# Creating ADRS with IMWG Criteria

# Introduction

This article describes creating an `ADRS` ADaM dataset in multiple myeloma (MM) studies based on International Myeloma Working Group (IMWG) criteria. It shows a similar way of deriving the endpoints presented in Creating ADRS (Including Non-standard Endpoints). Most of the endpoints are derived by calling `admiral::derive_extreme_event()`.

The hallmark of MM is the production of monoclonal immunoglobulins and/or light chains by the clonal plasma cells. Numerous parameters need to be considered while assessing response:

1. Monoclonal protein level (confirmatory assessment required):
   - SPEP - serum protein electrophoresis,
   - SIFE - serum immunofixation electrophoresis,
   - UPEP - urine protein electrophoresis,
   - UIFE - urine immunofixation electrophoresis,
   - SFLC - serum free light chains.
2. Marrow plasma cells: bone marrow aspirate/biopsy.
3. Plasmacytoma: imaging (PET/CT, CT or MRI).
4. Bone lesions: skeletal survey.

It is worth to mention:
Whenever more than one parameter is used to assess response, the overall assigned level of response is determined by the lowest level of response.
If a critical data point to establish a level of response is missing, the evaluation is downgraded to the next lower level.

For more information user may visit International Myeloma Working Group consensus criteria for response and minimal residual disease assessment in multiple myeloma.

Examples are currently presented and tested using `ADSL` (ADaM), `RS` and `SUPPRS` (SDTM) inputs. However, other domains could be used.

In IMWG criteria each status should be confirmed by second tests giving consistent results. Confirmation should be obtained for biochemical markers but is not necessary for bone marrow or imaging studies.

Two scenarios of response data collection in a clinical trial are possible:

- `RS` contains Confirmed Response,
- `RS` contains an unconfirmed response and the Confirmed Response should be derived.

In our example we will consider the second scenario.

Note: All examples assume CDISC SDTM and/or ADaM format as input unless otherwise specified.

# Programming Workflow

- Read in Data
- Pre-processing of Input Records
- Derive Confirmed Response Parameter
- Analysis flag derivation
- Derive Progressive Disease Parameter
- Define Events
- Derive Response Parameter
- Derive Clinical Benefit Parameter
- Derive Best Confirmed Overall Response Parameter
- Other Endpoints

## Read in Data

To start, all data frames needed for the creation of `ADRS` should be read into the environment. This will be a company specific process. Some of the data frames needed may be `ADSL`, `RS` and `TU`. For this vignette we assume that `RS` provides the response values `sCR`, `CR`, `VGPR`, `PR`,`MR`, `SD`, `PD`, and `NE`.

Label for non-evaluable response can vary between studies, i.e. it can be `NE`, `NA`, `UTD`, etc. In further considerations for non-evaluable responses, we use label `NE`. User will overwrite this value if necessary.

For example purpose, the SDTM and ADaM datasets (based on CDISC Pilot test data)—which are included in `{pharmaversesdtm}` and `{pharmaverseadam}`—are used.

    library(admiral)
    library(admiralonco)
    library(dplyr)
    library(pharmaverseadam)
    library(pharmaversesdtm)
    library(lubridate)
    library(stringr)
    library(metatools)
    library(cli)
    data("adsl")
    # IMWG sdtm data
    data("rs_onco_imwg")
    data("supprs_onco_imwg")

    rs <- rs_onco_imwg
    supprs <- supprs_onco_imwg

    rs <- combine_supp(rs, supprs)

    rs <- convert_blanks_to_na(rs)

USUBJID | RSTESTCD | RSSTRESC | VISIT | RSDTC | RSDY | PDOFL | DTHPDFL | NACTDT | PDIFL
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
01-701-1015 | OVRLRESP | PD | WEEK 6 | 2014-02-12 | 42 | Y | Y | NA | NA
01-701-1028 | OVRLRESP | sCR | WEEK 6 | 2013-08 | NA | NA | NA | NA | NA
01-701-1028 | OVRLRESP | sCR | WEEK 12 | 2013-10-09 | 84 | NA | NA | NA | NA
01-701-1028 | OVRLRESP | CR | WEEK 18 | 2013-11-20 | 126 | NA | NA | NA | NA
01-701-1034 | OVRLRESP | CR | WEEK 6 | 2014-08-11 | 42 | NA | NA | NA | NA
01-701-1034 | OVRLRESP | CR | WEEK 12 | 2014-09-25 | 84 | NA | NA | NA | NA
01-701-1034 | OVRLRESP | sCR | WEEK 18 | 2014-11-04 | 126 | NA | NA | NA | NA
01-701-1097 | OVRLRESP | PD | WEEK 6 | 2014-02-11 | 42 | Y | NA | 2014-02-10 | NA
01-701-1115 | OVRLRESP | PD | WEEK 6 | 2013-01-10 | 42 | NA | NA | NA | Y
01-701-1118 | OVRLRESP | sCR | WEEK 6 | 2014-04-23 | 42 | NA | NA | NA | NA

At this step, it may be useful to join `ADSL` to your `RS` domain. Only the `ADSL` variables used for derivations are selected at this step. The rest of the relevant `ADSL` variables would be added later.

    adsl_vars <- exprs(RANDDT, TRTSDT)
    adrs <- derive_vars_merged(
      rs,
      dataset_add = adsl,
      new_vars = adsl_vars,
      by_vars = get_admiral_option("subject_keys")
    )

