Nothing
## ----setup_vignette, eval = TRUE----------------------------------------------
knitr::opts_chunk$set(echo = TRUE, fig.width=5, fig.height=4)
## ----install_httk, eval = FALSE-----------------------------------------------
# install.packages("httk")
## ----write_privileges, eval = FALSE-------------------------------------------
# Depending on the account you are using and where you want to install the package on that computer, you may need “permission” from your local file system to install the package. See this help here:
#
# <https://stackoverflow.com/questions/42807247/installing-package-cannot-open-file-permission-denied>
#
# and here:
#
# <https://support.microsoft.com/en-us/topic/general-problem-installing-any-r-package-0bf1f9ba-ead2-6335-46ec-190f6af75e44>
## ----clear_memory, eval = TRUE------------------------------------------------
rm(list=ls())
## ----load_httk, eval = TRUE---------------------------------------------------
library(httk)
# Check what version you are using
packageVersion("httk")
## ----MC_samples, eval = TRUE--------------------------------------------------
NSAMP <- 25
## ----suppress_messages, eval = TRUE-------------------------------------------
css <- calc_analytic_css(chem.name = "Bisphenol A",
suppress.messages = FALSE)
css <- calc_analytic_css(chem.name = "Bisphenol A",
suppress.messages = TRUE)
## ----cheminfo_ex1, eval = TRUE------------------------------------------------
head(get_cheminfo(suppress.messages = TRUE))
## ----cheminfo_ex1a, eval = FALSE----------------------------------------------
# get_cheminfo(suppress.messages = TRUE)
## ----cheminfo_ex2, eval = TRUE------------------------------------------------
head(get_cheminfo(info = "all", median.only=TRUE,suppress.messages = TRUE))
## ----cheminfo_ex3, eval = TRUE------------------------------------------------
"80-05-7" %in% get_cheminfo(suppress.messages = TRUE)
## ----cheminfo_ex4, eval = TRUE------------------------------------------------
subset(get_cheminfo(info = "all",suppress.messages = TRUE),
Compound %in% c("A","B","C"))
## ----oral_equiv_ex, eval = TRUE-----------------------------------------------
calc_mc_oral_equiv(0.1,
chem.cas = "34256-82-1",
species = "human",
samples = NSAMP,
suppress.messages = TRUE)
calc_mc_oral_equiv(0.1,
chem.cas = "99-71-8",
species = "human",
samples = NSAMP,
suppress.messages = TRUE)
## ----tkstats_ex, eval = TRUE--------------------------------------------------
calc_tkstats(chem.cas = "34256-82-1",
species = "rat",
suppress.messages = TRUE)
calc_tkstats(chem.cas = "962-58-3",
species = "rat",
suppress.messages = TRUE)
## ----pbtk_ex, eval = TRUE-----------------------------------------------------
head(solve_pbtk(chem.name = "bisphenol a",
plots = TRUE,
days = 1,
suppress.messages = TRUE))
## ----subset_ex, eval = TRUE---------------------------------------------------
my_data <- subset(get_cheminfo(info = "all",suppress.messages = TRUE),
Compound %in% c("A","B","C"))
## ----writetodisk_ex, eval = TRUE----------------------------------------------
write.csv(my_data, file = "my_data.csv")
## ----fup_stats1, eval = TRUE--------------------------------------------------
library(httk)
fup.tab <- get_cheminfo(info="all",
median.only=TRUE,
model="schmitt",
suppress.messages = TRUE)
## ----fup_stats2, eval = TRUE--------------------------------------------------
median(as.numeric(fup.tab$Human.Funbound.plasma),na.rm=TRUE)
## ----fup_stats3, eval = TRUE--------------------------------------------------
mean(as.numeric(fup.tab$Human.Funbound.plasma),na.rm=TRUE)
## ----fup_stats4, eval = TRUE--------------------------------------------------
sum(!is.na(fup.tab$Human.Funbound.plasma))
## ----help1, eval = FALSE------------------------------------------------------
# help(httk)
## ----help2, eval = FALSE------------------------------------------------------
# help(package = httk)
## ----help3, eval = FALSE------------------------------------------------------
# vignette(package = "httk")
## ----help4, eval = FALSE------------------------------------------------------
# vignette("1_IntroToHTTK")
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