#' @name pistachio_anthracnose
#'
#' @title Characterization of \emph{Colletotrichum karstii} and
#' \emph{Colletotrichum fioriniae} the causal agent of the pistachio
#' anthracnose in California, United States.
#'
#' @description The object \code{pistachio_anthracnose} includes 9
#' tables that represent different experiments performed to
#' characterize the pathogen morphology, physiology and
#' pathogenicity.
#'
#' @format The object \code{pistachio_anthracnose} is a list containing
#' \code{data.frames}. Bellow each \code{data.frame} is documented.
#'
#' The \code{pistachio_anthracnose[["ogrotem"]]} stands for optimal
#' growth temperature. This \code{data.frame} contains 2646
#' observations and 8 variables (columns). In this experiment, 7
#' isolates were cultures onto acidified PDA (APDA) where mycelial
#' growth was daily measured during 7 sucessive days. Mycelial plug
#' of 4 mm was used. Experiment was performed 3 times.
#'
#' \strong{Objectives}: (1) Determine the optimum growth temperature
#' per isolate and compare their differences. (2) Compare the
#' isolate AUMGC for each temperature separately.
#'
#' \describe{
#'
#' \item{\code{exp}}{Integer variable for experiment. This study was
#' performed 3 times.}
#'
#' \item{\code{spp}}{Character variable for species. In total, two
#' species of \emph{Colletotrichum} were used: \emph{Colletotrichum
#' fioriniae} (Cf) and \emph{Colletotrichum karstii} (Ck).}
#'
#' \item{\code{iso}}{Character variable for isolate. In total, seven
#' isolates were used, Ck (n = 1, 3G23) and Cf (n = 6, 11J23, 11K11,
#' 11K17, 12D46, 12J05 and 12J41).}
#'
#' \item{\code{rep}}{Integer variable for repetition. In total, three
#' repetitions or experimental unit (petri plate) were used for each
#' combination of isolate and temperature.}
#'
#' \item{\code{tem}}{Integer variable for temperature. In total, six
#' temperatures were used to evaluate the mycelial growth of each
#' isolate. Temperatures were: 10, 15, 20, 25, 30, 35\eqn{^{o}}C.}
#'
#' \item{\code{day}}{Integer variable for day. In total, daily
#' measurements were made during seven sucessive days.}
#'
#' \item{\code{mm1l}}{Numeric variable for colony diameter 1 (mm). The
#' measurement 1 was taken from one perpendicular colony diameters
#' and recorded in mm. Mycelial plug of 4mm was used as inoculum.}
#'
#' \item{\code{mm2l}}{Numeric variable for colony diameter 2 (mm). The
#' measurement 1 was taken from one perpendicular colony diameters
#' (perpendicular to mm1) and recorded in mm. Mycelial plug of 4mm
#' was used as inoculum.}
#'
#' }
#'
#' The \code{pistachio_anthracnose[["ogertem"]]} stands for optimal
#' germination temperature. This \code{data.frame} contains 756
#' observations and 8 variables (columns). The percentual of
#' germinated conidia of \emph{Colletotrichum karstii} (Ck, n = 1)
#' and \emph{C. fioriniae} (Cf, n = 6) was evaluated after 6 and 12
#' hours from incubation, made at six different temperatures. For
#' each combination of isolate (n = 6) and temperature (n = 6), 50
#' \eqn{\mu}l of conidial suspension at concentration of
#' 10\eqn{^{5}} was transferred into three water agar plates (2\%
#' WA). Six and twelve hours after assay preparation the number of
#' germinated conidia was counted out of 50 conidias. Experiment
#' was performed three times.
#'
#' \strong{Objectives}: (1) Determine the optimum germination
#' temperature after 12 hours per isolate and their statistical
#' differences. (2) Compare the isolate frequency of germination for
#' each evaluation (6 and 12 hours) and temperature separately.
#'
#' \describe{
#'
#' \item{\code{exp}}{As previously described.}
#'
#' \item{\code{spp}}{As previously described.}
#'
#' \item{\code{tim}}{Integer variable for time. Two evaluations were
#' made for the same petri plates, the first after six incubation
#' hours and the second after 12 incubation hours at different
#' temperatures.}
#'
#' \item{\code{iso}}{As previously described.}
#'
#' \item{\code{tem}}{As previously described.}
#'
#' \item{\code{rep}}{As previously described.}
#'
#' \item{\code{gerl}}{Numeric variable germinated conidia. The conidia
#' is considered germinated when its germinative tube is equal or
#' greater than the conidia size. Missing values are reported as
#' \code{NA}.}
#'
#' \item{\code{of}}{Numeric variable for the total number conidia
#' counted. To determine the frequency of germinated conidia, 50
#' individual conidias were counted/accessed.}
#'
#' }
#'
#' The \code{pistachio_anthracnose[["ospotem"]]} stands for optimal
#' sporulation temperature. This \code{data.frame} contains 189
#' observations and 8 variables (columns). Following the mycelial
#' growth assay (ogrotem) isolates cultured at 20, 25 and
#' 30\eqn{^{o}}C had their conidia harvested. Each plate (reps = 3
#' per iso and tem) had 5 or 10 (it depends each case) 5mm mycelial
#' plugs removed from the colony edge. Mycelial plugs were placed
#' inside eppendorf tubes with 1 ml of water and vortexed to release
#' the conidia. Conidia were counted by using an Neubauer
#' Hematocitometer. The experiment was performed three times.
