## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(echo = TRUE, message=FALSE, eval=FALSE)
require(ubiquity)
require(deSolve)
require(ggplot2)
require(foreach)
require(doParallel)
require(rhandsontable)
## ----eval=FALSE---------------------------------------------------------------
# library(ubiquity)
# fr = workshop_fetch(section="Estimation", overwrite=TRUE)
## ----results="hide", message=FALSE--------------------------------------------
# library(ubiquity)
# system_new(file_name="system.txt", system_file="adapt", overwrite = TRUE)
# cfg = build_system(system_file = "system.txt")
## ----results="hide", message=FALSE--------------------------------------------
# system_fetch_template(cfg, template="Estimation")
## ----results="hide", echo=TRUE, warning=FALSE---------------------------------
# flowctl = 'estimate'
# archive_results = TRUE
# analysis_name = 'parent_d1030'
## ----results="hide", echo=TRUE------------------------------------------------
# pnames = c('Vp', 'Vt', 'CLp', 'Q')
# cfg = system_select_set(cfg, "default", pnames)
## ----results="hide", echo=TRUE------------------------------------------------
# cfg=system_set_option(cfg, group = "simulation",
# option = "output_times",
# seq(0,100,1))
## ----results="hide", echo=TRUE, warning=FALSE---------------------------------
# cfg = system_load_data(cfg, dsname = "pm_data",
# data_file = system.file("ubinc", "csv",
# "pm_data.csv",
# package = "ubiquity"))
## ----results="hide", echo=FALSE-----------------------------------------------
# dataset = read.csv(system.file("ubinc", "csv", "pm_data.csv", package = "ubiquity"))
## ----echo=FALSE, fig.align="center"-------------------------------------------
# rhandsontable(dataset, width=400, height=200)
## ----results="hide", echo=TRUE, warning=FALSE---------------------------------
# cfg = system_clear_cohorts(cfg)
## ----results="hide", echo=TRUE, warning=FALSE---------------------------------
# cohort = list(
# name = "dose_10",
# cf = list(DOSE = c(10)),
# inputs = NULL,
# outputs = NULL,
# dataset = "pm_data")
#
## ----results="hide", echo=TRUE, warning=FALSE---------------------------------
# cohort[["inputs"]][["bolus"]] = list()
# cohort[["inputs"]][["bolus"]][["Mpb"]] = list(TIME=NULL, AMT=NULL)
# cohort[["inputs"]][["bolus"]][["Mpb"]][["TIME"]] = c( 0) # hours
# cohort[["inputs"]][["bolus"]][["Mpb"]][["AMT"]] = c(10) # mpk
#
## ----results="hide", echo=TRUE, warning=FALSE---------------------------------
# cohort[["outputs"]][["Parent"]] = list()
#
# # Mapping to data set
# cohort[["outputs"]][["Parent"]][["obs"]] = list(
# time = "TIME",
# value = "PT",
# missing = -1)
#
# # Mapping to system file
# cohort[["outputs"]][["Parent"]][["model"]] = list(
# time = "hours",
# value = "Cpblood",
# variance = "1")
#
# # Plot formatting
# cohort[["outputs"]][["Parent"]][["options"]] = list(
# marker_color = "black",
# marker_shape = 1,
# marker_line = 2 )
## ----results="hide", echo=TRUE, warning=FALSE---------------------------------
# cohort[["outputs"]][["Parent"]][["options"]] = list(
# marker_color = "black",
# marker_shape = 1,
# marker_line = 2 )
## ----results="hide", echo=TRUE, warning=FALSE---------------------------------
# cfg = system_define_cohort(cfg, cohort)
## ----results="hide", echo=TRUE, warning=FALSE---------------------------------
# cohort = list(
# name = "dose_30",
# cf = list(DOSE = c(30)),
# dataset = "pm_data",
# inputs = NULL,
# outputs = NULL)
#
# # Bolus inputs for the cohort
