Adiciona do Lichtemberg o sensitivity_ake_b.

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#' @name sensitivity_ake_b
#' @title Effect of fungicide sprays programs and pistachio hedging on
#' sensitivity of \emph{Alternaria alternata} to fluopyram,
#' penthiopyrad and fluxapyroxad in \emph{Pistachio orchard} of
#' Tulare County, California.
#'
#' @description The experiment was established in a commercial pistachio
#' orchard in Tulare County, California. The total area sizes 2.9 ha
#' with density of 335 plants/ha. In total, 12 plots were set with
#' approximately 80 pistachio trees cv. Kerman spaced at 5.8 m
#' between rows and 5.2 m between plants. Each plot included four
#' rows in width (see Figure). In the year 2015, a heavy and
#' normal hedging were intercalated, resulting in 6 plots for each
#' hedging type. No hedging was made in 2016.
#'
#' Within each plot, a fungicide free sub-plot with 20 plants (4
#' rows by 5 plants) was set as a control. Along the plot central
#' rows, four plants (three inside the treated plot and one inside
#' the control sub-plot) were identified for isolate collection,
#' severity and defoliation assessments. In total, 48 plants were
#' identified.
#'
#' The fungicide treatment included three different programs,
#' described below.
#'
#' \describe{
#'
#' \item{treatment 1}{Merivon? (1st application) and Switch? (2nd
#' application).}
#'
#' \item{treatment 2}{FontelisTM (1st application) and Switch? (2nd
#' application).}
#'
#' \item{treatment 3}{Merivon? (1st application), Switch? (2nd
#' application) and Gem? (third application)}
#'
#' }
#'
#' The combination of spray program and hedging type allowed two
#' replication plots per treatment. In order to evaluate the
#' fungicide program effect on \emph{A. alternata} SDHI sensitivity,
#' four isolate populations were collected in two years of
#' experiment.
#'
#' In 2015, the population \strong{A} (\eqn{n = 59}) and \strong{B}
#' (\eqn{n = 59}) were collected in late-May and mid-September
#' respectively. In 2016, the population \strong{C} (\eqn{n = 79})
#' and \strong{D} (\eqn{n = 63}) were collected in early-May and
#' mid-September respectively.
#'
#' This arrangement allowed to sample isolates before (\strong{A}
#' and \strong{C}) and after (\strong{B} and \strong{D}) the spray
#' season. In our study, the sensitivity to SDHI was determined
#' throughout the effective concentration that inhibits mycelial
#' growth by 50\% (EC50, effective concentration). To obtain the
#' sensitivity values, three SDHI fungicides stock solutions were
#' prepared at 10 g a.i. liter-1 each. The fungicides used were:
#' technical grade fluopyram-fp (a.i. 99.13\%, Bayer CropScience)
#' and penthiopyrad-pe (a.i. 99.5\%, DuPont Company) diluted in
#' acetone; and the commercial product of fluxapyroxad-fd (Sercadis
#' 300 SC, BASF, The Chemical Company) diluted in sterile deionized
#' water.
#'
#' To determine an isolate's EC50, stock solution was diluted in
#' autoclaved YBA agar medium at concentrations of 0 (control),
#' 0.01, 0.03, 0.12, 0.48, 1.92, 7.68, 30.72 and 122.88
#' \eqn{\mu}g/ml. For each isolate tested, a 5 mm mycelial plug was
#' transferred from a 7-day-old colony and placed onto the YBA media
#' supplemented with one of the above fungicide
#' concentrations. Intercalate number of repetitions were prepared,
#' where 0 (control), 0.01, 0.12, 1.92, and 30.72 \eqn{\mu}g/ml
#' received two repetitions, and the other doses one.
#'
#' Plates were incubated in dark for seven days at room temperature
#' prior to colony measurement, taken from two perpendicular
#' diameters. For each concentration, the inhibition of colony
#' growth (\eqn{L_i}) of isolate \eqn{i} was calculated as \eqn{L_i
#' = (C_{ck}-C_i)/C_{ck}\times 100}, where \eqn{C_{ck}} is the mean
#' colony diameter of the control with no fungicide, and \eqn{C_i}
#' is the mean colony diameter of the isolate \eqn{i} on the
#' supplemented medium. The EC50 values were analysed by logarithm
#' (\eqn{log_{10}}) transforming the fungicide concentrations and
#' then performing linear regressions of the colony inhibition
#' values (\eqn{L}) by the \eqn{log_{10}} concentrations.
#'
#' @format Um \code{data.frame} 10920 observations of 11 variables
#' described below.