USUBJID | RSTESTCD | VISIT | RSDTC | RANDDT | TRTSDT
--- | --- | --- | --- | --- | ---
01-701-1015 | OVRLRESP | WEEK 6 | 2014-02-12 | 2014-01-02 | 2014-01-02
01-701-1028 | OVRLRESP | WEEK 6 | 2013-08 | 2013-07-19 | 2013-07-19
01-701-1028 | OVRLRESP | WEEK 12 | 2013-10-09 | 2013-07-19 | 2013-07-19
01-701-1028 | OVRLRESP | WEEK 18 | 2013-11-20 | 2013-07-19 | 2013-07-19
01-701-1034 | OVRLRESP | WEEK 6 | 2014-08-11 | 2014-07-01 | 2014-07-01
01-701-1034 | OVRLRESP | WEEK 12 | 2014-09-25 | 2014-07-01 | 2014-07-01
01-701-1034 | OVRLRESP | WEEK 18 | 2014-11-04 | 2014-07-01 | 2014-07-01
01-701-1097 | OVRLRESP | WEEK 6 | 2014-02-11 | 2014-01-01 | 2014-01-01
01-701-1115 | OVRLRESP | WEEK 6 | 2013-01-10 | 2012-11-30 | 2012-11-30
01-701-1118 | OVRLRESP | WEEK 6 | 2014-04-23 | 2014-03-12 | 2014-03-12

## Pre-processing of Input Records

The first step involves company-specific pre-processing of records for the required input to the downstream parameter functions. Note that this could be needed multiple times (e.g. once for investigator and once for Independent Review Facility (IRF)/Blinded Independent Central Review (BICR) records). It could even involve merging input data from other sources besides `RS`, such as `ADTR`/`TR`/`TU`.

This step would include any required selection/derivation of `ADT` or applying any necessary partial date imputations and updating `AVAL` (e.g. this should be ordered from worst to best response).

The below shows an example of a possible company-specific implementation of this step.

### Select Overall Response Records and Set Parameter Details

In this case we use the overall response records from `RS` from the investigator as our starting point. It is worth emphasizing again that responses are not confirmed. Confirmed values will be derived after further pre-processing.

The parameter details such as `PARAMCD`, `PARAM` etc will always be company-specific, but an example is shown below so that you can trace through how these records feed into the other parameter derivations.

    adrs <- adrs %>%
      filter(RSEVAL == "INVESTIGATOR" & RSTESTCD == "OVRLRESP") %>%
      mutate(
        PARAMCD = "OVR",
        PARAM = "Overall Response by Investigator",
        PARCAT1 = "Investigator",
        PARCAT2 = "IMWG"
      )

USUBJID | VISIT | RSTESTCD | RSEVAL | PARAMCD | PARAM | PARCAT1 | PARCAT2
--- | --- | --- | --- | --- | --- | --- | ---
01-701-1015 | WEEK 6 | OVRLRESP | INVESTIGATOR | OVR | Overall Response by Investigator | Investigator | IMWG
01-701-1028 | WEEK 6 | OVRLRESP | INVESTIGATOR | OVR | Overall Response by Investigator | Investigator | IMWG
01-701-1028 | WEEK 12 | OVRLRESP | INVESTIGATOR | OVR | Overall Response by Investigator | Investigator | IMWG
01-701-1028 | WEEK 18 | OVRLRESP | INVESTIGATOR | OVR | Overall Response by Investigator | Investigator | IMWG
01-701-1034 | WEEK 6 | OVRLRESP | INVESTIGATOR | OVR | Overall Response by Investigator | Investigator | IMWG
01-701-1034 | WEEK 12 | OVRLRESP | INVESTIGATOR | OVR | Overall Response by Investigator | Investigator | IMWG
01-701-1034 | WEEK 18 | OVRLRESP | INVESTIGATOR | OVR | Overall Response by Investigator | Investigator | IMWG
01-701-1097 | WEEK 6 | OVRLRESP | INVESTIGATOR | OVR | Overall Response by Investigator | Investigator | IMWG
01-701-1115 | WEEK 6 | OVRLRESP | INVESTIGATOR | OVR | Overall Response by Investigator | Investigator | IMWG
01-701-1118 | WEEK 6 | OVRLRESP | INVESTIGATOR | OVR | Overall Response by Investigator | Investigator | IMWG

### Partial Date Imputation and Deriving `ADT`, `ADTF`, `AVISIT` etc

If your data collection allows for partial dates, you could apply a company-specific imputation rule at this stage when deriving `ADT`. For this example, here we impute missing day to last possible date.

    adrs <- adrs %>%
      derive_vars_dt(
        dtc = RSDTC,
        new_vars_prefix = "A",
        highest_imputation = "D",
        date_imputation = "last"
      ) %>%
      derive_vars_dy(
        reference_date = TRTSDT,
        source_vars = exprs(ADT)
      ) %>%
      derive_vars_dtm(
        dtc = RSDTC,
        new_vars_prefix = "A",
        highest_imputation = "D",
        date_imputation = "last",
        flag_imputation = "time"
      ) %>%
      mutate(AVISIT = VISIT)

USUBJID | PARAMCD | VISIT | AVISIT | RSDTC | ADT | ADTF | ADY
--- | --- | --- | --- | --- | --- | --- | ---
01-701-1015 | OVR | WEEK 6 | WEEK 6 | 2014-02-12 | 2014-02-12 | NA | 42
01-701-1028 | OVR | WEEK 6 | WEEK 6 | 2013-08 | 2013-08-31 | D | 44
01-701-1028 | OVR | WEEK 12 | WEEK 12 | 2013-10-09 | 2013-10-09 | NA | 83
01-701-1028 | OVR | WEEK 18 | WEEK 18 | 2013-11-20 | 2013-11-20 | NA | 125
01-701-1034 | OVR | WEEK 6 | WEEK 6 | 2014-08-11 | 2014-08-11 | NA | 42
01-701-1034 | OVR | WEEK 12 | WEEK 12 | 2014-09-25 | 2014-09-25 | NA | 87
01-701-1034 | OVR | WEEK 18 | WEEK 18 | 2014-11-04 | 2014-11-04 | NA | 127
01-701-1097 | OVR | WEEK 6 | WEEK 6 | 2014-02-11 | 2014-02-11 | NA | 42
01-701-1115 | OVR | WEEK 6 | WEEK 6 | 2013-01-10 | 2013-01-10 | NA | 42
01-701-1118 | OVR | WEEK 6 | WEEK 6 | 2014-04-23 | 2014-04-23 | NA | 43