# cohort[["inputs"]][["bolus"]] = list()
# cohort[["inputs"]][["bolus"]][["Mpb"]] = list(TIME=NULL, AMT=NULL)
# cohort[["inputs"]][["bolus"]][["Mpb"]][["TIME"]] = c( 0) # hours
# cohort[["inputs"]][["bolus"]][["Mpb"]][["AMT"]] = c(30) # mpk
#
#
# # Defining Parent output
# cohort[["outputs"]][["Parent"]] = list()
#
# # Mapping to data set
# cohort[["outputs"]][["Parent"]][["obs"]] = list(
# time = "TIME",
# value = "PT",
# missing = -1)
#
# # Mapping to system file
# cohort[["outputs"]][["Parent"]][["model"]] = list(
# time = "hours",
# value = "Cpblood",
# variance = "1")
#
# # Plot formatting
# cohort[["outputs"]][["Parent"]][["options"]] = list(
# marker_color = "red",
# marker_shape = 2,
# marker_line = 2 )
# cfg = system_define_cohort(cfg, cohort)
## ----echo=FALSE, message=FALSE, warning=FALSE, results="hide"-----------------
# cfg = system_set_option(cfg, group = "estimation",
# option = "control",
# value = list(trace = TRUE,
# maxit = 10,
# REPORT = 10))
## ----echo=TRUE, message=FALSE, warning=FALSE, results="hide"------------------
# pest = system_estimate_parameters(cfg,
# flowctl = flowctl,
# analysis_name = analysis_name,
# archive_results = archive_results)
## ----results="hide", echo=TRUE, warning=FALSE---------------------------------
# cfg=system_set_option(cfg, group = "simulation",
# option = "output_times",
# seq(0,100,5))
## ----results="hide", echo=TRUE, warning=FALSE---------------------------------
# erp = system_simulate_estimation_results(pest = pest, cfg = cfg)
#
## ----results="hide", echo=TRUE, warning=FALSE, fig.align="center", fig.width=2----
# plot_opts = c()
# plot_opts$outputs$Parent$yscale = 'log'
## ----results="hide", echo=TRUE, warning=FALSE, message=FALSE------------------
# plinfo = system_plot_cohorts(erp, plot_opts, cfg, analysis_name=analysis_name)
## ----echo=FALSE---------------------------------------------------------------
# # Creating a reduced form of the estimation output to save it and use less disk space
# estout = list()
# estout$tc = plinfo$timecourse$Parent
# estout$op = plinfo$obs_pred$Parent
# ggsave(filename="Estimation-parent-tc.png", plot=estout$tc, height=4, width=7, units="in", dpi=72)
# ggsave(filename="Estimation-parent-op.png", plot=estout$op, height=4, width=7, units="in", dpi=72)
## ----results="hide", echo=TRUE, eval=FALSE------------------------------------
# cfg = system_rpt_read_template(cfg, template="PowerPoint")
# cfg = system_rpt_estimation(cfg=cfg, analysis_name=analysis_name)
# system_rpt_save_report(cfg=cfg,
# output_file=file.path("output",paste(analysis_name, "-report.pptx", sep="")))
## ----results="hide", echo=TRUE, eval=FALSE------------------------------------
# cfg = system_rpt_read_template(cfg, template="Word")
# cfg = system_rpt_estimation(cfg=cfg, analysis_name=analysis_name)
# system_rpt_save_report(cfg=cfg,
# output_file=file.path("output",paste(analysis_name, "-report.docx", sep="")))
## ----results="hide", echo=TRUE, eval=FALSE------------------------------------
# pnames = c('Vp',
# 'Vt',
# 'Vm',
# 'CLp',
# 'Q',
# 'CLm',
# 'slope_parent',
# 'slope_metabolite');
#
# cfg = system_select_set(cfg, "default", pnames)
## ----results="hide", echo=TRUE, eval=FALSE------------------------------------
# cohort = list(
# name = "dose_10",
# cf = list(DOSE = c(10)),
# inputs = NULL,
# outputs = NULL,
# dataset = "pm_data")
#
#
# # Bolus inputs for the cohort
# cohort[["inputs"]][["bolus"]] = list()
# cohort[["inputs"]][["bolus"]][["Mpb"]] = list(TIME=NULL, AMT=NULL)
