val = "Temperature",
    ct_spec = study_ct,
    ct_clst = "C67153",
    id_vars = oak_id_vars()
  ) %>%
  # Map VSORRES using assign_no_ct algorithm
  assign_no_ct(
    raw_dat = vs_raw,
    raw_var = "TEMP",
    tgt_var = "VSORRES",
    id_vars = oak_id_vars()
  ) %>%
  # Map VSORRESU using hardcode_ct algorithm
  hardcode_ct(
    raw_dat = vs_raw,
    raw_var = "TEMP",
    tgt_var = "VSORRESU",
    tgt_val = "C",
    ct_spec = study_ct,
    ct_clst = "C66770",
    id_vars = oak_id_vars()
  ) %>%
  # Map VSLOC from TEMPLOC using assign_ct
  assign_ct(
    raw_dat = vs_raw,
    raw_var = "TEMPLOC",
    tgt_var = "VSLOC",
    ct_spec = study_ct,
    ct_clst = "C74456",
    id_vars = oak_id_vars()
  )

# Map topic variable OXYSAT from raw variable OXY_SAT and its qualifiers.
vs_oxysat <-
  hardcode_ct(
    raw_dat = vs_raw,
    raw_var = "OXY_SAT",
    tgt_var = "VSTESTCD",
    tgt_val = "OXYSAT",
    ct_spec = study_ct,
    ct_clst = "C66741"
  ) %>%
  dplyr::filter(!is.na(.data$VSTESTCD)) %>%
  # Map VSTEST using hardcode_ct algorithm
  hardcode_ct(
    raw_dat = vs_raw,
    raw_var = "OXY_SAT",
    tgt_var = "VSTEST",
    tgt_val = "Oxygen Saturation",
    ct_spec = study_ct,
    ct_clst = "C67153",
    id_vars = oak_id_vars()
  ) %>%
  # Map VSORRES using assign_no_ct algorithm
  assign_no_ct(
    raw_dat = vs_raw,
    raw_var = "OXY_SAT",
    tgt_var = "VSORRES",
    id_vars = oak_id_vars()
  ) %>%
  # Map VSORRESU using hardcode_ct algorithm
  hardcode_ct(
    raw_dat = vs_raw,
    raw_var = "OXY_SAT",
    tgt_var = "VSORRESU",
    tgt_val = "%",
    ct_spec = study_ct,
    ct_clst = "C66770",
    id_vars = oak_id_vars()
  ) %>%
  # Map VSLAT using assign_ct from raw variable LAT
  assign_ct(
    raw_dat = vs_raw,
    raw_var = "LAT",
    tgt_var = "VSLAT",
    ct_spec = study_ct,
    ct_clst = "C99073",
    id_vars = oak_id_vars()
  ) %>%
  # Map VSLOC using assign_ct from raw variable LOC
  assign_ct(
    raw_dat = vs_raw,
    raw_var = "LOC",
    tgt_var = "VSLOC",
    ct_spec = study_ct,
    ct_clst = "C74456",
    id_vars = oak_id_vars()
  )

# Map topic variable VSALL from raw variable ASMNTDN with the logic if ASMNTDN  == 1 then VSTESTCD = VSALL
vs_vsall <-
  hardcode_ct(
    raw_dat = condition_add(vs_raw, ASMNTDN == 1L),
    raw_var = "ASMNTDN",
    tgt_var = "VSTESTCD",
    tgt_val = "VSALL",
    ct_spec = study_ct,
    ct_clst = "C66741"
  ) %>%
  dplyr::filter(!is.na(.data$VSTESTCD)) %>%
  # Map VSTEST using hardcode_ct algorithm
  hardcode_ct(
    raw_dat = vs_raw,
    raw_var = "ASMNTDN",
    tgt_var = "VSTEST",
    tgt_val = "Vital Signs",
    ct_spec = study_ct,
    ct_clst = "C67153",
    id_vars = oak_id_vars()
  )
```

Now that all the topic variable and its qualifier mappings are complete, combine all the datasets and proceed with mapping qualifiers, identifiers and timing variables applicable to all topic variables.

```{r, eval=TRUE}
# Combine all the topic variables into a single data frame and map qualifiers
# applicable to all topic variables
vs <- dplyr::bind_rows(
  vs_vsall, vs_sysbp, vs_diabp, vs_pulse, vs_resp,
  vs_temp, vs_oxysat
) %>%
  # Map qualifiers common to all topic variables
  # Map VSDTC using assign_ct algorithm
  assign_datetime(
    raw_dat = vs_raw,
    raw_var = c("VTLD", "VTLTM"),
    tgt_var = "VSDTC",
    raw_fmt = c(list(c("d-m-y", "dd-mmm-yyyy")), "H:M")
  ) %>%
  # Map VSTPT from TMPTC using assign_ct
  assign_ct(
    raw_dat = vs_raw,
    raw_var = "TMPTC",
    tgt_var = "VSTPT",
    ct_spec = study_ct,
    ct_clst = "TPT",
    id_vars = oak_id_vars()
  ) %>%
  # Map VSTPTNUM from TMPTC using assign_ct
  assign_ct(
    raw_dat = vs_raw,
    raw_var = "TMPTC",
    tgt_var = "VSTPTNUM",
    ct_spec = study_ct,
    ct_clst = "TPTNUM",
    id_vars = oak_id_vars()
  ) %>%
  # Map VISIT from INSTANCE using assign_ct
  assign_ct(
    raw_dat = vs_raw,
    raw_var = "INSTANCE",
    tgt_var = "VISIT",
    ct_spec = study_ct,
    ct_clst = "VISIT",
    id_vars = oak_id_vars()
  ) %>%
  # Map VISITNUM from INSTANCE using assign_ct
  assign_ct(
    raw_dat = vs_raw,
    raw_var = "INSTANCE",
    tgt_var = "VISITNUM",
    ct_spec = study_ct,
    ct_clst = "VISITNUM",
    id_vars = oak_id_vars()
  )
```

```{r, eval=TRUE, echo=FALSE}
sdtm.oak:::dataset_oak_vignette(
  vs,
  display_vars = exprs(
    oak_id, raw_source, patient_number, VSTESTCD, VSTEST, VSORRES, VSORRESU, VSPOS,
    VSLAT, VSDTC, VSTPT, VSTPTNUM, VISIT, VISITNUM
  )
)
```

## Create SDTM derived variables {#derivedvars}

Create derived variables applicable to all topic variables.

```{r eval=TRUE}
vs <- vs %>%
  dplyr::mutate(
    STUDYID = "test_study",
    DOMAIN = "VS",
    VSCAT = "VITAL SIGNS",
    USUBJID = paste0("test_study", "-", .data$patient_number)
  ) %>%
  # derive_seq(tgt_var = "VSSEQ",
  #            rec_vars= c("USUBJID", "VSTRT")) %>%
  derive_study_day(
    sdtm_in = .,
    dm_domain = dm,
    tgdt = "VSDTC",
    refdt = "RFXSTDTC",
    study_day_var = "VSDY"
  ) %>%
  dplyr::select("STUDYID", "DOMAIN", "USUBJID", everything())
```

```{r, eval=TRUE, echo=FALSE}
sdtm.oak:::dataset_oak_vignette(
  vs,
  display_vars = exprs(
    STUDYID, DOMAIN, USUBJID, VSTESTCD, VSTEST, VSORRES, VSORRESU, VSPOS,
    VSLAT, VSTPT, VSTPTNUM, VISIT, VISITNUM, VSDTC, VSDY
  )
)
```

## Add Labels and Attributes {#attributes}

Yet to be developed.