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Closes#134 update with derive_var_nfrlt #139

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ccff2e5
#134 update with derive_var_nfrlt
jeffreyad Jan 14, 2026
05feee7
#134 spelling and units
jeffreyad Jan 14, 2026
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31 changes: 19 additions & 12 deletions adam/adpc.R
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -56,8 +56,14 @@ pc_dates <- pc %>%
# Derive event ID and nominal relative time from first dose (NFRLT)
mutate(
EVID = 0,
DRUG = PCTEST,
NFRLT = if_else(PCTPTNUM < 0, 0, PCTPTNUM), .after = USUBJID
DRUG = PCTEST
) %>%
derive_var_nfrlt(
new_var = NFRLT,
new_var_unit = FRLTU,
out_unit = "HOURS",
tpt_var = PCTPT,
visit_day = VISITDY
)

## ----r------------------------------------------------------------------------
Expand Down Expand Up @@ -85,11 +91,13 @@ ex_dates <- ex %>%
) %>%
# Derive event ID and nominal relative time from first dose (NFRLT)
mutate(
EVID = 1,
NFRLT = case_when(
VISITDY == 1 ~ 0,
TRUE ~ 24 * VISITDY
)
EVID = 1
) %>%
derive_var_nfrlt(
new_var = NFRLT,
new_var_unit = FRLTU,
out_unit = "HOURS",
visit_day = VISITDY
) %>%
# Set missing end dates to start date
mutate(AENDTM = case_when(
Expand Down Expand Up @@ -233,16 +241,17 @@ adpc_arrlt <- bind_rows(adpc_nom_next, ex_exp) %>%
new_var = AFRLT,
start_date = FANLDTM,
end_date = ADTM,
out_unit = "hours",
out_unit = "HOURS",
floor_in = FALSE,
add_one = FALSE
) %>%
# Derive Actual Relative Time from Reference Dose (ARRLT)
derive_vars_duration(
new_var = ARRLT,
new_var_unit = RRLTU,
start_date = ADTM_prev,
end_date = ADTM,
out_unit = "hours",
out_unit = "HOURS",
floor_in = FALSE,
add_one = FALSE
) %>%
Expand All @@ -251,7 +260,7 @@ adpc_arrlt <- bind_rows(adpc_nom_next, ex_exp) %>%
new_var = AXRLT,
start_date = ADTM_next,
end_date = ADTM,
out_unit = "hours",
out_unit = "HOURS",
floor_in = FALSE,
add_one = FALSE
) %>%
Expand Down Expand Up @@ -330,8 +339,6 @@ adpc_aval <- adpc_nrrlt %>%
) %>%
# Derive relative time units
mutate(
FRLTU = "h",
RRLTU = "h",
# Derive PARAMCD
PARAMCD = coalesce(PCTESTCD, "DOSE"),
ALLOQ = PCLLOQ,
Expand Down
44 changes: 22 additions & 22 deletions adam/adpc.qmd
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ The Non-compartmental analysis (NCA) ADaM uses the CDISC Implementation Guide (<

## First Load Packages

First we will load the packages required for our project. We will use `{admiral}` for the creation of analysis data. `{admiral}` requires `{dplyr}`, `{lubridate}` and `{stringr}`. Find other `{admiral}` functions and related variables by searching [admiraldiscovery](<https://pharmaverse.github.io/admiraldiscovery/articles/reactable.html>). We will use `{metacore}` and `{metatools}` to store and manipulate metadata from our specifications. We will use `{xportr}` to perform checks on the final data and export to a transport file.
First we will load the packages required for our project. We will use `{admiral}` for the creation of analysis data. `{admiral}` requires `{dplyr}`, `{lubridate}` and `{stringr}`. Find other `{admiral}` functions and related variables by searching [admiraldiscovery](https://pharmaverse.github.io/admiraldiscovery/articles/reactable.html). We will use `{metacore}` and `{metatools}` to store and manipulate metadata from our specifications. We will use `{xportr}` to perform checks on the final data and export to a transport file.

The source SDTM data will come from the CDISC pilot study data stored in `{pharmaversesdtm}`.

