Nothing
## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(echo = TRUE, message=FALSE, eval=FALSE)
require(ubiquity)
require(ggplot2)
require(rhandsontable)
require(gridExtra)
require(flextable)
# The presim variable will contain presimulated data when eval is set to true
presim_loaded = FALSE
## ----echo=FALSE, results=FALSE------------------------------------------------
# presim= list()
# if(file.exists("NCA_presim.RData")){
# file.remove("NCA_presim.RData")
# }
## ----echo=FALSE, results=FALSE, eval=TRUE-------------------------------------
if(file.exists("NCA_presim.RData")){
load("NCA_presim.RData")
presim_loaded = TRUE
}
## ----warning=FALSE, message=FALSE, echo=FALSE, error=FALSE, results="hide", fig.width=8, fig.height=4----
# system_new(system_file="mab_pk", overwrite=TRUE)
# cfg = build_system()
# parameters = system_fetch_parameters(cfg)
# cfg = system_zero_inputs(cfg)
# cfg = system_set_bolus(cfg, state ="At",
# times = c( 0.0), # day
# values = c(400.0)) # mg
#
# cfg=system_set_option(cfg, group = "simulation",
# option = "output_times",
# linspace(0,30,100))
#
# som_smooth = run_simulation_ubiquity(parameters, cfg)
# som_smooth$simout$time_C_ng_ml = som_smooth$simout$C_ng_ml*som_smooth$simout$ts.days
#
# cfg=system_set_option(cfg, group = "simulation",
# option = "include_important_output_times",
# value = "no")
#
# cfg=system_set_option(cfg, group = "simulation",
# option = "output_times",
# c(0,.25, .5, 1, 2,7,14,21,28))
# som_sample = run_simulation_ubiquity(parameters, cfg)
# som_sample$simout$time_C_ng_ml = som_sample$simout$C_ng_ml*som_sample$simout$ts.days
#
#
# polydf = NULL
# for(tidx in 1:(nrow(som_sample$simout)-1)){
# xv = c(som_sample$simout$ts.days[tidx], som_sample$simout$ts.days[tidx+1], som_sample$simout$ts.days[tidx+1], som_sample$simout$ts.days[tidx] )
# yvC = c(som_sample$simout$C_ng_ml[tidx], som_sample$simout$C_ng_ml[tidx+1], 0, 0)
# yvTC = c(som_sample$simout$time_C_ng_ml[tidx], som_sample$simout$time_C_ng_ml[tidx+1], 0, 0)
# tmpdf = data.frame(xv = xv, yvC=yvC, yvTC=yvTC, sp=tidx)
# if(is.null(polydf)){
# polydf = tmpdf
# } else {
# polydf = rbind(tmpdf, polydf)
# }
# }
## ----results="hide", warning=FALSE, echo=FALSE--------------------------------
# # When eval is set to TRUE we save the presimulated results
# presim$plots$som_smooth = som_smooth
# presim$plots$som_sample = som_sample
# presim$plots$polydf = polydf
## ----results="hide", warning=FALSE, echo=FALSE, eval=TRUE---------------------
if(presim_loaded){
som_smooth = presim$plots$som_smooth
som_sample = presim$plots$som_sample
polydf = presim$plots$polydf
}
## ----warning=FALSE, message=FALSE, echo=FALSE, error=FALSE, eval=TRUE, results="hide", fig.width=8, fig.height=4----
p_C = ggplot()
p_C = p_C + geom_line(data=som_smooth$simout, aes(x=ts.days, y=C_ng_ml))
p_C = p_C + geom_point(data=som_sample$simout, aes(x=ts.days, y=C_ng_ml), color="blue")
p_C = p_C + xlab("Time") + ylab("Concentration") + ggtitle("AUC")
p_C = p_C + geom_polygon(data=polydf, aes(x=xv, y=yvC, group=sp), color="blue", linetype='dashed', fill="lightblue")
p_C = p_C + theme(plot.title = element_text(hjust = 0.5))