### Derive `AVALC` and `AVAL`

Here we populate `AVALC` and create the numeric version as `AVAL` (ordered from worst to best response, followed by `NE`). The `AVAL` values are not considered in the parameter derivations below, and so changing `AVAL` here would not change the result of those derivations. However, please note that the ordering of `AVAL` will be used to determine `ANL01FL` in the subsequent step, ensure that the appropriate `mode` is being set in the `admiral::derive_var_extreme_flag()`.

IMWG ordering will be used or if you’d like to provide your own company-specific ordering here you could do this as follows:

    aval_resp_imwg <- function(arg) {
      case_match(
        arg,
        "NE" ~ 8,
        "sCR" ~ 7,
        "CR" ~ 6,
        "VGPR" ~ 5,
        "PR" ~ 4,
        "MR" ~ 3,
        "SD" ~ 2,
        "PD" ~ 1,
        NA ~ NA_real_
      )
    }

    adrs <- adrs %>%
      mutate(
        AVALC = RSSTRESC,
        AVAL = aval_resp_imwg(AVALC)
      )
    #> Warning: There was 1 warning in `mutate()`.
    #> i In argument: `AVAL = aval_resp_imwg(AVALC)`.
    #> Caused by warning:
    #> ! `case_match()` was deprecated in dplyr 1.2.0.
    #> i Please use `recode_values()` instead.

USUBJID | PARAMCD | AVISIT | ADT | AVAL | AVALC
--- | --- | --- | --- | --- | ---
01-701-1015 | OVR | WEEK 6 | 2014-02-12 | 1 | PD
01-701-1028 | OVR | WEEK 6 | 2013-08-31 | 7 | sCR
01-701-1028 | OVR | WEEK 12 | 2013-10-09 | 7 | sCR
01-701-1028 | OVR | WEEK 18 | 2013-11-20 | 6 | CR
01-701-1034 | OVR | WEEK 6 | 2014-08-11 | 6 | CR
01-701-1034 | OVR | WEEK 12 | 2014-09-25 | 6 | CR
01-701-1034 | OVR | WEEK 18 | 2014-11-04 | 7 | sCR
01-701-1097 | OVR | WEEK 6 | 2014-02-11 | 1 | PD
01-701-1115 | OVR | WEEK 6 | 2013-01-10 | 1 | PD
01-701-1118 | OVR | WEEK 6 | 2014-04-23 | 7 | sCR

## Derive Confirmed Response Parameter

Confirmation of response require two consecutive readings of applicable disease parameters (biochemical analyses). No minimal time interval, but a different sample is required for the confirmation assessment. Bone marrow assessments and imaging do not need to be confirmed.

If `RS` contains unconfirmed response and confirmation is performed at next scheduled visit we can derive Confirmed Response based on response at subsequent visit.

While deriving Confirmed Response, the following should be taken into consideration:

Note: Patients will continue in the last Confirmed Response category until there is confirmation of progression or improvement to a higher response status.

Let’s define a function `aval_resp_conf` that maps numerical values to the responses, so that `PD` is prioritized and concept of “higher response status” is understandable:

    aval_resp_conf <- function(arg) {
      case_match(
        arg,
        "PD" ~ 8,
        "sCR" ~ 7,
        "CR" ~ 6,
        "VGPR" ~ 5,
        "PR" ~ 4,
        "MR" ~ 3,
        "SD" ~ 2,
        "NE" ~ 1,
        NA ~ 0
      )
    }

Below table provides a summary of the Confirmed Response status calculation at each time point. The maximum refers to numeric values previously defined in `aval_resp_conf` function.

Response at 1st time point | Response at 2nd time point | Confirmed Response at 1st time point
--- | --- | ---
sCR | sCR | sCR
CR | sCR/CR | max(CR, last Confirmed Response)
VGPR | sCR/CR/VGPR | max(VGPR, last Confirmed Response)
PR | sCR/CR/VGPR/PR | max(PR, last Confirmed Response)
MR | sCR/CR/VGPR/PR/MR | max(MR, last Confirmed Response)
sCR | CR | max(CR, last Confirmed Response)
sCR/CR | VGPR | max(VGPR, last Confirmed Response)
sCR/CR/VGPR | PR | max(PR, last Confirmed Response)
sCR/CR/VGPR/PR | MR | max(MR, last Confirmed Response)
sCR/CR/VGPR/PR/MR | SD/PD/NE/NA | max(SD, last Confirmed Response)
SD | any | max(SD, last Confirmed Response)
NE | any | max(NE, last Confirmed Response)
PD reason imaging | any | PD
PD reason serum/urine | PD/death | PD
PD reason serum/urine | sCR/CR/VGPR/PR/MR/SD/NE/NA | max(NE, last Confirmed Response)

### Handling Non-Evaluable Responses

IMWG criteria article does not define exactly what is the time interval needed to confirm a response and whether non-evaluable (`NE`) records can be ignored when confirming a response. Detailed guidelines on this topic should be specified in SAP.

We assumed in our next steps that non-evaluable records are ignored when deriving Confirmed Response. That is, to confirm response at a visit we use the response from the first subsequent visit, which had an answer other than `NE`.