Expand Down Expand Up @@ -71,7 +71,7 @@ vs <- convert_blanks_to_na(vs)

### Derive PC Dates

Here we use `{admiral}` functions for working with dates and we will also create a nominal time from first dose `NFRLT` for `PC` data based on `PCTPTNUM`.
Here we use `{admiral}` functions for working with dates and we will also create a nominal time from first dose `NFRLT` for `PC` data using `derive_var_nfrlt()`.

```{r}
#| label: PC Dates
Expand Down Expand Up @@ -101,8 +101,14 @@ pc_dates <- pc %>%
# Derive event ID and nominal relative time from first dose (NFRLT)
mutate(
EVID = 0,
DRUG = PCTEST,
NFRLT = if_else(PCTPTNUM < 0, 0, PCTPTNUM), .after = USUBJID
DRUG = PCTEST
) %>%
derive_var_nfrlt(
new_var = NFRLT,
new_var_unit = FRLTU,
out_unit = "HOURS",
tpt_var = PCTPT,
visit_day = VISITDY
)
```

Expand All @@ -112,7 +118,7 @@ print_df(pc_dates %>% select(USUBJID, PCTEST, ADTM, VISIT, PCTPT, NFRLT))

### Get Dosing Information

Here we also create nominal time from first dose `NFRLT` for `EX` data based on `VISITDY`.
Here we also create nominal time from first dose `NFRLT` for `EX` data based on `VISITDY` using `derive_var_nfrlt()`.

```{r}
#| label: Dosing
Expand Down Expand Up @@ -141,11 +147,13 @@ ex_dates <- ex %>%
) %>%
# Derive event ID and nominal relative time from first dose (NFRLT)
mutate(
EVID = 1,
NFRLT = case_when(
VISITDY == 1 ~ 0,
TRUE ~ 24 * VISITDY
)
EVID = 1
) %>%
derive_var_nfrlt(
new_var = NFRLT,
new_var_unit = FRLTU,
out_unit = "HOURS",
visit_day = VISITDY
) %>%
# Set missing end dates to start date
mutate(AENDTM = case_when(
Expand Down Expand Up @@ -230,8 +238,6 @@ adpc_first_dose <- pc_dates %>%
)
```



```{r eval=TRUE, echo=FALSE, purl=FALSE}
print_df(adpc_first_dose %>% select(USUBJID, FANLDTM, NFRLT, ADTM, AVISITN, AVISIT, PCTPT))
```
Expand Down Expand Up @@ -318,7 +324,6 @@ adpc_nom_next <- adpc_nom_prev %>%
print_df(adpc_nom_prev %>% select(USUBJID, NFRLT, AVISIT, PCTPT, NFRLT_prev))
```


### Combine PC and EX Data

Combine `PC` and `EX` records and derive the additional relative time variables.
Expand All @@ -341,16 +346,17 @@ adpc_arrlt <- bind_rows(adpc_nom_next, ex_exp) %>%
new_var = AFRLT,
start_date = FANLDTM,
end_date = ADTM,
out_unit = "hours",
out_unit = "HOURS",
floor_in = FALSE,
add_one = FALSE
) %>%
# Derive Actual Relative Time from Reference Dose (ARRLT)
derive_vars_duration(
new_var = ARRLT,
new_var_unit = RRLTU,
start_date = ADTM_prev,
end_date = ADTM,
out_unit = "hours",
out_unit = "HOURS",
floor_in = FALSE,
add_one = FALSE
) %>%
Expand All @@ -359,7 +365,7 @@ adpc_arrlt <- bind_rows(adpc_nom_next, ex_exp) %>%
new_var = AXRLT,
start_date = ADTM_next,
end_date = ADTM,
out_unit = "hours",
out_unit = "HOURS",
floor_in = FALSE,
add_one = FALSE
) %>%
Expand Down Expand Up @@ -406,12 +412,10 @@ adpc_nrrlt <- adpc_arrlt %>%
)
```


```{r eval=TRUE, echo=FALSE, purl=FALSE}
print_df(adpc_nrrlt %>% select(USUBJID, NFRLT, NRRLT, AVISIT, PCTPT))
```


### Derive Analysis Variables

Here we derive the analysis variables such as `AVAL` and `ATPTREF`.
Expand Down Expand Up @@ -458,8 +462,6 @@ adpc_aval <- adpc_nrrlt %>%
) %>%
# Derive relative time units
mutate(
FRLTU = "h",
RRLTU = "h",
# Derive PARAMCD
PARAMCD = coalesce(PCTESTCD, "DOSE"),
ALLOQ = PCLLOQ,
Expand Down Expand Up @@ -512,12 +514,10 @@ dtype <- adpc_aval %>%
derive_vars_dtm_to_tm(exprs(PCRFTDTM))
```