#'
#' \describe{
#'
#' \item{\code{yr}}{A 2-level factor variable to indicate the year of
#' experiment.}
#'
#' \item{\code{pop}}{A 4-level factor variable to indicate the isolate
#' population collected in 2015, "A" and "B", and 2016, "C" and
#' "D". Each population was collected before and after the spray
#' season in field, for this reason they belong to the same location
#' but the individuals inside the each population are unique,
#' meaning that isolate number one, tested for the population "A"
#' will never be tested in a different population.}
#'
#' \item{\code{hed}}{A 2-factor variable to indicate the hedging type on
#' trees. The hedging is the shape the branchs and limbs are
#' pruned. they can be heavy (severe pruning) or normal (regular
#' pruning).}
#'
#' \item{\code{tra}}{A factor variable to indicate the fungicide
#' treatment on field, already described above. the treatment
#' combines the use of one SDHI fungicide (Merivon or Fontelis) and
#' one or two additional chemical group.}
#'
#' \item{\code{plot}}{Not an important variable to consider in the
#' analysis. The plot code simply indicate the location of
#' experimental plots, they represent the treatment and hedging
#' combination in field.}
#'
#' \item{\code{iso}}{A factor variable to differenciate the isolates
#' collected during the preparation of populations "A", "B", "C" and
#' "D". They will never repeat because each isolate is collected
#' only one in the field. So, this is an unique ID for isolates.}
#'
#' \item{\code{fun}}{A factor variable to indicate the SDHI fungicide
#' tested in laboratory. Each isolate collected in field was tested
#' \emph{in vitro} for its sensitivity of fluopyram "FP",
#' fluxapyroxad "FD", and penthiopyrad "PE". The shift in
#' sensitivity for "FP", "PE", and "FD" is the information we aimed
#' to have at the end of this experiment to know, which combination
#' of \code{tra} and \code{hed} affected more or less the
#' sensitivity of \code{fun}.}
#'
#' \item{\code{dos}}{A numeric factor variable to indicate the dose of
#' fungicide prepared inside the petri plate. Each dose was prepared
#' by the dilution of fungicide stock solution on YBA media. The
#' measure unit for fungicide dose is \eqn{\mu}g/ml.}
#'
#' \item{\code{rep}}{A numeric variable to indicate the repetition of
#' fungicide dose used to calculate the EC50 (sensitivity) of each
#' isolate. The repetitions were intercalate, two and one plate per
#' dose. Control received two repetitions as well.}
#'
#' \item{\code{d1}}{A numeric response variable for the first colony
#' diameter measured in mm. However the data on the table need to
#' be divided by 100. Decimals were ignored to facilitate the typing
#' of collected data.}
#'
#' \item{\code{d2}}{A numeric response variable for the second colony
#' diameter measured in mm. However the data on the table need to
#' be divided by 100. Decimals were ignored to facilitate the typing
#' of collected data.}
#'
#' }
#'
#' @source P. S. F. Lichtemberg\eqn{^1}
#' (\url{http://lattes.cnpq.br/8132272273348880});
#' R. D. Puckett\eqn{^1} (\url{http://kare.ucanr.edu/});
#' W. M. Zeviani\eqn{^2} (\url{http://www.leg.ufpr.br/~walmes});
#' C. G. Cunningham\eqn{^1} (\url{http://kare.ucanr.edu/});
#' T. J. Michailides\eqn{^1}
#' (\url{http://ucanr.edu/?facultyid=1535}). University of
#' \eqn{^1}California, Department of Plant Pathology, Kearney
#' agricultural, research and extension center, 9240 S Riverbend
#' Ave, Parlier, California, US. \eqn{^2}Universidade Federal do
#' Paran?, Departamento de Estat?stica,
#'
#' @examples
#'
#' # Load and view data.
#' data(sensitivity_ake_b)
#' str(sensitivity_ake_b)
#'
#' library(lattice)
#'
#' xyplot(d1 ~ d2 | as.factor(dos),
#' groups = tra,
#' data = sensitivity_ake_b,
#' as.table = TRUE,
#' scales = "free")
#'
#' # Unique levels of fungicide dose.
#' x <- sort(unique(sensitivity_ake_b$dos))
#'
#' # Variance of distance between doses.
#' esp <- function(p) {
#' u <- x^p
#' u <- (u - min(u))
#' u <- u/max(u)
#' var(diff(u))
#' }
#'
#' # Optimise de power parameter to the most equally spaced set.
