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inst/doc/Titration.R
In ubiquity: PKPD, PBPK, and Systems Pharmacology Modeling Tools
## ----setup, include=FALSE, eval=TRUE------------------------------------------
knitr::opts_chunk$set(echo = TRUE, message=FALSE, eval=FALSE)
require(ubiquity)
require(deSolve)
require(ggplot2)
require(foreach)
require(doParallel)
require(rhandsontable)
# The presim variable will contain presimualted data when eval is set to true
presim_loaded = FALSE
## ----echo=FALSE, results=FALSE------------------------------------------------
# presim= list()
# if(file.exists("Titration_presim.RData")){
# file.remove("Titration_presim.RData")
# }
## ----echo=FALSE, results=FALSE, eval=TRUE-------------------------------------
if(file.exists("Titration_presim.RData")){
load("Titration_presim.RData")
presim_loaded = TRUE
}
## ----eval=FALSE---------------------------------------------------------------
# library(ubiquity)
# fr = workshop_fetch(section="Titration", overwrite=TRUE)
## ----results="hide", message=FALSE, echo=FALSE--------------------------------
# library(ubiquity)
# system_new(file_name="system.txt", system_file="mab_pk", overwrite = TRUE)
## ----results="hide", message=FALSE, warning=FALSE-----------------------------
# cfg = build_system()
# cfg = system_select_set(cfg, "default")
# parameters = system_fetch_parameters(cfg)
# cfg=system_set_option(cfg,group = "simulation", option = "solver", value = "lsoda")
# cfg=system_set_option(cfg, group = "simulation", option = "output_times", seq(0,10*7,1))
# cfg = system_zero_inputs(cfg)
# cfg = system_set_bolus(cfg, state = "Cc",
# times = c(0, 14, 28, 42, 56),
# values = c(500, 500, 500, 500, 500))
# som_fix = run_simulation_ubiquity(parameters, cfg)
## ----results="hide", message=FALSE--------------------------------------------
# cfg=system_set_option(cfg,
# group = "titration",
# option = "titrate",
# value = TRUE)
## ----results="hide", message=FALSE--------------------------------------------
# cfg=system_new_tt_rule(cfg,
# name = "ivdose",
# times = c(0, 2, 4, 6, 8),
# timescale = "weeks")
## ----results="hide", message=FALSE--------------------------------------------
# cfg=system_set_tt_cond(cfg,
# name = "ivdose",
# cond = "TRUE",
# action = "SI_TT_BOLUS[state='Cc', values=500, times=0]",
# value = "1")
## ----results="hide", message=FALSE--------------------------------------------
# som_tt = run_simulation_titrate(parameters, cfg)
## ----results="hide", warning=FALSE, echo=FALSE--------------------------------
# # When eval is set to TRUE we save the presimulated results
# presim$bolus$som_tt$simout = data.frame(ts.days = som_tt$simout$ts.days,
# Cc = som_tt$simout$Cc)
# presim$bolus$som_fix$simout = data.frame(ts.days = som_fix$simout$ts.days,
# Cc = som_fix$simout$Cc)
## ----results="hide", warning=FALSE, echo=FALSE, eval=TRUE---------------------
if(presim_loaded){
som_tt = presim$bolus$som_tt
som_fix = presim$bolus$som_fix
}
## ----warning=FALSE, message=FALSE, fig.width=7, fig.height=3, eval=TRUE-------
myfig = ggplot() +
geom_line(data=som_fix$simout, aes(x=ts.days, y=Cc, color="Fixed Dosing"), linetype=1) +
geom_line(data=som_tt$simout, aes(x=ts.days, y=Cc, color="Titration" ), linetype=2) +
scale_colour_manual(values=c("Fixed Dosing"="darkblue", "Titration"="firebrick3")) +
theme(legend.title = element_blank()) +
theme(legend.position = 'bottom')
myfig = prepare_figure('present', myfig)
print(myfig)