p_C = prepare_figure(fo=p_C, purpose="shiny")
p_TC = ggplot()
p_TC = p_TC + geom_line(data=som_smooth$simout, aes(x=ts.days, y=time_C_ng_ml))
p_TC = p_TC + geom_point(data=som_sample$simout, aes(x=ts.days, y=time_C_ng_ml), color="blue")
p_TC = p_TC + xlab("Time") + ylab("Time x Concentration") + ggtitle("AUMC")
p_TC = p_TC + geom_polygon(data=polydf, aes(x=xv, y=yvTC, group=sp), color="blue", linetype='dashed', fill="lightblue")
p_TC = p_TC + theme(plot.title = element_text(hjust = 0.5))
p_TC = prepare_figure(fo=p_TC, purpose="shiny")
p_AUC = p_C
p_AUMC = p_TC
## ----warning=FALSE, message=FALSE, echo=FALSE, error=FALSE, eval=TRUE, fig.width=8, fig.height=3.5----
gridExtra::grid.arrange(p_AUC, p_AUMC, ncol=2)
## ----warning=FALSE, message=FALSE, echo=TRUE, error=FALSE, results="hide", fig.width=8, fig.height=4----
# library(ubiquity)
# fr = workshop_fetch(section="NCA", overwrite=TRUE)
## ----warning=FALSE, message=FALSE, echo=TRUE, error=FALSE, results="hide", fig.width=8, fig.height=4----
# library(ubiquity)
# cfg = build_system()
# fr = system_fetch_template(cfg, template = "NCA")
## ----warning=FALSE, message=FALSE, echo=TRUE, error=FALSE, results="hide", fig.width=8, fig.height=4----
# cfg = build_system(system_file="system.txt")
# cfg = system_load_data(cfg, dsname = "PKDATA",
# data_file = "pk_all_sd.csv")
## ----echo=FALSE, fig.align="center", eval=TRUE--------------------------------
rhandsontable(read.csv(system.file("ubinc", "csv", "pk_all_sd.csv" , package="ubiquity")), width="100%", height=200)
## ----warning=FALSE, message=FALSE, echo=TRUE, error=FALSE, results="hide", fig.width=8, fig.height=4----
# cfg = system_nca_run(cfg, dsname = "PKDATA",
# dscale = 1e6,
# analysis_name = "pk_single_dose",
# extrap_C0 = FALSE,
# dsmap = list(TIME = "TIME_HR",
# NTIME = "TIME_HR",
# CONC = "C_ng_ml",
# DOSE = "DOSE",
# ROUTE = "ROUTE",
# ID = "ID"),
# NCA_options = list(max.aucinf.pext = 10) )
## ----warning=FALSE, message=FALSE, echo=TRUE, error=FALSE, eval=FALSE, results="hide", fig.width=8, fig.height=4----
# NCA_results = system_fetch_nca(cfg, analysis_name = "pk_single_dose")
## ----warning=FALSE, message=FALSE, echo=FALSE, error=FALSE--------------------
# nca_summary = read.csv(file.path("output", "pk_single_dose-nca_summary-pknca.csv"))
# presim$sd$nca_summary = nca_summary
## ----results="hide", warning=FALSE, echo=FALSE, eval=TRUE---------------------
if(presim_loaded){
nca_summary = presim$sd$nca_summary
}
## ----echo=FALSE, fig.align="center", eval=TRUE--------------------------------
rhandsontable(nca_summary, width="100%", height=200)
## ----warning=FALSE, message=FALSE, echo=TRUE, error=FALSE, eval=FALSE, results="hide", fig.width=8, fig.height=4----
# nca_cols = system_fetch_nca_columns(cfg, "pk_single_dose")
# rhandsontable(nca_cols[["NCA_col_summary"]], width="100%", height=200)
## ----warning=FALSE, message=FALSE, echo=FALSE, error=FALSE--------------------
# nca_cols = system_fetch_nca_columns(cfg, "pk_single_dose")
# presim$sd$nca_cols = nca_cols
## ----results="hide", warning=FALSE, echo=FALSE, eval=TRUE---------------------
if(presim_loaded){
nca_summary = presim$sd$nca_summary