#'
#' \strong{Objectives}: (1) Determine the optimum sporulation
#' temperature per isolate and their statistical differences. (2)
#' Compare the isolate sporulation for each temperature separately.
#'
#' \describe{
#'
#' \item{\code{exp}}{As previously described.}
#'
#' \item{\code{spp}}{As previously described.}
#'
#' \item{\code{tem}}{Integer variable for temperature. In this
#' experiment three temperatures were used: 20, 25, and
#' 30\eqn{^{o}}C.}
#'
#' \item{\code{iso}}{As previously described.}
#'
#' \item{\code{rep}}{As previously described.}
#'
#' \item{\code{spo}}{Numeric variable for sporulation. The value
#' represent the total number of conidia counted.}
#'
#' \item{\code{index}}{Numeric variable used to calculate the conidia
#' concentration according the hematocitometer chambers used. For
#' instance: when I count conidia from the "a" chamber the index
#' used was 1.6x10\eqn{^{5}}. When I count conidia from the "A" the
#' index used was 1x10\eqn{^{4}}. The "A" chamber is located at the
#' four corners of the hematocitometer slide, where one "A" chamber
#' correspond to 16 "a". The "a" = 1/16, then "A" = 0.0625
#' square-mm. When using the "a" to count conidia I have counted 16
#' "a" compartments. When using "A" to count conidia I counted 64
#' "a".}
#'
#' \item{\code{slice}}{Numeric variable for the mycelial plug area. The
#' equation used to determine the plug area was: \eqn{A =
#' \pi r^{2}}, where A = area, \eqn{\pi} = 3.1416, r = plug radius
#' 0.25cm. The plug area was multiplied by the number of plugs used,
#' 10 or 5 plugs.}
#'
#' \item{\code{nsq}}{Numeric variable for the number of squares. The
#' number of squares "a" and "A" counted. The "a" above mentioned
#' corresponde to 16 squares while "A" corresponde to 64 "a".}
#'
#' }
#'
#' The \code{pistachio_anthracnose[["cs"]]} stands for conidia
#' size. This \code{data.frame} contains 370 observations and 6
#' variables (columns). Isolates were cultured in APDA for 7 days.
#' After that, conidia was harvested and taken to a microscopy
#' attached to a camera. Pictures were taken and conidia size lenght
#' (len) by width (wid) were measured for 25 single isolates per
#' isolate:experiment by using the software piximetre v
#' 5.2. Experiment was performed two times.
#'
#' \strong{Objectives}: (1) Compare the lenght, width and volume of
#' different isolates.
#'
#' \describe{
#'
#' \item{\code{exp}}{As previously described.}
#'
#' \item{\code{spp}}{As previously described.}
#'
#' \item{\code{iso}}{As previously described.}
#'
#' \item{\code{len}}{Numeric variable for conidia lenght. longitudinal
#' size of conidia measured in micrometre (\eqn{\mu}m).}
#'
#' \item{\code{wid}}{Numeric variable for conidia width. Transversal
#' size of conidia measured in micrometre (\eqn{\mu}m).}
#'
#' \item{\code{vol}}{Numeric variable for conidia volume. To obtain the
#' conidia volume we used the following formula: Vol =
#' \eqn{\pi}((wid/2)^2)len. The unit would be \eqn{\mu}m\eqn{^{3}}.}
#'
#' }
#'
#' The \code{pistachio_anthracnose[["af"]]} stands for appressorium
#' formation. This \code{data.frame} contains 28 observations and 6
#' variables (columns). Isolates were cultured in APDA for 7
#' days. After that, conidia were harvested and adjusted to
#' 10\eqn{^{5}} conidia/ml. From the conidia suspension 10 ul was
#' transferred to the surface of a microscopy cover slide that was
#' placed inside a Petri plate contaning 2\% WA poured in both plate
#' sides (lid and bottom). Plates were closed and incubated for 24
#' hours at 25 \eqn{^{o}}C prior to count the number of germinated
#' conidia forming the appressorium structure. In total 100
#' germinated conidia were counted. Evaluation was made on
#' microscopy and experiment was performed two times.