## ----warning=FALSE, message=FALSE, echo=FALSE---------------------------------
# # resetting everything for the repeat infusion example
# cfg = system_select_set(cfg, "default")
# parameters = system_fetch_parameters(cfg)
# cfg=system_set_option(cfg,group = "simulation", option = "solver", value = "lsoda")
# cfg=system_set_option(cfg, group = "simulation",
# option = "output_times",
# seq(0,10*7,.5))
## ----warning=FALSE, message=FALSE---------------------------------------------
# cfg = system_zero_inputs(cfg)
# cfg = system_set_rate(cfg, rate = "Dinf",
# times = c( 0, 30, 20160, 20190, 40320, 40350, 60480, 60510, 80640, 80670),
# levels = c(15 , 0, 15, 0, 15, 0, 15, 0, 15, 0))
# som_fix = run_simulation_ubiquity(parameters, cfg)
## ----warning=FALSE, message=FALSE---------------------------------------------
# cfg=system_set_option(cfg, group = "titration", option = "titrate", value = TRUE)
# cfg=system_new_tt_rule(cfg, name = "ivdose", times = c(0, 2, 4, 6, 8), timescale = "weeks")
## ----warning=FALSE, message=FALSE---------------------------------------------
# cfg=system_set_tt_cond(cfg,
# name = "ivdose",
# cond = "TRUE",
# action = "SI_TT_RATE[rate='Dinf', times=c(0,30), levels=c(15,0)]",
# value = "1")
## ----warning=FALSE, message=FALSE---------------------------------------------
# som_tt = run_simulation_titrate(parameters, cfg)
## ----results="hide", warning=FALSE, echo=FALSE--------------------------------
# # When eval is set to TRUE we save the presimulated results
# presim$infusion$som_tt$simout = data.frame(ts.days = som_tt$simout$ts.days,
# Cc = som_tt$simout$Cc)
# presim$infusion$som_fix$simout = data.frame(ts.days = som_fix$simout$ts.days,
# Cc = som_fix$simout$Cc)
## ----results="hide", warning=FALSE, echo=FALSE, eval=TRUE---------------------
if(presim_loaded){
som_tt = presim$infusion$som_tt
som_fix = presim$infusion$som_fix
}
## ----warning=FALSE, message=FALSE, fig.width=7, fig.height=3, eval=TRUE-------
myfig = ggplot() +
geom_line(data=som_fix$simout, aes(x=ts.days, y=Cc, color="Fixed Dosing"), linetype=1) +
geom_line(data=som_tt$simout, aes(x=ts.days, y=Cc, color="Titration" ), linetype=2) +
scale_colour_manual(values=c("Fixed Dosing"="darkblue", "Titration"="firebrick3")) +
theme(legend.title = element_blank()) +
theme(legend.position = 'bottom')
myfig = prepare_figure('present', myfig)
print(myfig)
## ----warning=FALSE, message=FALSE, echo=FALSE---------------------------------
# cfg = system_select_set(cfg, "default")
# parameters = system_fetch_parameters(cfg)
# cfg=system_set_option(cfg,group = "simulation", option = "solver", value = "lsoda")
# cfg=system_set_option(cfg, group = "simulation",
# option = "output_times",
# seq(0,28*7*4,8))
# cfg=system_set_option(cfg,
# group = "titration",
# option = "titrate",
# value = TRUE)
## ----warning=FALSE, message=FALSE---------------------------------------------
# cfg=system_new_tt_rule(cfg,
# name = "ivdose",
# times = c(0, 6, 12, 18, 24),
# timescale = "months")
# cfg=system_set_tt_cond(cfg,
# name = "ivdose",
# cond = "Cc < 900",
# action = "SI_TT_BOLUS[state='At', values=700, times=0, repdose='last', number=11, interval=14]",
# value = "700")
# cfg=system_set_tt_cond(cfg,
# name = "ivdose",
# cond = "Cc > 900",
# action = "SI_TT_BOLUS[state='At', values=600, times=0, repdose='last', number=11, interval=14]",
# value = "600")
#
# som_tt = run_simulation_titrate(parameters, cfg)
## ----results="hide", warning=FALSE, echo=FALSE--------------------------------
# # When eval is set to TRUE we save the presimulated results
# presim$visit$som_tt$simout = data.frame(ts.days = som_tt$simout$ts.days,
# ts.weeks = som_tt$simout$ts.weeks,
# Cc = som_tt$simout$Cc)
# presim$visit$som_tt$titration = som_tt$titration[1:100,]
# presim$visit$som_tt$titration_history = som_tt$titration_history
## ----results="hide", warning=FALSE, echo=FALSE, eval=TRUE---------------------
if(presim_loaded){