### Additional Variables

To derive Confirmed Response we are using variables from `SUPPRS` dataset included in `{pharmaversesdtm}` package.

Variable Name | Variable Label
--- | ---
PDOFL | Progressive Disease: Other
PDIFL | Progressive Disease: Imaging
DTHPDFL | Death Due to Progressive Disease
NACTDT | New Anti-Cancer Therapy Date

User will overwrite variable names if necessary.

1. `PDOFL`, `PDIFL`, `DTHPDFL` variables are used in derivation of `PD` as Confirmed Response. If `PD` comes from imaging assessment (`PDIFL = "Y"`) or participant died due to disease under study before further adequate assessment could be performed (`DTHPDFL = "Y"`) or `PD` comes from biochemical markers and is followed by another `PD` (`PDOFL = "Y" and AVALC.next = "PD"`), we report `PD` as Confirmed Progression.

2. `NACTDT` variable is used to exclude assessments after start day of subsequent therapy while confirming responses (`sCR`, `CR`, `VGPR`. `PR`, `MR`). However, testing during subsequent therapy can be used to confirm `PD`.

### Definition of `derive_confirmed_response` Function

`derive_confirmed_response` function defined below takes as an argument dataset with Overall Responses and returns dataset with Confirmed Responses.

In brief, the function performs the following steps:

1. Remove records with response of `NE` and derive intermediate response.
2. Display a warning if responses used for confirmation are more than `confirmed_period` apart. User can set `confirmed_period` freely - there is no time limit on the sample we use to confirm the response.
3. Add records with response of `NE`.
4. Derive best Confirmed Response so far.
5. Assign `AVAL` and `AVALC`, remove unnecessary variables.

    confirmation_period <- 84

    derive_confirmed_response <- function(datain) {
      data_adrs <- datain %>%
        arrange(USUBJID, ADTM) %>%
        filter(AVALC != "NE") %>%
        group_by(USUBJID) %>%
        mutate(
          AVALC.next = lead(AVALC),
          AVAL.next = lead(AVAL),
          ADT.next = lead(ADT)
        ) %>%
        ungroup() %>%
        mutate(AVALC.confirmed = case_when(
          # better response
          AVALC %in% c("sCR", "CR", "VGPR", "PR", "MR") &
            AVALC.next %in% c("sCR", "CR", "VGPR", "PR", "MR") &
            (is.na(NACTDT) | ADT.next <= NACTDT) &
            AVAL.next >= AVAL ~ AVALC,
          # worse response
          AVALC %in% c("sCR", "CR", "VGPR", "PR", "MR") &
            AVALC.next %in% c("sCR", "CR", "VGPR", "PR", "MR", "SD") &
            (is.na(NACTDT) | ADT.next <= NACTDT) &
            AVAL.next < AVAL ~ AVALC.next,
          # next assessment PD, NA or after subsequent therapy
          AVALC %in% c("sCR", "CR", "VGPR", "PR", "MR") &
            (AVALC.next == "PD" | is.na(AVALC.next) |
              !is.na(NACTDT) & ADT.next > NACTDT) ~ "SD",
          # no need to confirm SD
          AVALC %in% c("SD") ~ AVALC,
          # confirmed progression
          AVALC == "PD" &
            (PDIFL == "Y" | DTHPDFL == "Y" | PDOFL == "Y" & AVALC.next == "PD") ~
            AVALC,
          # unconfirmed progression
          AVALC == "PD" & is.na(DTHPDFL) & PDOFL == "Y" &
            (AVALC.next %in% c("sCR", "CR", "VGPR", "PR", "MR", "SD") |
              is.na(AVALC.next)) ~ "NE"
        ))

      data_adrs_check <- data_adrs %>%
        mutate(diff_days = as.numeric(difftime(ADT.next, ADT, units = "days"))) %>%
        filter(diff_days > confirmation_period) %>%
        mutate(warn = paste(
          "For USUBJID", USUBJID, "to confirm", AVISIT,
          "visit, a visit that took place", diff_days, "days later was used."
        )) %>%
        pull(warn)

      if (length(data_adrs_check) > 0) {
        cli_warn("{data_adrs_check}")
      }

      data_adrs_ne <- datain %>%
        filter(AVALC == "NE") %>%
        mutate(AVALC.confirmed = AVALC)

      data_adrs_all <- bind_rows(data_adrs, data_adrs_ne) %>%
        arrange(USUBJID, ADTM) %>%
        mutate(AVAL.confirmed = aval_resp_conf(AVALC.confirmed)) %>%
        group_by(USUBJID) %>%
        # best Confirmed Response so far
        mutate(AVAL.confirmed = cummax(AVAL.confirmed)) %>%
        ungroup(USUBJID)

      # char mapping to go back to AVALC values
      avalc_resp_conf <- function(arg) {
        case_match(
          arg,
          8 ~ "PD",
          7 ~ "sCR",
          6 ~ "CR",
          5 ~ "VGPR",
          4 ~ "PR",
          3 ~ "MR",
          2 ~ "SD",
          1 ~ "NE",
          NA_real_ ~ NA
        )
      }

      data_adrs_all <- data_adrs_all %>%
        mutate(AVALC.confirmed = avalc_resp_conf(AVAL.confirmed)) %>%
        select(
          -AVAL, -AVALC, -AVAL.next, -AVALC.next, -ADT.next,
          -AVAL.confirmed
        ) %>%
        rename(AVALC = AVALC.confirmed) %>%
        mutate(AVAL = aval_resp_imwg(AVALC)) %>%
        mutate(
          PARAMCD = "COVR",
          PARAM = "Confirmed Response at Time Point by Investigator",
          PARCAT1 = "Investigator",
          PARCAT2 = "IMWG"
        )
    }
    adrs_imwg <- derive_confirmed_response(adrs)