nca_cols = presim$sd$nca_cols
}
## ----echo=FALSE, fig.align="center", eval=TRUE--------------------------------
HT = rhandsontable(nca_cols[["NCA_col_summary"]], width="100%", height=200)
HT = hot_cols(HT, colWidths = c(80, 80,100, 450))
HT
## ----warning=FALSE, message=FALSE, eval=FALSE, echo=TRUE, error=FALSE, results="hide", fig.width=8, fig.height=4----
# cfg = system_rpt_read_template(cfg, template="PowerPoint")
# cfg = system_rpt_add_slide(cfg,
# template = "title_slide",
# elements = list( title= list(content = "NCA Single Dose PK", type = "text")))
# cfg = system_rpt_nca(cfg=cfg, analysis_name="pk_single_dose")
# system_rpt_save_report(cfg=cfg, output_file=file.path("output","pk_single_dose-report.pptx"))
## ----warning=FALSE, message=FALSE, eval=FALSE, echo=TRUE, error=FALSE, results="hide", fig.width=8, fig.height=4----
# cfg = system_rpt_read_template(cfg, template="Word")
# cfg = system_rpt_nca(cfg=cfg, analysis_name="pk_single_dose")
# system_rpt_save_report(cfg=cfg, output_file=file.path("output","pk_single_dose-report.docx"))
## ----warning=FALSE, message=FALSE, echo=TRUE, error=FALSE---------------------
# nca_table = system_nca_summary(cfg,
# analysis_name = "pk_single_dose",
# params_include = c( "ID", "cmax", "tmax", "half.life", "auclast"),
# params_header = list(cmax = c( "<label>", "(ng/ml)")),
# ds_wrangle = "NCA_sum = NCA_sum %>% dplyr::filter(Dose == 30)",
# summary_stats = list("<MEAN> (<STD>)" = c("auclast", "half.life"),
# "<MEDIAN>" = c("tmax")),
# summary_labels = list(MEAN = "Mean",
# STD = "Std Dev",
# N = "N obs",
# MEDIAN = "Median",
# SE = "Std Err."),
# summary_location = "ID")
#
# nca_table[["vignette"]] = set_table_properties(nca_table$nca_summary_ft,layout = "autofit")
## ----warning=FALSE, message=FALSE, echo=FALSE, error=FALSE--------------------
# presim$sd$nca_table = nca_table
## ----results="hide", warning=FALSE, echo=FALSE, eval=TRUE---------------------
if(presim_loaded){
nca_table = presim$sd$nca_table
}
## ----warning=FALSE, echo=FALSE, eval=TRUE-------------------------------------
knitr::knit_print(nca_table[["vignette"]])
## ----warning=FALSE, message=FALSE, echo=TRUE, error=FALSE, results="hide", fig.width=8, fig.height=4----
# cfg = build_system(system_file="system.txt")
# cfg = system_load_data(cfg, dsname = "PKDATA",
# data_file = "pk_all_md.csv")
## ----echo=FALSE, fig.align="center", eval=TRUE--------------------------------
rhandsontable(read.csv(system.file("ubinc", "csv", "pk_all_md.csv" , package="ubiquity")), width="100%", height=200)
## ----warning=FALSE, message=FALSE, echo=FALSE, error=FALSE, results="hide", fig.width=8, fig.height=4----
# cfg = system_nca_run(cfg, dsname = "PKDATA",
# dscale = 1e6,
# analysis_name = "pk_multiple_dose",
# dsmap = list(TIME = "TIME_HR",
# NTIME = "NTIME_HR",
# CONC = "C_ng_ml",
# DOSE = "DOSE",
# ROUTE = "ROUTE",
# ID = "ID",
# DOSENUM = "DOSENUM",
# EXTRAP = "EXTRAP"))
## ----warning=FALSE, eval=FALSE, message=FALSE, echo=TRUE, error=FALSE, results="hide", fig.width=8, fig.height=4----
# cfg = system_nca_run(cfg, dsname = "PKDATA",
# dscale = 1e6,
# analysis_name = "pk_multiple_dose",
