lastdose appears to have a side effect of changing AMT column in data frame it is ran on

[andersone1]

library(tidyverse)

pk <- 
  Theoph %>% 
  transmute(
    ID = dense_rank(Subject),
    WTBL = Wt,
    DOSE = Dose,
    TIME = Time,
    DV = conc,
    EVID = 0
  ) 

dosing <-
  pk %>%
  distinct(ID, DOSE, TIME, WTBL) %>%
  mutate(EVID = 1, AMT = DOSE)

pk$AMT <- NA_real_
  
nm_1 <-
  bind_rows(pk, dosing) %>%
  arrange(ID, TIME) %>% 
  as_tibble()

# nm_1 has NA AMT (which is OK)
head(nm_1$AMT) # NA  4 NA  4 NA  4

# Create nm_2
nm_2 <- lastdose::lastdose(nm_1, include_tafd = TRUE)

# nm_2 has new AMT (which is OK)
head(nm_2$AMT) #  0 4 0 4 0 4

# nm_1 has new AMT (not OK?)
head(nm_1$AMT) #  0 4 0 4 0 4

[kylebaron]

Reproducing this:

library(tidyverse)

pk <- 
  Theoph %>% 
  transmute(
    ID = dense_rank(Subject),
    WTBL = Wt,
    DOSE = Dose,
    TIME = Time,
    DV = conc,
    EVID = 0
  ) 

dosing <-
  pk %>%
  distinct(ID, DOSE, TIME, WTBL) %>%
  mutate(EVID = 1, AMT = DOSE)

pk$AMT <- NA_real_

nm_1 <-
  bind_rows(pk, dosing) %>%
  arrange(ID, TIME) %>% 
  as_tibble()

# nm_1 has NA AMT (which is OK)
head(nm_1$AMT) # NA  4 NA  4 NA  4
#> [1] NA  4 NA  4 NA  4

# Create nm_2
nm_2 <- lastdose::lastdose(nm_1, include_tafd = TRUE)

# nm_2 has new AMT (which is OK)
head(nm_2$AMT) #  0 4 0 4 0 4
#> [1] 0 4 0 4 0 4

# nm_1 has new AMT (not OK?)
head(nm_1$AMT) #  0 4 0 4 0 4
#> [1] 0 4 0 4 0 4

^{Created on 2023-09-22 with reprex v2.0.2}

[kylebaron]

This is now fixed with d5cfec7

library(tidyverse)

pk <-
  Theoph %>%
  transmute(
    ID = dense_rank(Subject),
    WTBL = Wt,
    DOSE = Dose,
    TIME = Time,
    DV = conc,
    EVID = 0
  )

dosing <-
  pk %>%
  distinct(ID, DOSE, TIME, WTBL) %>%
  mutate(EVID = 1, AMT = DOSE)

pk$AMT <- NA_real_

nm_1 <-
  bind_rows(pk, dosing) %>%
  arrange(ID, TIME) %>%
  as_tibble()

# nm_1 has NA AMT (which is OK)
head(nm_1$AMT) # NA  4 NA  4 NA  4
#> [1] NA  4 NA  4 NA  4

# Create nm_2
nm_2 <- lastdose::lastdose(nm_1, include_tafd = TRUE)

# nm_2 has same AMT
head(nm_2$AMT) #  0 4 0 4 0 4
#> [1] NA  4 NA  4 NA  4

# nm_1 has same AMT
head(nm_1$AMT) #  0 4 0 4 0 4
#> [1] NA  4 NA  4 NA  4

^{Created on 2023-09-22 with reprex v2.0.2}

[andersone1]

@kylebaron Will this fix be released to a new version that will make it MPN?

[kylebaron]

Hi @andersone1 - we can release it.

[andersone1]

Sounds good @kylebaron . I am OK closing this issue if you are.