#' op <- optim(par = c(p = 0.5), fn = esp)
#'
#' p <- seq(0, 1, by = 0.01)
#' v <- sapply(p, esp)
#' plot(log(v) ~ p, type = "o")
#' abline(v = op$par)
#'
#' # Sensitivity plot of each isolate.
#' xyplot(d1 ~ dos^0.2 | factor(iso),
#' strip = FALSE,
#' data = sensitivity_ake_b,
#' groups = fun,
#' type = c("p", "a"),
#' as.table = TRUE,
#' scales = list(draw = FALSE))
#'
NULL
This diff is collapsed.
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/sensitivity_ake_b.R
\name{sensitivity_ake_b}
\alias{sensitivity_ake_b}
\title{Effect of fungicide sprays programs and pistachio hedging on
sensitivity of \emph{Alternaria alternata} to fluopyram,
penthiopyrad and fluxapyroxad in \emph{Pistachio orchard} of
Tulare County, California.}
\format{Um \code{data.frame} 10920 observations of 11 variables
described below.
\describe{
\item{\code{yr}}{A 2-level factor variable to indicate the year of
experiment.}
\item{\code{pop}}{A 4-level factor variable to indicate the isolate
population collected in 2015, "A" and "B", and 2016, "C" and
"D". Each population was collected before and after the spray
season in field, for this reason they belong to the same location
but the individuals inside the each population are unique,
meaning that isolate number one, tested for the population "A"
will never be tested in a different population.}
\item{\code{hed}}{A 2-factor variable to indicate the hedging type on
trees. The hedging is the shape the branchs and limbs are
pruned. they can be heavy (severe pruning) or normal (regular
pruning).}
\item{\code{tra}}{A factor variable to indicate the fungicide
treatment on field, already described above. the treatment
combines the use of one SDHI fungicide (Merivon or Fontelis) and
one or two additional chemical group.}
\item{\code{plot}}{Not an important variable to consider in the
analysis. The plot code simply indicate the location of
experimental plots, they represent the treatment and hedging
combination in field.}
\item{\code{iso}}{A factor variable to differenciate the isolates
collected during the preparation of populations "A", "B", "C" and
"D". They will never repeat because each isolate is collected
only one in the field. So, this is an unique ID for isolates.}
\item{\code{fun}}{A factor variable to indicate the SDHI fungicide
tested in laboratory. Each isolate collected in field was tested
\emph{in vitro} for its sensitivity of fluopyram "FP",
fluxapyroxad "FD", and penthiopyrad "PE". The shift in
sensitivity for "FP", "PE", and "FD" is the information we aimed
to have at the end of this experiment to know, which combination
of \code{tra} and \code{hed} affected more or less the
sensitivity of \code{fun}.}
\item{\code{dos}}{A numeric factor variable to indicate the dose of
fungicide prepared inside the petri plate. Each dose was prepared
by the dilution of fungicide stock solution on YBA media. The
measure unit for fungicide dose is \eqn{\mu}g/ml.}
\item{\code{rep}}{A numeric variable to indicate the repetition of
fungicide dose used to calculate the EC50 (sensitivity) of each
isolate. The repetitions were intercalate, two and one plate per
dose. Control received two repetitions as well.}
\item{\code{d1}}{A numeric response variable for the first colony
diameter measured in mm. However the data on the table need to
be divided by 100. Decimals were ignored to facilitate the typing
of collected data.}
\item{\code{d2}}{A numeric response variable for the second colony
diameter measured in mm. However the data on the table need to
be divided by 100. Decimals were ignored to facilitate the typing
of collected data.}
}}
\source{
P. S. F. Lichtemberg\eqn{^1}
(\url{http://lattes.cnpq.br/8132272273348880});
R. D. Puckett\eqn{^1} (\url{http://kare.ucanr.edu/});
W. M. Zeviani\eqn{^2} (\url{http://www.leg.ufpr.br/~walmes});
C. G. Cunningham\eqn{^1} (\url{http://kare.ucanr.edu/});
T. J. Michailides\eqn{^1}
(\url{http://ucanr.edu/?facultyid=1535}). University of
\eqn{^1}California, Department of Plant Pathology, Kearney
agricultural, research and extension center, 9240 S Riverbend
Ave, Parlier, California, US. \eqn{^2}Universidade Federal do
Paran?, Departamento de Estat?stica,
}
\description{
The experiment was established in a commercial pistachio
orchard in Tulare County, California. The total area sizes 2.9 ha
with density of 335 plants/ha. In total, 12 plots were set with
approximately 80 pistachio trees cv. Kerman spaced at 5.8 m
between rows and 5.2 m between plants. Each plot included four
rows in width (see Figure). In the year 2015, a heavy and
normal hedging were intercalated, resulting in 6 plots for each
hedging type. No hedging was made in 2016.