# dsmap = list(TIME = "TIME_HR",
# NTIME = "NTIME_HR",
# CONC = "C_ng_ml",
# DOSE = "DOSE",
# ROUTE = "ROUTE",
# ID = "ID",
# DOSENUM = "DOSENUM",
# EXTRAP = "EXTRAP"))
# cfg = system_rpt_read_template(cfg, template="PowerPoint")
# cfg = system_rpt_nca(cfg=cfg, analysis_name="pk_multiple_dose")
# system_rpt_save_report(cfg=cfg, output_file=file.path("output","pk_multiple_dose-report.pptx"))
#
## ----warning=FALSE, message=FALSE, echo=FALSE, error=FALSE--------------------
# nca_summary = read.csv(file.path("output", "pk_multiple_dose-nca_summary-pknca.csv"))
# presim$md$nca_summary = nca_summary
## ----results="hide", warning=FALSE, echo=FALSE, eval=TRUE---------------------
if(presim_loaded){
nca_summary = presim$md$nca_summary
}
## ----echo=FALSE, fig.align="center", eval=TRUE--------------------------------
rhandsontable(nca_summary, width="100%", height=200)
## ----warning=FALSE, message=FALSE, echo=TRUE, error=FALSE, results="hide", fig.width=8, fig.height=4----
# cfg = build_system(system_file="system.txt")
# cfg = system_load_data(cfg, dsname = "PKDATA",
# data_file = "pk_sparse_sd.csv")
## ----echo=FALSE, fig.align="center", eval=TRUE--------------------------------
rhandsontable(read.csv(system.file("ubinc", "csv", "pk_sparse_sd.csv" , package="ubiquity")), width="100%", height=200)
## ----warning=FALSE, message=FALSE, echo=FALSE, error=FALSE, results="hide", fig.width=8, fig.height=4----
# cfg = system_nca_run(cfg, dsname = "PKDATA",
# dscale = 1e6,
# analysis_name = "pk_sparse",
# sparse = TRUE,
# dsmap = list(TIME = "TIME_HR",
# NTIME = "TIME_HR",
# CONC = "C_ng_ml",
# DOSE = "DOSE",
# ROUTE = "ROUTE",
# ID = "ID",
# SPARSEGROUP = "DOSE"))
#
#
# cfg = system_rpt_read_template(cfg, template="PowerPoint")
## ----warning=FALSE, message=FALSE, eval=FALSE, echo=TRUE, error=FALSE, results="hide", fig.width=8, fig.height=4----
# cfg = system_nca_run(cfg, dsname = "PKDATA",
# dscale = 1e6,
# analysis_name = "pk_sparse",
# sparse = TRUE,
# dsmap = list(TIME = "TIME_HR",
# NTIME = "TIME_HR",
# CONC = "C_ng_ml",
# DOSE = "DOSE",
# ROUTE = "ROUTE",
# ID = "ID",
# SPARSEGROUP = "DOSE"))
# cfg = system_rpt_read_template(cfg, template="PowerPoint")
# cfg = system_rpt_add_slide(cfg,
# template = "title_slide",
# elements = list( title= list(content = "NCA of Sparsely Sampled PK", type = "text")))
# cfg = system_rpt_nca(cfg=cfg, analysis_name="pk_sparse")
# system_rpt_save_report(cfg=cfg, output_file=file.path("output","pk_sparse-report.pptx"))
## ----warning=FALSE, message=FALSE, echo=FALSE, error=FALSE--------------------
# nca_summary = read.csv(file.path("output", "pk_sparse-nca_summary-pknca.csv"))
# presim$sparse$nca_summary = nca_summary
## ----results="hide", warning=FALSE, echo=FALSE, eval=TRUE---------------------
if(presim_loaded){
nca_summary = presim$sparse$nca_summary
}
## ----echo=FALSE, fig.align="center", eval=TRUE--------------------------------
rhandsontable(nca_summary, height=150, width="100%")
## ----warning=FALSE, message=FALSE, echo=FALSE---------------------------------
# save(presim, file="NCA_presim.RData")
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