USUBJID | PARAMCD | AVISIT | ADT | AVALC
--- | --- | --- | --- | ---
01-701-1015 | COVR | WEEK 6 | 2014-02-12 | PD
01-701-1028 | COVR | WEEK 6 | 2013-08-31 | sCR
01-701-1028 | COVR | WEEK 12 | 2013-10-09 | sCR
01-701-1028 | COVR | WEEK 18 | 2013-11-20 | sCR
01-701-1034 | COVR | WEEK 6 | 2014-08-11 | CR
01-701-1034 | COVR | WEEK 12 | 2014-09-25 | CR
01-701-1034 | COVR | WEEK 18 | 2014-11-04 | CR
01-701-1097 | COVR | WEEK 6 | 2014-02-11 | NE
01-701-1115 | COVR | WEEK 6 | 2013-01-10 | PD
01-701-1118 | COVR | WEEK 6 | 2014-04-23 | VGPR

### Check Number of `NE` Values Between Responses

If user would like to receive a warning that there is a certain number of `NE`s between responses, this can be done using `filter_consecutive_vals` function defined below.

    filter_consecutive_vals <- function(dataset, by_vars, order, var, val, n) {
      var <- enexpr(var)
      var_join <- sym(paste0(as.character(var), ".join"))
      data <- derive_var_obs_number(dataset, by_vars = by_vars, order = order, new_var = temp_seq)

      left_join(
        data, select(data, !!!by_vars, temp_seq, !!var),
        by = admiraldev::vars2chr(by_vars),
        suffix = c("", ".join"),
        relationship = "many-to-many"
      ) %>%
        filter(temp_seq <= temp_seq.join & !!var == !!val) %>%
        filter_relative(
          by_vars = c(by_vars, expr(temp_seq)),
          order = exprs(temp_seq.join),
          condition = !!var_join != !!val,
          mode = "first",
          selection = "before",
          keep_no_ref_groups = TRUE,
          inclusive = FALSE
        ) %>%
        derive_var_merged_summary(
          dataset = .,
          dataset_add = .,
          by_vars = c(by_vars, expr(temp_seq)),
          new_vars = exprs(nr_vals = n())
        ) %>%
        filter(nr_vals >= n) %>%
        filter_extreme(
          by_vars = c(by_vars, expr(temp_seq)),
          order = exprs(temp_seq.join),
          mode = "first",
          check_type = "none"
        ) %>%
        select(-temp_seq, -temp_seq.join, -!!var_join, -nr_vals)
    }

    # filter on three or more NEs in a row
    many_nes <- filter_consecutive_vals(
      adrs,
      by_vars = get_admiral_option("subject_keys"),
      order = exprs(ADTM),
      var = AVALC,
      val = "NE",
      n = 3
    )
    #> `derive_var_merged_summary()` was deprecated in admiral 1.4.
    #> i Please use `derive_vars_merged_summary()` instead.
    #> x Function is brought inline with our programming strategy - warning will be
    #>   issued in January 2027
    #> i See admiral's deprecation guidance:
    #>   https://pharmaverse.github.io/admiraldev/dev/articles/programming_strategy.html#deprecation

    if (nrow(many_nes) > 0) {
      cli_warn("There are subjects with more than three NEs in a row.")
    }

## Analysis Flag Derivation

### Flag One Assessment at Each Analysis Visit (`ANL01FL`)

To get Confirm Responses on each visit, we took into account all assessments - including those that took place after a new therapy was started or after progression.

When deriving `ANL01FL` this is an opportunity to exclude any records that should not contribute to any downstream parameter derivations.

Common options for `ANL01FL` would be to set null for invalid assessments or those occurring after new anti-cancer therapy, or to only flag assessments on or after date of first treatment/randomization, or rules to cover the case when a patient has multiple observations per visit/date (e.g. by selecting the worst value). Another consideration could be extra potential protocol-specific sources of Progressive Disease such as radiological assessments, which could be pre-processed here to create a PD record to feed downstream derivations.

For the derivation of the parameters it is expected that the subject identifier variables (usually `STUDYID` and `USUBJID`) and `ADT` are a unique key.

In the below example we consider only valid assessments and those occurring on or after randomization date. If there is more than one assessment at a date, the worst one is flagged.

    adrs_imwg <- adrs_imwg %>%
      restrict_derivation(
        derivation = derive_var_extreme_flag,
        args = params(
          by_vars = exprs(!!!get_admiral_option("subject_keys"), ADT),
          order = exprs(AVAL, RSSEQ),
          new_var = ANL01FL,
          mode = "first"
        ),
        filter = !is.na(AVAL) & AVALC != "MISSING" & ADT >= RANDDT
      )

### Exclude Assessments After New Anti-Cancer Therapy (`ANL02FL`)

Here is an alternative example where those records occurring after new anti-cancer therapy are additionally excluded (where `NACTDT` would be pre-derived as first date of new anti-cancer therapy.
In our example `NACTDT` is present in `SUPPRS` domain. If not available, see `{admiralonco}` Creating and Using New Anti-Cancer Start Date for deriving this variable).

    adrs_imwg <- adrs_imwg %>%
      mutate(
        ANL02FL = case_when(
          !is.na(AVAL) & ADT >= RANDDT & ADT < NACTDT ~ "Y",
          is.na(NACTDT) ~ "Y",
          TRUE ~ NA_character_
        )
      )

### Flag Assessments up to First PD (`ANL03FL`)

To restrict response data up to and including first reported progressive disease `ANL03FL` flag could be created by using `{admiral}` function `admiral::derive_var_relative_flag()`.

