#'---
#'output:
#' pdf_document:
#' keep_tex: yes
#' latex_engine: xelatex
#'params:
#' set_title: "My Title!"
#' set_date: "My Date!"
#' data_file: "test"
#' max.conc: "test"
#' species: "test"
#' negative_control_col: "test"
#' positive_control_col: "test"
#' highest_conc_col: "test"
#' lowest_conc_col: "test"
#' number_of_lines: "test"
#' startRow: "test"
#' endRow: "test"
#'title: "`r params$set_title`"
#'date: "`r params$set_date` "
#'author: no
#'---
#+ echo=F,warning=F,results='hide',error=F,message=FALSE
library("knitr")
library("stargazerCustom")
library("wellexplainer")
data <- extract_MIC_OD_data(
params$data_file,
params$max.conc,
params$startRow,
params$endRow
)
inhib <- calculate_MIC_OD_inhib(data,
params$negative_control_col,
params$positive_control_col,
params$highest_conc_col,
params$lowest_conc_col,
params$number_of_lines,
species=params$species)
plots <- plot_MIC_OD(data)
summary <- summary_MIC_inhib(inhib,
number_of_lines = params$number_of_lines,
species = params$species)
results_by_strain <- summary[[2]]
#+ Strain by strain results, echo = F, results='asis'
for (i in 1:length(results_by_strain))
{
stargazer(
results_by_strain[[i]],
header = F,
summary = F,
digit.separator = " ",
digits=2,
no.space = TRUE,
notes = c("Concentrations en µg/mL"),
rownames = F,
title = paste0("Résultats ", names(results_by_strain)[i])
)
}
#+ Plots, echo = F, results='asis'
for (j in 1:length(plots))
{
print(plots[[j]])
}
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