![[Stable]](figures/lifecycle-stable.svg)
Follows PsN coding conventions to add covariates into a model. The advantage
is no need to create a .scm file, just directly modify the NONMEM control
file contents. This function is used by covariate_step_tibble() for
stepwise covariate model development.
add_cov(
ctl,
param,
cov,
state = 2,
continuous = TRUE,
time_varying,
additional_state_text = list(),
id_var = "ID",
force = FALSE,
force_TV_var = FALSE,
init,
lower,
upper
)
remove_cov(
ctl,
param,
cov,
state = 2,
continuous = TRUE,
time_varying,
id_var = "ID"
)Arguments
- ctl
An nm object or an object coercible to
ctl_list.- param
Character. Name of parameter.
- cov
Character. Name of covariate.
- state
Numeric or character. Number or name of state (see details).
- continuous
Logical (default =
TRUE). Is covariate continuous?- time_varying
Optional logical. is the covariate time varying?
- additional_state_text
Optional character (default = empty). Custom state variable to be passed to
param_cov_text.- id_var
Character (default =
"ID"). Needed if time_varying is missing.- force
Logical (default = `FALSE``). Force covariate in even if missing values found.
- force_TV_var
Logical (default =
FALSE). Force covariates only onTVnotation parameters.- init
Optional numeric/character vector. Initial estimate of additional parameters.
- lower
Optional numeric/character vector. lower bound of additional parameters.
- upper
Optional numeric/character vector. Upper bound of additional parameters.
Value
An nm object with modified ctl_contents field.
Details
Available states:
- "2" or "linear"
PARCOV= ( 1 + THETA(1)*(COV -median))
- "3" or "hockey-stick"
IF(COV.LE.median) PARCOV = ( 1 + THETA(1)*(COV - median)) IF(COV.GT.median) PARCOV = ( 1 + THETA(2)*(COV - median))
- "4" or "exponential"
PARCOV= EXP(THETA(1)*(COV - median))
- "5" or "power"
PARCOV= ((COV/median)**THETA(1))
- "power1"
PARCOV= ((COV/median))
- "power0.75"
PARCOV= ((COV/median)**0.75)
- "6" or "log-linear"
PARCOV= ( 1 + THETA(1)*(LOG(COV) - log(median)))
remove_cov only works with covariates added with add_cov.
See also
Examples
# create example object m1 from package demo files
exdir <- system.file("extdata", "examples", "theopp", package = "NMproject")
m1 <- new_nm(run_id = "m1",
based_on = file.path(exdir, "Models", "ADVAN2.mod"),
data_path = file.path(exdir, "SourceData", "THEOPP.csv"))
temp_data_file <- paste0(tempfile(), ".csv")
## dataset has missing WTs so create a new one and assign this to the run
input_data(m1) %>%
dplyr::group_by(ID) %>%
dplyr::mutate(WT = na.omit(WT)) %>%
write_derived_data(temp_data_file)
#> written:
#> /var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T//RtmpHHBXcI/file375b3bb8e517.RDS
#> /var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T//RtmpHHBXcI/file375b3bb8e517.csv
m1 <- m1 %>% data_path(temp_data_file)
m1WT <- m1 %>% child("m1WT") %>%
add_cov(param = "V", cov = "WT", state = "power")
m1 %>% dollar("PK")
#> $`execute.Models/m1`
#> 1| $PK
#> 2|
#> 3| TVKA=EXP(THETA(1))
#> 4| MU_1=LOG(TVKA)
#> 5| KA = EXP(MU_1+ETA(1))
#> 6|
#> 7| TVK=EXP(THETA(2))
#> 8| MU_2=LOG(TVK)
#> 9| K = EXP(MU_2+ETA(2))
#> 10|
#> 11| TVV=EXP(THETA(3))
#> 12| MU_3=LOG(TVV)
#> 13| V = EXP(MU_3+ETA(3))
#> 14|
#> 15| CL = K*V
#> 16|
#> 17| S2 = V
#> 18|
#>
m1WT %>% dollar("PK") ## notice SCM style code added
#> $`execute.Models/m1WT`
#> 1| $PK
#> 2|
#> 3| ;;; TVVWT-DEFINITION START
#> 4| TVVWT= ((WT/70.5)**THETA(4))
#> 5| ;;; TVVWT-DEFINITION END
