Type: Package
Title: An Automated Way to Estimate EC50 for Stratified Datasets
Version: 0.1.0
Date: 2020-09-07
Maintainer: Kaique dos S. Alves <kaiquedsalves@gmail.com>
Description: An implementation for estimating Effective control to 50% of growth inhibition (EC50) for multi isolates and stratified datasets. It implements functions from the drc package in a way that is displayed a tidy data.frame as output. Info about the drc package is available in Ritz C, Baty F, Streibig JC, Gerhard D (2015) <doi:10.1371/journal.pone.0146021>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: dplyr, tidyr, tibble, magrittr, drc
RoxygenNote: 7.0.2
VignetteBuilder: knitr
Suggests: knitr, rmarkdown, ggplot2, ggridges, cowplot
URL: https://github.com/AlvesKS/ec50estimator
BugReports: https://github.com/AlvesKS/ec50estimator/issues
NeedsCompilation: no
Packaged: 2020-09-07 19:08:46 UTC; kai-q
Author: Kaique dos S. Alves ORCID iD [aut, cre]
Repository: CRAN
Date/Publication: 2020-09-15 09:40:06 UTC

Estimate Efective dose (EC50) for multi isolate data set

Description

Estimate Efective dose (EC50) for multi isolate stratified data set.

Usage

estimate_EC50(formula, data, EC_lvl = 50, isolate_col,
strata_col = NULL,
fct,interval = c("none", "delta", "fls", "tfls"))

Arguments

formula

An object of class "formula.(e.g. growth ~ dose")

data

A data.frame in which the dose-response data is in

EC_lvl

Define the EC level. Default is 50

isolate_col

indicate the isolate colunm. Indicate the name inside "". (e.g. "isolates")

strata_col

indicate the strata colunms. If there are more then one colunms, indicate as a vector (e.g. c("region", "field"))

fct

A list with three or more elements specifying the non-linear function. Please, inform the model function with the :: operator to inform the drc package (e.g. drc::LL.4()). For more info, see "drm".

interval

A character string specifying the type of confidence intervals to be supplied. For more information see "ED"

Examples

# Load data
data(multi_isolate)

df_ec50 = estimate_EC50(growth~dose,
                        data =multi_isolate,
                        isolate_col = "isolate",
                        strata_col =  c("field","fungicida"),
                        interval = "delta",
                        fct = drc::LL.3())
head(df_ec50)

Multi isolate dataset

Description

Dataset containing simulated data of mycelial growth under increasing fungicide doses for 50 fungal isolates, two types of field (conventional and organic), and two different fungicides.

Usage

data("multi_isolate")

Format

A data frame with 3500 observations on the following 5 variables.

isolate

a numeric vector

field

a factor with levels Conventional Organic

fungicida

a factor with levels Fungicide A Fungicide B

dose

a numeric vector

growth

a numeric vector

Examples

data(multi_isolate)
## maybe str(multi_isolate) ; plot(multi_isolate) ...