#'
#' \strong{Objectives}: (1) Compare the frequency of appressorium
#' formation per isolates.
#'
#' \describe{
#'
#' \item{\code{exp}}{As previously described.}
#'
#' \item{\code{iso}}{As previously described.}
#'
#' \item{\code{spp}}{As previously described.}
#'
#' \item{\code{rep}}{As previously described.}
#'
#' \item{\code{app}}{Numeric variable for appressorium.}
#'
#' \item{\code{tot}}{Numeric variable for total number of conidia
#' counted. For each combination of isolate and repetition 100
#' conidias were counted.}
#'
#' }
#'
#' The \code{pistachio_anthracnose[["tos"]]} stands for time of
#' susceptibility. This \code{data.frame} contains 660 observations
#' and 10 variables (columns). In this study, periodical pistachio
#' cluster inoculations were made every month by using conidial
#' suspensions of 10\eqn{^{5}} for each pathogen species
#' (n = 2). Clusters were covered with plastic and paper bags
#' overnight to allow better infection process and removed in the
#' following morning. Prior to harvest (September) clusters were
#' harvested and each single nut was evaluated for symptoms of
#' anthracnose. The month corresponding to higher blighted nut
#' frequency is the most susceptible period for pathogen
#' infection. The documentation includes data for 2017 and 2018. In
#' September 2019 we will provide the third year results.
#'
#' \strong{Objectives}: (1) Determine the period of higher cultivar
#' susceptibility to \emph{Colletotrichum karstii} and
#' \emph{Colletotrichum fioriniae} infection for each crop year
#' separately.
#'
#' \describe{
#'
#' \item{\code{yr}}{Integer variable for year. The year where this
#' experiment was performed.}
#'
#' \item{\code{mo}}{Integer variable for month. The month correspond to
#' the period of the year that inoculation was made. In 2017, we
#' have three periods of inoculations (June, July and August), while
#' in 2018 we have five periods of inoculation (April, May, June,
#' July and August).}
#'
#' \item{\code{cv}}{Factor variable for cultivar. In 2017 we inoculated
#' Kerman and Red Aleppo cultivars (n = 2) and in 2018 only Red
#' Aleppo was inoculated (n = 1).}
#'
#' \item{\code{spp}}{As previously described.}
#'
#' \item{\code{fla}}{Factor variable for flag. different flag colors
#' were used to identify spp and period of inoculation used. They
#' dont need to be considered on the analises.}
#'
#' \item{\code{arb}}{Integer variable for tree. Every month, three trees
#' were used per combination of cultivar and specie.}
#'
#' \item{\code{clu}}{Integer variable cluster. Each combination of
#' \code{mo:cv:spp:arb} include 10 pistachio clusters that were
#' inoculated. The cluster can be used as a repetition for each
#' tree.}
#'
#' \item{\code{bli}}{Numeric variable blighted nuts. Its the number of
#' nuts that were blighted due to the pathogen infection. Missing
#' values are reported as \code{NA}.}
#'
#' \item{\code{hea}}{numeric variable for healthy nuts. Its the number
#' of nuts that were found to be healthy meaning: no symptoms of
#' anthracnose were observed. Missing values are reported as
#' \code{NA}.}
#'
#' \item{\code{tot}}{numeric variable for total number of nuts counted
#' per cluster. The number may vary from cluster to cluster. Missing
#' values are reported as \code{NA}.}
#'
#' }
#'
#' The \code{pistachio_anthracnose[["pato_vv"]]} stands for
#' pathogenicity performed \emph{in vivo}. This \code{data.frame}
#' contains 360 observations and 10 variables (columns). In 2017 and
#' 2018, inoculations were performed as described for (tos). The
#' following data set include the inoculation made on June for each
#' year on different pistachio cultivars. Data for 2019 will be
#' available in September this year.
#'
#' \strong{Objectives}: (1) Compare the cultivar susceptibility to
#' \emph{Colletotrichum karstii} and \emph{Colletotrichum fioriniae}
#' infection.