```{r eval=TRUE, echo=FALSE, purl=FALSE}
print_df(dtype %>% select(USUBJID, DTYPE, BASETYPE, ATPT, NFRLT, NRRLT, AFRLT, ARRLT))
```


### Combine Original and DTYPE Copy

Now the duplicated records are combined with the original records.
Expand Down
26 changes: 17 additions & 9 deletions adam/adppk.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -59,8 +59,14 @@ pc_dates <- pc %>%
# Derive event ID and nominal relative time from first dose (NFRLT)
mutate(
EVID = 0,
DRUG = PCTEST,
NFRLT = if_else(PCTPTNUM < 0, 0, PCTPTNUM), .after = USUBJID
DRUG = PCTEST
) %>%
derive_var_nfrlt(
new_var = NFRLT,
new_var_unit = FRLTU,
out_unit = "HOURS",
tpt_var = PCTPT,
visit_day = VISITDY
)

## ----r------------------------------------------------------------------------
Expand Down Expand Up @@ -90,11 +96,13 @@ ex_dates <- ex %>%
) %>%
# Derive event ID and nominal relative time from first dose (NFRLT)
mutate(
EVID = 1,
NFRLT = case_when(
VISITDY == 1 ~ 0,
TRUE ~ 24 * VISITDY
)
EVID = 1
) %>%
derive_var_nfrlt(
new_var = NFRLT,
new_var_unit = FRLTU,
out_unit = "HOURS",
visit_day = VISITDY
) %>%
# Set missing end dates to start date
mutate(AENDTM = case_when(
Expand Down Expand Up @@ -211,7 +219,7 @@ adppk_aprlt <- bind_rows(adppk_nom_prev, ex_exp) %>%
new_var = AFRLT,
start_date = FANLDTM,
end_date = ADTM,
out_unit = "hours",
out_unit = "HOURS",
floor_in = FALSE,
add_one = FALSE
) %>%
Expand All @@ -220,7 +228,7 @@ adppk_aprlt <- bind_rows(adppk_nom_prev, ex_exp) %>%
new_var = APRLT,
start_date = ADTM_prev,
end_date = ADTM,
out_unit = "hours",
out_unit = "HOURS",
floor_in = FALSE,
add_one = FALSE
) %>%
Expand Down
30 changes: 19 additions & 11 deletions adam/adppk.qmd
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -73,7 +73,7 @@ lb <- convert_blanks_to_na(lb)

### Derive PC Dates

Here we use `{admiral}` functions for working with dates and we will also create a nominal time from first dose `NFRLT` for `PC` data based on `PCTPTNUM`.
Here we use `{admiral}` functions for working with dates and we will also create a nominal time from first dose `NFRLT` for `PC` data using `derive_var_nfrlt()`.

```{r}
#| label: PC Dates
Expand Down Expand Up @@ -103,8 +103,14 @@ pc_dates <- pc %>%
# Derive event ID and nominal relative time from first dose (NFRLT)
mutate(
EVID = 0,
DRUG = PCTEST,
NFRLT = if_else(PCTPTNUM < 0, 0, PCTPTNUM), .after = USUBJID
DRUG = PCTEST
) %>%
derive_var_nfrlt(
new_var = NFRLT,
new_var_unit = FRLTU,
out_unit = "HOURS",
tpt_var = PCTPT,
visit_day = VISITDY
)
```

Expand All @@ -115,7 +121,7 @@ print_df(pc_dates %>% select(USUBJID, PCTEST, ADTM, VISIT, PCTPT, NFRLT))

### Get Dosing Information

Here we also create nominal time from first dose `NFRLT` for `EX` data based on `VISITDY`.
Here we also create nominal time from first dose `NFRLT` for `EX` data based on `VISITDY` using `derive_var_nfrlt()`.

```{r}
#| label: Dosing
Expand Down Expand Up @@ -145,11 +151,13 @@ ex_dates <- ex %>%
) %>%
# Derive event ID and nominal relative time from first dose (NFRLT)
mutate(
EVID = 1,
NFRLT = case_when(
VISITDY == 1 ~ 0,
TRUE ~ 24 * VISITDY
)
EVID = 1
) %>%
derive_var_nfrlt(
new_var = NFRLT,
new_var_unit = FRLTU,
out_unit = "HOURS",
visit_day = VISITDY
) %>%
# Set missing end dates to start date
mutate(AENDTM = case_when(
Expand Down Expand Up @@ -328,7 +336,7 @@ adppk_aprlt <- bind_rows(adppk_nom_prev, ex_exp) %>%
new_var = AFRLT,
start_date = FANLDTM,
end_date = ADTM,
out_unit = "hours",
out_unit = "HOURS",
floor_in = FALSE,
add_one = FALSE
) %>%
Expand All @@ -337,7 +345,7 @@ adppk_aprlt <- bind_rows(adppk_nom_prev, ex_exp) %>%
new_var = APRLT,
start_date = ADTM_prev,
end_date = ADTM,
out_unit = "hours",
out_unit = "HOURS",
floor_in = FALSE,
add_one = FALSE
) %>%
Expand Down
2 changes: 2 additions & 0 deletions inst/WORDLIST
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Original file line number Diff line number Diff line change
Expand Up @@ -464,6 +464,7 @@ NCA
nDate
nDose
nestcolor
nfrlt
NFRLT
nFrom
nLTRs
Expand Down Expand Up @@ -733,6 +734,7 @@ TMPTC
toc
topleft
toupper
tpt
TPT
TPTNUM
traceback
Expand Down