    adrs_imwg <- adrs_imwg %>%
      derive_var_relative_flag(
        by_vars = get_admiral_option("subject_keys"),
        order = exprs(ADT, RSSEQ),
        new_var = ANL03FL,
        condition = AVALC == "PD",
        mode = "first",
        selection = "before",
        inclusive = TRUE
      )

USUBJID | AVISIT | PARAMCD | AVALC | ADT | ANL01FL | ANL02FL | ANL03FL
--- | --- | --- | --- | --- | --- | --- | ---
01-701-1015 | WEEK 6 | COVR | PD | 2014-02-12 | Y | Y | Y
01-701-1028 | WEEK 6 | COVR | sCR | 2013-08-31 | Y | Y | Y
01-701-1028 | WEEK 12 | COVR | sCR | 2013-10-09 | Y | Y | Y
01-701-1028 | WEEK 18 | COVR | sCR | 2013-11-20 | Y | Y | Y
01-701-1034 | WEEK 6 | COVR | CR | 2014-08-11 | Y | Y | Y
01-701-1034 | WEEK 12 | COVR | CR | 2014-09-25 | Y | Y | Y
01-701-1034 | WEEK 18 | COVR | CR | 2014-11-04 | Y | Y | Y
01-701-1097 | WEEK 6 | COVR | NE | 2014-02-11 | Y | NA | Y
01-701-1115 | WEEK 6 | COVR | PD | 2013-01-10 | Y | Y | Y
01-701-1118 | WEEK 6 | COVR | VGPR | 2014-04-23 | Y | Y | Y

### Select Source Assessments for Parameter derivations

For next parameter derivations we consider only Confirmed Responses (`PARAMCD = "COVR"`). We take post-baseline records (`ANL01FL = "Y"`) before start of new anti-cancer therapy (`ANL02FL = "Y"`) and up to and including first PD (`ANL03FL = "Y"`).

    ovr <- filter(adrs_imwg, PARAMCD == "COVR" & ANL01FL == "Y" & ANL02FL == "Y" & ANL03FL == "Y")

    adrs <- bind_rows(adrs, adrs_imwg)

USUBJID | AVISIT | AVALC | ADT | RANDDT
--- | --- | --- | --- | ---
01-701-1015 | WEEK 6 | PD | 2014-02-12 | 2014-01-02
01-701-1028 | WEEK 6 | sCR | 2013-08-31 | 2013-07-19
01-701-1028 | WEEK 12 | sCR | 2013-10-09 | 2013-07-19
01-701-1028 | WEEK 18 | sCR | 2013-11-20 | 2013-07-19
01-701-1034 | WEEK 6 | CR | 2014-08-11 | 2014-07-01
01-701-1034 | WEEK 12 | CR | 2014-09-25 | 2014-07-01
01-701-1034 | WEEK 18 | CR | 2014-11-04 | 2014-07-01
01-701-1115 | WEEK 6 | PD | 2013-01-10 | 2012-11-30
01-701-1118 | WEEK 6 | VGPR | 2014-04-23 | 2014-03-12
01-701-1118 | WEEK 12 | VGPR | 2014-06-05 | 2014-03-12

## Derive Progressive Disease Parameter

Now that we have the input records prepared above with any company-specific requirements, we can start to derive new parameter records. For the parameter derivations, all values except those overwritten by `set_values_to` argument are kept from the earliest occurring input record fulfilling the required criteria.

The function `admiral::derive_extreme_records()` can be used to find the date of first PD.

    adrs <- adrs %>%
      derive_extreme_records(
        dataset_ref = adsl,
        dataset_add = ovr,
        by_vars = get_admiral_option("subject_keys"),
        filter_add = PARAMCD == "COVR" & AVALC == "PD",
        order = exprs(ADT),
        mode = "first",
        exist_flag = AVALC,
        false_value = "N",
        set_values_to = exprs(
          PARAMCD = "PD",
          PARAM = "Disease Progression by Investigator",
          PARCAT1 = "Investigator",
          PARCAT2 = "IMWG",
          AVAL = yn_to_numeric(AVALC),
          ANL01FL = "Y",
          ANL02FL = "Y",
          ANL03FL = "Y"
        )
      )

USUBJID | AVISIT | PARAMCD | AVALC | ADT
--- | --- | --- | --- | ---
01-701-1015 | WEEK 6 | PD | Y | 2014-02-12
01-701-1115 | WEEK 6 | PD | Y | 2013-01-10
01-701-1287 | WEEK 18 | PD | Y | 2014-05-29
01-701-1302 | WEEK 6 | PD | Y | 2013-10-08
01-701-1023 | NA | PD | N | NA
01-701-1028 | NA | PD | N | NA
01-701-1033 | NA | PD | N | NA
01-701-1034 | NA | PD | N | NA
01-701-1047 | NA | PD | N | NA
01-701-1057 | NA | PD | N | NA

For progressive disease and response shown in steps here and below, in our examples we show these as `ADRS` parameters, but they could equally be achieved via `ADSL` dates or `ADEVENT` parameters. If you prefer to store as an ADSL date, then the function `admiral::derive_var_extreme_dt()` could be used to find the date of first `PD` as a variable, rather than as a new parameter record.

## Define Events

The building blocks for the events that contribute to deriving common endpoints like what constitutes a responder, or a Best Overall Response of complete response (CR), … are predefined in admiralonco for RECIST 1.1 (see Pre-Defined Response Event Objects).

