#clearing the workspace
rm(list=ls())
graphics.off()
options(show.error.locations = TRUE)
# If we are in a stand alone ubiquity distribution we run
# from there otherwise we try to load the package
if(file.exists(file.path('library', 'r_general', 'ubiquity.R'))){
source(file.path('library', 'r_general', 'ubiquity.R'))
} else {
library(ubiquity) }
analysis_name = 'parent_d1030'
# flowctl = 'previous estimate as guess'
# flowctl = 'plot previous estimate'
# flowctl = 'plot guess'
flowctl = 'estimate'
archive_results = TRUE
# For documentation explaining how to modify the commands below
# See the "R Workflow" section at the link below:
# http://presentation.ubiquity.grok.tv
# Rebuilding the system (R scripts and compiling C code)
cfg = build_system(output_directory = file.path(".", "output"),
temporary_directory = file.path(".", "transient"))
# set name | Description
# -------------------------------------------------------
# default | TMDD: Membrane bound target
pnames = c('Vp', 'Vt', 'CLp', 'Q')
cfg = system_select_set(cfg, "default", pnames)
# #
# # Simulation options
# #
#
# Specify the output times used for smooth profiles
cfg=system_set_option(cfg, group = "simulation",
option = "output_times",
seq(0,100,1))
cfg = system_load_data(cfg, dsname = "pm_data",
data_file = "pm_data.csv")
# cat(system_view(cfg, 'datasets'))
# Defining the cohorts
#
# Clearing all of the cohorts
cfg = system_clear_cohorts(cfg)
#-------------------------------------------------------
# 10 mpk cohort
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 = "1")
# Plot formatting
cohort[["outputs"]][["Parent"]][["options"]] = list(
marker_color = "black",
marker_shape = 1,
marker_line = 2 )
cfg = system_define_cohort(cfg, cohort)
#-------------------------------------------------------
#-------------------------------------------------------
# 30 mpk cohort
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)
#-------------------------------------------------------
#cat(system_view(cfg, field="datasets"))
#cat(system_view(cfg, field="cohorts"))
#cat(system_view(cfg, field="estimation"))
#cat(system_view(cfg, field="simulation"))
# cfg = system_set_option(cfg, group="estimation",
# option="method",
# value = "BFGS")
#
#
# cfg = system_set_option(cfg, group="estimation",
# option="optimizer",
# value = "optimx")
#
#
# performing estimation or loading guess/previous results
pest = system_estimate_parameters(cfg,
flowctl = flowctl,
analysis_name = analysis_name,
archive_results = archive_results)
# Simulating the system at the estimate
erp = system_simulate_estimation_results(pest = pest, cfg = cfg)
plot_opts = c()
plot_opts$outputs$Parent$yscale = 'log'
plot_opts$outputs$Metabolite$yscale = 'linear'
# plot_opts$outputs$ONAME$yscale = 'linear' # 'linear' or 'log'
# plot_opts$outputs$ONAME$ylim = c(0,1) # NULL
# plot_opts$outputs$ONAME$xlim = c(0,1) # NULL
system_plot_cohorts(erp, plot_opts, cfg, analysis_name=analysis_name)
#-------------------------------------------------------
# Writing the results to a PowerPoint report
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="")))
#-------------------------------------------------------
# Writing the results to a Word report
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="")))
#-------------------------------------------------------
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