som_tt = presim$visit$som_tt
}
## ----warning=FALSE, message=FALSE, fig.width=7, fig.height=3, eval=TRUE-------
myfig = ggplot() +
geom_line(data=som_tt$simout, aes(x=ts.weeks, y=Cc), color="blue")
myfig = prepare_figure('present', myfig)
print(myfig)
## ----echo=FALSE, fig.align="center", eval=TRUE--------------------------------
rhandsontable(som_tt$titration, width=550)
## ----echo=FALSE, fig.align="center", eval=TRUE--------------------------------
rhandsontable(som_tt$titration_history, width=550)
## ----echo=TRUE, message=FALSE, results=FALSE, warning=FALSE-------------------
# cfg = system_set_option(cfg, group="stochastic", option="nsub", value=20)
# som= simulate_subjects(parameters, cfg)
## ----results="hide", warning=FALSE, echo=FALSE--------------------------------
# # When eval is set to TRUE we save the presimulated results
# sdf = som_to_df(cfg, som)
# sdf = sdf[1:100,]
# #presim$visit$som = som
# presim$visit$sdf = sdf
## ----results="hide", warning=FALSE, echo=FALSE, eval=TRUE---------------------
if(presim_loaded){
#som = presim$visit$som
sdf = presim$visit$sdf
}
## ----message=FALSE, results=FALSE, eval=FALSE---------------------------------
# sdf = som_to_df(cfg, som)
## ----echo=FALSE, eval=TRUE----------------------------------------------------
rhandsontable(sdf, width=600, height=300)
## ----warning=FALSE, message=FALSE, echo=FALSE---------------------------------
# cfg = system_select_set(cfg, "default")
# parameters = system_fetch_parameters(cfg)
# cfg=system_set_option(cfg,group = "simulation", option = "solver", value = "lsoda")
# cfg=system_set_option(cfg, group = "simulation",
# option = "output_times",
# seq(0,10*7,1))
# cfg=system_set_option(cfg,
# group = "titration",
# option = "titrate",
# value = TRUE)
## ----message=FALSE, results=FALSE---------------------------------------------
# cfg=system_new_tt_rule(cfg,
# name = "ivdose",
# times = c(0, 2, 4, 6, 8),
# timescale = "weeks")
#
# cfg=system_set_tt_cond(cfg,
# name = "ivdose",
# cond = 'TRUE',
# action = "SI_TT_BOLUS[state='Cc', values=500, times=0]",
# value = "5")
## ----message=FALSE, results=FALSE---------------------------------------------
# cfg=system_new_tt_rule(cfg,
# name = "state_reset",
# times = c(3),
# timescale = "weeks")
# cfg=system_set_tt_cond(cfg,
# name = "state_reset",
# cond = 'TRUE',
# action = "SI_TT_STATE[Cc][0.5*Cc]",
# value = "0")
# cfg=system_set_tt_cond(cfg,
# name = "state_reset",
# cond = 'TRUE',
# action = "SI_TT_STATE[Cp][0.5*Cp]",
# value = "0")
# som_tt = run_simulation_titrate(parameters, cfg)
## ----results="hide", warning=FALSE, echo=FALSE--------------------------------
# # When eval is set to TRUE we save the presimulated results
# presim$state$som_tt$simout = data.frame(ts.weeks = som_tt$simout$ts.weeks,
# Cc = som_tt$simout$Cc)
## ----results="hide", warning=FALSE, echo=FALSE, eval=TRUE---------------------
if(presim_loaded){
som_tt = presim$state$som_tt
}
## ----warning=FALSE, message=FALSE, fig.width=7, fig.height=3, eval=TRUE-------
myfig = ggplot() +
geom_line(data=som_tt$simout, aes(x=ts.weeks, y=Cc), color="red")
myfig = prepare_figure('present', myfig)
print(myfig)
## ----warning=FALSE, message=FALSE, echo=FALSE---------------------------------
# save(presim, file="Titration_presim.RData")
## ----echo=FALSE, comment='', message=TRUE, eval=TRUE--------------------------
cat(readLines(system.file("ubinc", "systems","system-mab_pk.txt", package="ubiquity")), sep="\n")
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ubiquity documentation built on Nov. 2, 2023, 6:26 p.m.