New events need to be defined for the IMWG criteria.
Below are definitions of non-response events used in the derivations of all parameters.
Parameter-specific events are defined right before the parameter derivation.

    no_data_n <- event(
      description = "Define no response for all patients in adsl (should be used as last event)",
      dataset_name = "adsl",
      condition = TRUE,
      set_values_to = exprs(AVALC = "N"),
      keep_source_vars = adsl_vars
    )

    no_data_missing <- event(
      description = paste(
        "Define missing response (MISSING) for all patients in adsl (should be used",
        "as last event)"
      ),
      dataset_name = "adsl",
      condition = TRUE,
      set_values_to = exprs(AVALC = "MISSING"),
      keep_source_vars = adsl_vars
    )

## Derive Response Parameter

The function `admiral::derive_extreme_event()` can then be used to find the date of first response. In the below example, the response condition has been defined as `PR` or better via the event `rsp_y_imwg` that was created for IMWG.

    rsp_y_imwg <- event(
      description = "Define sCR, CR, VGPR or PR as response",
      dataset_name = "ovr",
      condition = AVALC %in% c("sCR", "CR", "VGPR", "PR"),
      set_values_to = exprs(AVALC = "Y")
    )

    adrs <- adrs %>%
      derive_extreme_event(
        by_vars = get_admiral_option("subject_keys"),
        order = exprs(ADT),
        mode = "first",
        events = list(rsp_y_imwg, no_data_n),
        source_datasets = list(
          ovr = ovr,
          adsl = adsl
        ),
        set_values_to = exprs(
          PARAMCD = "RSP",
          PARAM = "IMWG Response by Investigator",
          PARCAT1 = "Investigator",
          PARCAT2 = "IMWG",
          AVAL = yn_to_numeric(AVALC),
          ANL01FL = "Y",
          ANL02FL = "Y",
          ANL03FL = "Y"
        )
      )

USUBJID | RSORRES | AVISIT | PARAMCD | AVALC | ADT
--- | --- | --- | --- | --- | ---
01-701-1028 | sCR | WEEK 6 | RSP | Y | 2013-08-31
01-701-1034 | CR | WEEK 6 | RSP | Y | 2014-08-11
01-701-1118 | sCR | WEEK 6 | RSP | Y | 2014-04-23
01-701-1130 | VGPR | WEEK 6 | RSP | Y | 2014-03-29
01-701-1133 | sCR | WEEK 6 | RSP | Y | 2012-12-11
01-701-1148 | VGPR | WEEK 6 | RSP | Y | 2013-10-03
01-701-1287 | PR | WEEK 6 | RSP | Y | 2014-03-06

## Derive Clinical Benefit Parameter

The function `admiral::derive_extreme_event()` can then be used to derive the clinical benefit parameter, which we define as a patient having had a response or a sustained period of time before first `PD`. This could also be known as disease control. In this example the “sustained period” has been defined as 42 days after randomization date via the created `cb_y_imwg` event.

    sustained_period <- 42

    cb_y_imwg <- event(
      description = paste(
        "Define sCR, CR, VGPR, PR, MR or SD occuring at least",
        sustained_period,
        "days after randomization as clinical benefit"
      ),
      dataset_name = "ovr",
      condition = AVALC %in% c("sCR", "CR", "VGPR", "PR", "MR", "SD") &
        ADT >= RANDDT + days(sustained_period),
      set_values_to = exprs(AVALC = "Y")
    )

Please note that the result `AVALC = "Y"` is defined by the first two events specified for `events`. For subjects with observations fulfilling both events the one with the earlier date should be selected (and not the first one in the list). Thus `ignore_event_order` and `tmp_event_nr_var` are not specified.

    adrs <- adrs %>%
      derive_extreme_event(
        by_vars = get_admiral_option("subject_keys"),
        order = exprs(desc(AVALC), ADT),
        mode = "first",
        events = list(rsp_y_imwg, cb_y_imwg, no_data_n),
        source_datasets = list(
          ovr = ovr,
          adsl = adsl
        ),
        set_values_to = exprs(
          PARAMCD = "CB",
          PARAM = "IMWG Clinical Benefit by Investigator",
          PARCAT1 = "Investigator",
          PARCAT2 = "IMWG",
          AVAL = yn_to_numeric(AVALC),
          ANL01FL = "Y",
          ANL02FL = "Y",
          ANL03FL = "Y"
        ),
        check_type = "none"
      )

USUBJID | RSORRES | AVISIT | PARAMCD | AVALC | ADT
--- | --- | --- | --- | --- | ---
01-701-1028 | sCR | WEEK 6 | CB | Y | 2013-08-31
01-701-1034 | CR | WEEK 6 | CB | Y | 2014-08-11
01-701-1118 | sCR | WEEK 6 | CB | Y | 2014-04-23
01-701-1130 | VGPR | WEEK 6 | CB | Y | 2014-03-29
01-701-1133 | sCR | WEEK 6 | CB | Y | 2012-12-11
01-701-1148 | VGPR | WEEK 6 | CB | Y | 2013-10-03
01-701-1153 | sCR | WEEK 6 | CB | Y | 2013-11-04
01-701-1203 | CR | WEEK 6 | CB | Y | 2013-03-16
01-701-1211 | MR | WEEK 12 | CB | Y | 2013-01-14
01-701-1239 | MR | WEEK 12 | CB | Y | 2014-04-02

Similarly, we can define the parameters:

- CR or better response (`PARAMCD` = `CRRSP`),
- VGPR or better response (`PARAMCD` =`VGPRRSP`).