#'
#' \describe{
#'
#' \item{\code{yr}}{As previously described.}
#'
#' \item{\code{mo}}{Integer variable for month.}
#'
#' \item{\code{cv}}{Factor variable for cultivar. in 2017 we inoculated
#' Kerman, Golden Hills and Red Aleppo cultivars. In 2018 we
#' inoculated Kerman, Golden Hills and Red Aleppo. In 2019 (data not
#' yet available) we inoculated Kerman, Golden Hills, Lost Hills and
#' Red Aleppo.}
#'
#' \item{\code{spp}}{As previously described.}
#'
#' \item{\code{fla}}{As previously described.}
#'
#' \item{\code{arb}}{As previously described.}
#'
#' \item{\code{clu}}{As previously described.}
#'
#' \item{\code{bli}}{As previously described.}
#'
#' \item{\code{hea}}{As previously described.}
#'
#' \item{\code{tot}}{As previously described.}
#'
#' }
#'
#' The \code{pistachio_anthracnose[["pato_vt"]]} stands for
#' pathogenicity \emph{in vitro}. This \code{data.frame} contains
#' 5760 observations and 10 variables (columns). The study was
#' performed on detached leaves of Kerman and Red Aleppo
#' cultivars. Each cultivar was inoculated with mycelial plugs (4mm)
#' of \emph{Colletotrichum karstii} and \emph{Colletotrichum
#' fioriniae} incubated at 20, 25 and 30 \eqn{^{o}}C. For each
#' combination of temperature, species and cultivar 30 leaves were
#' prepared. Lesion size was measured at 3, 5, 7 and 10 days after
#' inoculation. The study separate kerman from red aleppo, but
#' randomized species within cultivars. The experiment 1 was the
#' only experiment replication that was not randomized, meaning that
#' each crysper (plastic container) held a single cultivar and
#' specie.
#'
#' \strong{Objectives}: (1) Determine the optimum temperature for
#' lesion growth for \emph{Colletotrichum karstii} and
#' \emph{Colletotrichum fioriniae} inoculated on Red Aleppo and
#' Kerman separately. (2) Compare the susceptibility of cultivar to
#' each species separately.
#'
#' \describe{
#'
#' \item{\code{exp}}{As previously described.}
#'
#' \item{\code{tem}}{As previously described.}
#'
#' \item{\code{cv}}{As previously described.}
#'
#' \item{\code{cri}}{Integer variable for crysper. The crysper is the
#' plastic container that holds 10 leaves each.}
#'
#' \item{\code{lea}}{Integer variable for leaf. The leaf is the
#' experimental unit from where lesion size was measured.}
#'
#' \item{\code{spp}}{As previously described.}
#'
#' \item{\code{iso}}{As previously described.}
#'
#' \item{\code{day}}{As previously described.}
#'
#' \item{\code{mm1}}{As previously described. Notice that measurement
#' need to be divided by 100 to obtain the correct size in
#' mm. Missing values are reported as \code{NA}.}
#'
#' \item{\code{mm2}}{As previously described.Notice that measurement
#' need to be divided by 100 to obtain the correct size in
#' mm. Missing values are reported as \code{NA}.}
#'
#' }
#'
#' The \code{pistachio_anthracnose[["spo_vt"]]} stands for
#' sporulation \emph{in vitro}. This \code{data.frame} contains 108
#' observations and 10 variables (columns). Following the
#' pathogenicity study \emph{in vitro} (above described) 10 lesions
#' caused by \emph{Colletotrichum karstii} and \emph{Colletotrichum
#' fioriniae} were detached from the leaves and combined into three
#' new repetitions, according the temperature used. For instance:
#' The 30 Ck lesions obtained at 20\eqn{^{o}}C on Kerman cv
#' originated three reps of 10 lesions combined and placed in
#' different flasks. Water was added to release the spores from the
#' lesions. Sporulation was performed according conventional
#' protocol above described.
#'
#' \strong{Objectives}: (1) Determine the optimum sporulation
#' temperature for \emph{Colletotrichum karstii} and
#' \emph{Colletotrichum fioriniae} on Red Aleppo and Kerman
#' cultivar. (2) Compare sporulation capacity of Ck and Cf at
#' different temperatures and cultivars.
#'
#' \describe{
#'
#' \item{\code{exp}}{As previously described.}
#'
#' \item{\code{spp}}{As previously described.}
#'
#' \item{\code{tem}}{As previously described.}
#'
#' \item{\code{iso}}{As previously described.}
#'
#' \item{\code{rep}}{As previously described.}
#'
#' \item{\code{cv}}{As previously described.}
#'
#' \item{\code{spo}}{As previously described.}
#'
#' \item{\code{index}}{As previously described.}
#'
#' \item{\code{slice}}{As previously described. Sum of lesion size
#' combined (n = 10)}
#'
#' \item{\code{ml}}{Integer variable for water volume used to harvest
#' conidia from leaf lesion.}
#'
#' }
#'
#' @source Paulo S.F. Lichtemberg (\email{plichtemberg@@ucdavis.edu}),
#' Thiago A. Carraro (\email{thiagoacarraro@@gmail.com}), Walmes
#' M. Zeviani (\email{walmes@@ufpr.br}), Themis J. Michailides
#' (\email{tjmichailides@@ucanr.edu}).
#'
#' @examples
#'
#' data(pistachio_anthracnose, package = "RDASC")
#' str(pistachio_anthracnose)
#'
"pistachio_anthracnose"
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