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## ----setup, include=FALSE, eval=TRUE------------------------------------------
knitr::opts_chunk$set(echo = TRUE, message=FALSE, eval=FALSE)
require(ubiquity)
require(deSolve)
require(ggplot2)
require(foreach)
require(doParallel)
require(rhandsontable)
# The presim variable will contain presimualted data when eval is set to true
presim_loaded = FALSE
## ----echo=FALSE, results=FALSE------------------------------------------------
# presim= list()
# if(file.exists("Titration_presim.RData")){
# file.remove("Titration_presim.RData")
# }
## ----echo=FALSE, results=FALSE, eval=TRUE-------------------------------------
if(file.exists("Titration_presim.RData")){
load("Titration_presim.RData")
presim_loaded = TRUE
}
## ----eval=FALSE---------------------------------------------------------------
# library(ubiquity)
# fr = workshop_fetch(section="Titration", overwrite=TRUE)
## ----results="hide", message=FALSE, echo=FALSE--------------------------------
# library(ubiquity)
# system_new(file_name="system.txt", system_file="mab_pk", overwrite = TRUE)
## ----results="hide", message=FALSE, warning=FALSE-----------------------------
# cfg = build_system()
# cfg = system_select_set(cfg, "default")
# parameters = system_fetch_parameters(cfg)
# cfg=system_set_option(cfg,group = "simulation", option = "solver", value = "lsoda")
# cfg=system_set_option(cfg, group = "simulation", option = "output_times", seq(0,10*7,1))
# cfg = system_zero_inputs(cfg)
# cfg = system_set_bolus(cfg, state = "Cc",
# times = c(0, 14, 28, 42, 56),
# values = c(500, 500, 500, 500, 500))
# som_fix = run_simulation_ubiquity(parameters, cfg)
## ----results="hide", message=FALSE--------------------------------------------
# cfg=system_set_option(cfg,
# group = "titration",
# option = "titrate",
# value = TRUE)
## ----results="hide", message=FALSE--------------------------------------------
# cfg=system_new_tt_rule(cfg,
# name = "ivdose",
# times = c(0, 2, 4, 6, 8),
# timescale = "weeks")
## ----results="hide", message=FALSE--------------------------------------------
# cfg=system_set_tt_cond(cfg,
# name = "ivdose",
# cond = "TRUE",
# action = "SI_TT_BOLUS[state='Cc', values=500, times=0]",
# value = "1")
## ----results="hide", message=FALSE--------------------------------------------
# som_tt = run_simulation_titrate(parameters, cfg)
## ----results="hide", warning=FALSE, echo=FALSE--------------------------------
# # When eval is set to TRUE we save the presimulated results
# presim$bolus$som_tt$simout = data.frame(ts.days = som_tt$simout$ts.days,
# Cc = som_tt$simout$Cc)
# presim$bolus$som_fix$simout = data.frame(ts.days = som_fix$simout$ts.days,
# Cc = som_fix$simout$Cc)
## ----results="hide", warning=FALSE, echo=FALSE, eval=TRUE---------------------
if(presim_loaded){
som_tt = presim$bolus$som_tt
som_fix = presim$bolus$som_fix
}
## ----warning=FALSE, message=FALSE, fig.width=7, fig.height=3, eval=TRUE-------
myfig = ggplot() +
geom_line(data=som_fix$simout, aes(x=ts.days, y=Cc, color="Fixed Dosing"), linetype=1) +
geom_line(data=som_tt$simout, aes(x=ts.days, y=Cc, color="Titration" ), linetype=2) +
scale_colour_manual(values=c("Fixed Dosing"="darkblue", "Titration"="firebrick3")) +
theme(legend.title = element_blank()) +
theme(legend.position = 'bottom')
myfig = prepare_figure('present', myfig)
print(myfig)