    cr_y_imwg <- event(
      description = "Define sCR or CR as response",
      dataset_name = "ovr",
      condition = AVALC %in% c("sCR", "CR"),
      set_values_to = exprs(AVALC = "Y")
    )

    adrs <- adrs %>%
      derive_extreme_event(
        by_vars = get_admiral_option("subject_keys"),
        order = exprs(desc(AVALC), ADT),
        mode = "first",
        events = list(cr_y_imwg, no_data_n),
        source_datasets = list(
          ovr = ovr,
          adsl = adsl
        ),
        set_values_to = exprs(
          PARAMCD = "CRRSP",
          PARAM = "IMWG Complete Response by Investigator",
          PARCAT1 = "Investigator",
          PARCAT2 = "IMWG",
          AVAL = yn_to_numeric(AVALC),
          ANL01FL = "Y",
          ANL02FL = "Y",
          ANL03FL = "Y"
        ),
        check_type = "none"
      )

    vgpr_y_imwg <- event(
      description = "Define sCR, CR or VGPR as response",
      dataset_name = "ovr",
      condition = AVALC %in% c("sCR", "CR", "VGPR"),
      set_values_to = exprs(AVALC = "Y")
    )

    adrs <- adrs %>%
      derive_extreme_event(
        by_vars = get_admiral_option("subject_keys"),
        order = exprs(desc(AVALC), ADT),
        mode = "first",
        events = list(vgpr_y_imwg, no_data_n),
        source_datasets = list(
          ovr = ovr,
          adsl = adsl
        ),
        set_values_to = exprs(
          PARAMCD = "VGPRRSP",
          PARAM = "IMWG VGPR Response by Investigator",
          PARCAT1 = "Investigator",
          PARCAT2 = "IMWG",
          AVAL = yn_to_numeric(AVALC),
          ANL01FL = "Y",
          ANL02FL = "Y",
          ANL03FL = "Y"
        ),
        check_type = "none"
      )

USUBJID | RSORRES | AVISIT | PARAMCD | AVALC | ADT
--- | --- | --- | --- | --- | ---
01-701-1028 | sCR | WEEK 6 | CRRSP | Y | 2013-08-31
01-701-1034 | CR | WEEK 6 | CRRSP | Y | 2014-08-11
01-701-1028 | sCR | WEEK 6 | VGPRRSP | Y | 2013-08-31
01-701-1034 | CR | WEEK 6 | VGPRRSP | Y | 2014-08-11
01-701-1118 | sCR | WEEK 6 | VGPRRSP | Y | 2014-04-23
01-701-1130 | VGPR | WEEK 6 | VGPRRSP | Y | 2014-03-29

## Derive Best Confirmed Overall Response Parameter

The function `admiral::derive_extreme_event()` can be used to derive the best confirmed overall response parameter.

Please note that the order of the events specified for `events` is important. For example, a subject with `PR`, `PR`, `CR` qualifies for both `bor_cr` and `bor_pr`. As `bor_cr` is listed before `bor_pr`, `CR` is selected as best overall response for this subject.

Some events such as `bor_cr`, `bor_pr` have been defined in {admiralonco}. Missing events specific to IMWG criteria are defined below.
Note: For `SD`, it is not required as for RECIST1.1 that the response occurs after a protocol-defined number of days.

    bor_scr <- event(
      description = "Define stringent complete response (sCR) for best overall response
      (BOR)",
      dataset_name = "ovr",
      condition = AVALC == "sCR",
      set_values_to = exprs(AVALC = "sCR")
    )

    bor_vgpr <- event(
      description = "Define very good partial response (VGPR) for best overall response
      (BOR)",
      dataset_name = "ovr",
      condition = AVALC == "VGPR",
      set_values_to = exprs(AVALC = "VGPR")
    )

    bor_mr <- event(
      description = "Define minimal response (MR) for best overall response (BOR)",
      dataset_name = "ovr",
      condition = AVALC == "MR",
      set_values_to = exprs(AVALC = "MR")
    )

    bor_sd_imwg <- event(
      description = "Define stable disease (SD) for best overall response (BOR)",
      dataset_name = "ovr",
      condition = AVALC == "SD",
      set_values_to = exprs(AVALC = "SD")
    )

    bor_ne_imwg <- event(
      description = "Define not evaluable (NE) for best overall response (BOR)",
      dataset_name = "ovr",
      condition = AVALC == "NE",
      set_values_to = exprs(AVALC = "NE")
    )

    adrs <- adrs %>%
      derive_extreme_event(
        by_vars = get_admiral_option("subject_keys"),
        tmp_event_nr_var = event_nr,
        order = exprs(event_nr, ADT),
        mode = "first",
        source_datasets = list(
          ovr = ovr,
          adsl = adsl
        ),
        events = list(
          bor_scr, bor_cr, bor_vgpr, bor_pr, bor_mr, bor_sd_imwg, bor_pd, bor_ne_imwg,
          no_data_missing
        ),
        set_values_to = exprs(
          PARAMCD = "CBOR",
          PARAM = "IMWG Best Confirmed Overall Response by Investigator",
          PARCAT1 = "Investigator",
          PARCAT2 = "IMWG",
          AVAL = aval_resp_imwg(AVALC),
          ANL01FL = "Y",
          ANL02FL = "Y",
          ANL03FL = "Y"
        )
      )

USUBJID | AVISIT | PARAMCD | AVALC | ADT
--- | --- | --- | --- | ---
01-701-1015 | WEEK 6 | CBOR | PD | 2014-02-12
01-701-1028 | WEEK 6 | CBOR | sCR | 2013-08-31
01-701-1034 | WEEK 6 | CBOR | CR | 2014-08-11
01-701-1115 | WEEK 6 | CBOR | PD | 2013-01-10
01-701-1118 | WEEK 6 | CBOR | VGPR | 2014-04-23
01-701-1130 | WEEK 6 | CBOR | VGPR | 2014-03-29
01-701-1133 | WEEK 6 | CBOR | PR | 2012-12-11
01-701-1146 | WEEK 6 | CBOR | NE | 2013-06-30
01-701-1148 | WEEK 6 | CBOR | PR | 2013-10-03
01-701-1153 | WEEK 6 | CBOR | MR | 2013-11-04

## Other Endpoints

For examples on the additional endpoints, please see Creating ADRS (Including Non-standard Endpoints).