Within each plot, a fungicide free sub-plot with 20 plants (4
rows by 5 plants) was set as a control. Along the plot central
rows, four plants (three inside the treated plot and one inside
the control sub-plot) were identified for isolate collection,
severity and defoliation assessments. In total, 48 plants were
identified.
The fungicide treatment included three different programs,
described below.
\describe{
\item{treatment 1}{Merivon? (1st application) and Switch? (2nd
application).}
\item{treatment 2}{FontelisTM (1st application) and Switch? (2nd
application).}
\item{treatment 3}{Merivon? (1st application), Switch? (2nd
application) and Gem? (third application)}
}
The combination of spray program and hedging type allowed two
replication plots per treatment. In order to evaluate the
fungicide program effect on \emph{A. alternata} SDHI sensitivity,
four isolate populations were collected in two years of
experiment.
In 2015, the population \strong{A} (\eqn{n = 59}) and \strong{B}
(\eqn{n = 59}) were collected in late-May and mid-September
respectively. In 2016, the population \strong{C} (\eqn{n = 79})
and \strong{D} (\eqn{n = 63}) were collected in early-May and
mid-September respectively.
This arrangement allowed to sample isolates before (\strong{A}
and \strong{C}) and after (\strong{B} and \strong{D}) the spray
season. In our study, the sensitivity to SDHI was determined
throughout the effective concentration that inhibits mycelial
growth by 50\% (EC50, effective concentration). To obtain the
sensitivity values, three SDHI fungicides stock solutions were
prepared at 10 g a.i. liter-1 each. The fungicides used were:
technical grade fluopyram-fp (a.i. 99.13\%, Bayer CropScience)
and penthiopyrad-pe (a.i. 99.5\%, DuPont Company) diluted in
acetone; and the commercial product of fluxapyroxad-fd (Sercadis
300 SC, BASF, The Chemical Company) diluted in sterile deionized
water.
To determine an isolate's EC50, stock solution was diluted in
autoclaved YBA agar medium at concentrations of 0 (control),
0.01, 0.03, 0.12, 0.48, 1.92, 7.68, 30.72 and 122.88
\eqn{\mu}g/ml. For each isolate tested, a 5 mm mycelial plug was
transferred from a 7-day-old colony and placed onto the YBA media
supplemented with one of the above fungicide
concentrations. Intercalate number of repetitions were prepared,
where 0 (control), 0.01, 0.12, 1.92, and 30.72 \eqn{\mu}g/ml
received two repetitions, and the other doses one.
Plates were incubated in dark for seven days at room temperature
prior to colony measurement, taken from two perpendicular
diameters. For each concentration, the inhibition of colony
growth (\eqn{L_i}) of isolate \eqn{i} was calculated as \eqn{L_i
= (C_{ck}-C_i)/C_{ck}\times 100}, where \eqn{C_{ck}} is the mean
colony diameter of the control with no fungicide, and \eqn{C_i}
is the mean colony diameter of the isolate \eqn{i} on the
supplemented medium. The EC50 values were analysed by logarithm
(\eqn{log_{10}}) transforming the fungicide concentrations and
then performing linear regressions of the colony inhibition
values (\eqn{L}) by the \eqn{log_{10}} concentrations.
}
\examples{
# Load and view data.
data(sensitivity_ake_b)
str(sensitivity_ake_b)
library(lattice)
xyplot(d1 ~ d2 | as.factor(dos),
groups = tra,
data = sensitivity_ake_b,
as.table = TRUE,
scales = "free")
# Unique levels of fungicide dose.
x <- sort(unique(sensitivity_ake_b$dos))
# Variance of distance between doses.
esp <- function(p) {
u <- x^p
u <- (u - min(u))
u <- u/max(u)
var(diff(u))
}
# Optimise de power parameter to the most equally spaced set.
op <- optim(par = c(p = 0.5), fn = esp)
p <- seq(0, 1, by = 0.01)
v <- sapply(p, esp)
plot(log(v) ~ p, type = "o")
abline(v = op$par)
# Sensitivity plot of each isolate.
xyplot(d1 ~ dos^0.2 | factor(iso),
strip = FALSE,
data = sensitivity_ake_b,
groups = fun,
type = c("p", "a"),
as.table = TRUE,
scales = list(draw = FALSE))
}
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