## ----warning=FALSE, message=FALSE, echo=FALSE---------------------------------
# # resetting everything for the repeat infusion example
# cfg = system_select_set(cfg, "default")
# parameters = system_fetch_parameters(cfg)
# cfg=system_set_option(cfg,group = "simulation", option = "solver", value = "lsoda")
# cfg=system_set_option(cfg, group = "simulation",
# option = "output_times",
# seq(0,10*7,.5))
## ----warning=FALSE, message=FALSE---------------------------------------------
# cfg = system_zero_inputs(cfg)
# cfg = system_set_rate(cfg, rate = "Dinf",
# times = c( 0, 30, 20160, 20190, 40320, 40350, 60480, 60510, 80640, 80670),
# levels = c(15 , 0, 15, 0, 15, 0, 15, 0, 15, 0))
# som_fix = run_simulation_ubiquity(parameters, cfg)
## ----warning=FALSE, message=FALSE---------------------------------------------
# cfg=system_set_option(cfg, group = "titration", option = "titrate", value = TRUE)
# cfg=system_new_tt_rule(cfg, name = "ivdose", times = c(0, 2, 4, 6, 8), timescale = "weeks")
## ----warning=FALSE, message=FALSE---------------------------------------------
# cfg=system_set_tt_cond(cfg,
# name = "ivdose",
# cond = "TRUE",
# action = "SI_TT_RATE[rate='Dinf', times=c(0,30), levels=c(15,0)]",
# value = "1")
## ----warning=FALSE, message=FALSE---------------------------------------------
# som_tt = run_simulation_titrate(parameters, cfg)
## ----results="hide", warning=FALSE, echo=FALSE--------------------------------
# # When eval is set to TRUE we save the presimulated results
# presim$infusion$som_tt$simout = data.frame(ts.days = som_tt$simout$ts.days,
# Cc = som_tt$simout$Cc)
# presim$infusion$som_fix$simout = data.frame(ts.days = som_fix$simout$ts.days,
# Cc = som_fix$simout$Cc)
## ----results="hide", warning=FALSE, echo=FALSE, eval=TRUE---------------------
if(presim_loaded){
som_tt = presim$infusion$som_tt
som_fix = presim$infusion$som_fix
}
## ----warning=FALSE, message=FALSE, fig.width=7, fig.height=3, eval=TRUE-------
myfig = ggplot() +
geom_line(data=som_fix$simout, aes(x=ts.days, y=Cc, color="Fixed Dosing"), linetype=1) +
geom_line(data=som_tt$simout, aes(x=ts.days, y=Cc, color="Titration" ), linetype=2) +
scale_colour_manual(values=c("Fixed Dosing"="darkblue", "Titration"="firebrick3")) +
theme(legend.title = element_blank()) +
theme(legend.position = 'bottom')
myfig = prepare_figure('present', myfig)
print(myfig)
## ----warning=FALSE, message=FALSE, echo=FALSE---------------------------------
# cfg = system_select_set(cfg, "default")
# parameters = system_fetch_parameters(cfg)
# cfg=system_set_option(cfg,group = "simulation", option = "solver", value = "lsoda")
# cfg=system_set_option(cfg, group = "simulation",
# option = "output_times",
# seq(0,28*7*4,8))
# cfg=system_set_option(cfg,
# group = "titration",
# option = "titrate",
# value = TRUE)
## ----warning=FALSE, message=FALSE---------------------------------------------
# cfg=system_new_tt_rule(cfg,
# name = "ivdose",
# times = c(0, 6, 12, 18, 24),
# timescale = "months")
# cfg=system_set_tt_cond(cfg,
# name = "ivdose",
# cond = "Cc < 900",
# action = "SI_TT_BOLUS[state='At', values=700, times=0, repdose='last', number=11, interval=14]",
# value = "700")
# cfg=system_set_tt_cond(cfg,
# name = "ivdose",
# cond = "Cc > 900",
# action = "SI_TT_BOLUS[state='At', values=600, times=0, repdose='last', number=11, interval=14]",
# value = "600")
#
# som_tt = run_simulation_titrate(parameters, cfg)
## ----results="hide", warning=FALSE, echo=FALSE--------------------------------
# # When eval is set to TRUE we save the presimulated results
# presim$visit$som_tt$simout = data.frame(ts.days = som_tt$simout$ts.days,
# ts.weeks = som_tt$simout$ts.weeks,
# Cc = som_tt$simout$Cc)
# presim$visit$som_tt$titration = som_tt$titration[1:100,]
# presim$visit$som_tt$titration_history = som_tt$titration_history
## ----results="hide", warning=FALSE, echo=FALSE, eval=TRUE---------------------
if(presim_loaded){