# cohort[["inputs"]][["bolus"]][["Mpb"]][["TIME"]] = c( 0) # hours
# cohort[["inputs"]][["bolus"]][["Mpb"]][["AMT"]] = c(10) # mpk
#
#
# # Defining Parent output
# cohort[["outputs"]][["Parent"]] = list()
#
# # Mapping to data set
# cohort[["outputs"]][["Parent"]][["obs"]] = list(
# time = "TIME",
# value = "PT",
# missing = -1)
#
# # Mapping to system file
# cohort[["outputs"]][["Parent"]][["model"]] = list(
# time = "hours",
# value = "Cpblood",
# variance = "slope_parent*PRED^2")
#
# # Plot formatting
# cohort[["outputs"]][["Parent"]][["options"]] = list(
# marker_color = "black",
# marker_shape = 1,
# marker_line = 1 )
#
# # Defining Metabolite output
# cohort[["outputs"]][["Metabolite"]] = list()
#
# # Mapping to data set
# cohort[["outputs"]][["Metabolite"]][["obs"]] = list(
# time = "TIME",
# value = "MT",
# missing = -1)
#
# # Mapping to system file
# cohort[["outputs"]][["Metabolite"]][["model"]] = list(
# time = "hours",
# value = "Cmblood",
# variance = "slope_metabolite*PRED^2")
#
# # Plot formatting
# cohort[["outputs"]][["Metabolite"]][["options"]] = list(
# marker_color = "blue",
# marker_shape = 1,
# marker_line = 1 )
#
# cfg = system_define_cohort(cfg, cohort)
## ----eval=FALSE---------------------------------------------------------------
# cfg = system_set_option(cfg, group = "estimation",
# option = "method",
# value = "SANN")
## ----eval=FALSE---------------------------------------------------------------
# library(pso)
# cfg = system_set_option(cfg, group = "estimation",
# option = "optimizer",
# value = "pso")
#
# cfg = system_set_option(cfg, group = "estimation",
# option = "method",
# value = "psoptim")
## ----eval=FALSE---------------------------------------------------------------
# library(GA)
#
# cfg = system_set_option(cfg, group = "estimation",
# option = "optimizer",
# value = "ga")
#
# cfg = system_set_option(cfg, group = "estimation",
# option = "method",
# value = "ga")
#
# cfg = system_set_option(cfg, group = "estimation",
# option = "control",
# value = list(maxiter = 10000,
# optimArgs = list(method = "Nelder-Mead",
# maxiter = 1000)))
## ----eval=FALSE---------------------------------------------------------------
# cfg = system_load_data(cfg, dsname = "nm_pm_data",
# data_file = system.file("ubinc", "csv",
# "nm_data.csv",
# package = "ubiquity"))
# cfg = system_clear_cohorts(cfg);
## ----eval=FALSE---------------------------------------------------------------
# filter = list()
# filter$DOSE = c(10, 30)
## ----eval=FALSE---------------------------------------------------------------
# OBSMAP = list()
# OBSMAP$PT = list(variance = 'slope_parent*PRED^2',
# CMT = 1,
# output = 'Cpblood',
# missing = -1 )
#
# OBSMAP$MT = list(variance = 'slope_metabolite*PRED^2',
# CMT = 2,
# output = 'Cmblood',
# missing = -1 )
## ----eval=FALSE---------------------------------------------------------------
# INPUTMAP = list()
# INPUTMAP$bolus$Mpb$CMT_NUM = 1
## ----eval=FALSE---------------------------------------------------------------
# cfg = system_define_cohorts_nm(cfg,
# DS = 'nm_pm_data',
# col_ID = 'ID', col_CMT = 'CMT', col_DV = 'DV',
# col_TIME = 'TIME', col_AMT = 'AMT', col_RATE = 'RATE',
# col_EVID = 'EVID', col_GROUP= 'DOSE',
# filter = filter,
# INPUTS = INPUTMAP,
# OBS = OBSMAP,
# group = FALSE)
## ----echo=FALSE, comment='', message=TRUE, eval=TRUE--------------------------
cat(readLines(system.file("ubinc", "systems","system-adapt.txt", package="ubiquity")), sep="\n")