#> 6|
#> 7| ;;; TVV-RELATION START
#> 8| TVVCOV=TVVWT
#> 9| ;;; TVV-RELATION END
#> 10|
#> 11| TVKA=EXP(THETA(1))
#> 12| MU_1=LOG(TVKA)
#> 13| KA = EXP(MU_1+ETA(1))
#> 14|
#> 15| TVK=EXP(THETA(2))
#> 16| MU_2=LOG(TVK)
#> 17| K = EXP(MU_2+ETA(2))
#> 18|
#> 19| TVV=EXP(THETA(3))
#> 20|
#> 21| TVV = TVVCOV*TVV
#> 22| MU_3=LOG(TVV)
#> 23| V = EXP(MU_3+ETA(3))
#> 24|
#> 25| CL = K*V
#> 26|
#> 27| S2 = V
#> 28|
#>
nm_diff(m1WT)
#> < old_ctl
#> > new_ctl
#> @@ 28,4 / 28,12 @@
#> $PK
#>
#> > ;;; TVVWT-DEFINITION START
#> > TVVWT= ((WT/70.5)**THETA(4))
#> > ;;; TVVWT-DEFINITION END
#> >
#> > ;;; TVV-RELATION START
#> > TVVCOV=TVVWT
#> > ;;; TVV-RELATION END
#> >
#> TVKA=EXP(THETA(1))
#> MU_1=LOG(TVKA)
#> @@ 37,4 / 45,6 @@
#>
#> TVV=EXP(THETA(3))
#> >
#> > TVV = TVVCOV*TVV
#> MU_3=LOG(TVV)
#> V = EXP(MU_3+ETA(3))
#> @@ 58,4 / 68,5 @@
#> ..... ; V ; L ; LOG
#>
#> > $THETA (-1,0.8,5) ; TVVWTpower
#> $OMEGA
#> 0.1 ; IIV_KA ; LOG
if (FALSE) {
run_nm(c(m1, m1WT))
rr(c(m1, m1WT))
summary_wide(c(m1, m1WT))
}
unlink(temp_data_file)
# create example object m1 from package demo files
exdir <- system.file("extdata", "examples", "theopp", package = "NMproject")
m1 <- new_nm(run_id = "m1",
based_on = file.path(exdir, "Models", "ADVAN2.mod"),
data_path = file.path(exdir, "SourceData", "THEOPP.csv"))
temp_data_file <- paste0(tempfile(), ".csv")
## dataset has missing WTs so create a new one and assign this to the run
input_data(m1) %>%
dplyr::group_by(ID) %>%
dplyr::mutate(WT = na.omit(WT)) %>%
write_derived_data(temp_data_file)
#> written:
#> /var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T//RtmpHHBXcI/file375b67c867a2.RDS
#> /var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T//RtmpHHBXcI/file375b67c867a2.csv
m1 <- m1 %>% data_path(temp_data_file)
m1WT <- m1 %>% child("m1WT") %>%
add_cov(param = "V", cov = "WT", state = "power")
m1 %>% dollar("PK")
#> $`execute.Models/m1`
#> 1| $PK
#> 2|
#> 3| TVKA=EXP(THETA(1))
#> 4| MU_1=LOG(TVKA)
#> 5| KA = EXP(MU_1+ETA(1))
#> 6|
#> 7| TVK=EXP(THETA(2))
#> 8| MU_2=LOG(TVK)
#> 9| K = EXP(MU_2+ETA(2))
#> 10|
#> 11| TVV=EXP(THETA(3))
#> 12| MU_3=LOG(TVV)
#> 13| V = EXP(MU_3+ETA(3))
#> 14|
#> 15| CL = K*V
#> 16|
#> 17| S2 = V
#> 18|
#>
m1WT %>% dollar("PK") ## notice SCM style code added
#> $`execute.Models/m1WT`
#> 1| $PK
#> 2|
#> 3| ;;; TVVWT-DEFINITION START
#> 4| TVVWT= ((WT/70.5)**THETA(4))
#> 5| ;;; TVVWT-DEFINITION END
#> 6|
#> 7| ;;; TVV-RELATION START
#> 8| TVVCOV=TVVWT
#> 9| ;;; TVV-RELATION END
#> 10|
#> 11| TVKA=EXP(THETA(1))
#> 12| MU_1=LOG(TVKA)
#> 13| KA = EXP(MU_1+ETA(1))
#> 14|
#> 15| TVK=EXP(THETA(2))
#> 16| MU_2=LOG(TVK)
#> 17| K = EXP(MU_2+ETA(2))
#> 18|
#> 19| TVV=EXP(THETA(3))
#> 20|
#> 21| TVV = TVVCOV*TVV
#> 22| MU_3=LOG(TVV)
#> 23| V = EXP(MU_3+ETA(3))
#> 24|
#> 25| CL = K*V
#> 26|
#> 27| S2 = V
#> 28|
#>
## reverse this by removing WT
m1noWT <- m1WT %>% child("m1noWT") %>%
remove_cov(param = "V", cov = "WT")
m1noWT %>% dollar("PK")
#> $`execute.Models/m1noWT`
#> 1| $PK
#> 2|
#> 3|
#> 4|
#> 5| TVKA=EXP(THETA(1))
#> 6| MU_1=LOG(TVKA)
#> 7| KA = EXP(MU_1+ETA(1))
#> 8|
#> 9| TVK=EXP(THETA(2))
#> 10| MU_2=LOG(TVK)
#> 11| K = EXP(MU_2+ETA(2))
#> 12|
#> 13| TVV=EXP(THETA(3))
#> 14|
#> 15| MU_3=LOG(TVV)
#> 16| V = EXP(MU_3+ETA(3))
#> 17|
#> 18| CL = K*V
#> 19|
#> 20| S2 = V
#> 21|
#>
m1noWT %>% dollar("THETA")
#> $`execute.Models/m1noWT`
#> 1| $THETA
#> 2| ..... ; KA ; h-1 ; LOG
#> 3| ..... ; K ; h-1 ; LOG
#> 4| ..... ; V ; L ; LOG
#> 5|
#>
unlink(temp_data_file)