som_tt = presim$visit$som_tt
}
## ----warning=FALSE, message=FALSE, fig.width=7, fig.height=3, eval=TRUE-------
myfig = ggplot() +
geom_line(data=som_tt$simout, aes(x=ts.weeks, y=Cc), color="blue")
myfig = prepare_figure('present', myfig)
print(myfig)
## ----echo=FALSE, fig.align="center", eval=TRUE--------------------------------
rhandsontable(som_tt$titration, width=550)
## ----echo=FALSE, fig.align="center", eval=TRUE--------------------------------
rhandsontable(som_tt$titration_history, width=550)
## ----echo=TRUE, message=FALSE, results=FALSE, warning=FALSE-------------------
# cfg = system_set_option(cfg, group="stochastic", option="nsub", value=20)
# som= simulate_subjects(parameters, cfg)
## ----results="hide", warning=FALSE, echo=FALSE--------------------------------
# # When eval is set to TRUE we save the presimulated results
# sdf = som_to_df(cfg, som)
# sdf = sdf[1:100,]
# #presim$visit$som = som
# presim$visit$sdf = sdf
## ----results="hide", warning=FALSE, echo=FALSE, eval=TRUE---------------------
if(presim_loaded){
#som = presim$visit$som
sdf = presim$visit$sdf
}
## ----message=FALSE, results=FALSE, eval=FALSE---------------------------------
# sdf = som_to_df(cfg, som)
## ----echo=FALSE, eval=TRUE----------------------------------------------------
rhandsontable(sdf, width=600, height=300)
## ----warning=FALSE, message=FALSE, echo=FALSE---------------------------------
# cfg = system_select_set(cfg, "default")
# parameters = system_fetch_parameters(cfg)
# cfg=system_set_option(cfg,group = "simulation", option = "solver", value = "lsoda")
# cfg=system_set_option(cfg, group = "simulation",
# option = "output_times",
# seq(0,10*7,1))
# cfg=system_set_option(cfg,
# group = "titration",
# option = "titrate",
# value = TRUE)
## ----message=FALSE, results=FALSE---------------------------------------------
# cfg=system_new_tt_rule(cfg,
# name = "ivdose",
# times = c(0, 2, 4, 6, 8),
# timescale = "weeks")
#
# cfg=system_set_tt_cond(cfg,
# name = "ivdose",
# cond = 'TRUE',
# action = "SI_TT_BOLUS[state='Cc', values=500, times=0]",
# value = "5")
## ----message=FALSE, results=FALSE---------------------------------------------
# cfg=system_new_tt_rule(cfg,
# name = "state_reset",
# times = c(3),
# timescale = "weeks")
# cfg=system_set_tt_cond(cfg,
# name = "state_reset",
# cond = 'TRUE',
# action = "SI_TT_STATE[Cc][0.5*Cc]",
# value = "0")
# cfg=system_set_tt_cond(cfg,
# name = "state_reset",
# cond = 'TRUE',
# action = "SI_TT_STATE[Cp][0.5*Cp]",
# value = "0")
# som_tt = run_simulation_titrate(parameters, cfg)
## ----results="hide", warning=FALSE, echo=FALSE--------------------------------
# # When eval is set to TRUE we save the presimulated results
# presim$state$som_tt$simout = data.frame(ts.weeks = som_tt$simout$ts.weeks,
# Cc = som_tt$simout$Cc)
## ----results="hide", warning=FALSE, echo=FALSE, eval=TRUE---------------------
if(presim_loaded){
som_tt = presim$state$som_tt
}
## ----warning=FALSE, message=FALSE, fig.width=7, fig.height=3, eval=TRUE-------
myfig = ggplot() +
geom_line(data=som_tt$simout, aes(x=ts.weeks, y=Cc), color="red")
myfig = prepare_figure('present', myfig)
print(myfig)
## ----warning=FALSE, message=FALSE, echo=FALSE---------------------------------
# save(presim, file="Titration_presim.RData")
## ----echo=FALSE, comment='', message=TRUE, eval=TRUE--------------------------
cat(readLines(system.file("ubinc", "systems","system-mab_pk.txt", package="ubiquity")), sep="\n")
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