Nothing
## ----setup, include=FALSE, echo=FALSE-----------------------------------------
knitr::opts_chunk$set(
echo = TRUE,
warning = FALSE,
message = FALSE,
comment = "# >"
)
data.table::setDTthreads(2)
## ----packages-----------------------------------------------------------------
library(envalysis)
library(data.table)
library(ggplot2)
## ---- echo=F------------------------------------------------------------------
knitr::kable(phenolics$seq[c(1:4,73:74,76,78,80,83:84),], "simple",
row.names = F)
## ---- echo=F------------------------------------------------------------------
knitr::kable(phenolics$samples[c(1:2,4,41:42),], "simple",
row.names = F)
## ----data---------------------------------------------------------------------
data("phenolics")
str(phenolics)
## ----simple_calibration, fig.align="center"-----------------------------------
tyrosol_1 <- subset(phenolics$seq, Compound == "Tyrosol" & Batch == 1)
cal_1 <- calibration(Area ~ `Spec Conc`,
data = subset(tyrosol_1, Type == "Standard"))
print(cal_1)
plot(cal_1)
## ----simple_inv_predict-------------------------------------------------------
tyrosol_1$`Calc Conc` <- inv_predict(cal_1, tyrosol_1$Area, below_lod = 0)
head(tyrosol_1)
## ----data.table---------------------------------------------------------------
dt <- lapply(phenolics, as.data.table)
## ----calibration--------------------------------------------------------------
dt$seq[, `Calc Conc` := calibration(Area ~ `Spec Conc`, .SD[Type == "Standard"]) |>
inv_predict(Area, below_lod = 0),
by = .(Compound, Batch)]
head(dt$seq)
## ----parameters---------------------------------------------------------------
dt$cal <- dt$seq[Type == "Standard", calibration(Area ~ `Spec Conc`) |>
as.list(c("coef", "adj.r.squared", "lod", "loq")),
by = .(Compound, Batch)]
print(dt$cal)
## ----blank_subtr--------------------------------------------------------------
dt$seq[, `Clean Conc` := `Calc Conc` - mean(
`Calc Conc`[Type == "Extraction blank"], na.rm = T),
by = .(Batch, Compound)]
## ----merging------------------------------------------------------------------
dt$res <- merge(dt$seq, dt$samples, by = "Name")
dt$res[, Content := `Clean Conc` * (Extract / Weight) * Dilution]
head(dt$res)
## ----plotting, fig.align="center", fig.height=3.5-----------------------------
dt$sum <- dt$res[, .(Content = mean(Content, na.rm = T),
CI = CI(Content, na.rm = T)),
by = .(Compound, Treatment, Day)]
ggplot(dt$sum, aes(x = Day, y = Content)) +
geom_errorbar(aes(ymin = Content - CI, ymax = Content + CI, group = Treatment),
width = 1, position = position_dodge(1)) +
geom_point(aes(shape = Treatment, fill = Treatment),
position = position_dodge(1)) +
xlab("Day of incubation") +
ylab(expression("Phenolic content"~"["*mg~kg^-1*"]")) +
facet_wrap(~ Compound, ncol = 2, scales = "free") +
scale_shape_manual(values = c(21,24)) +
scale_fill_manual(values = c("black", "white")) +
theme_publish()
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