R/pistachio_anthracnose.R

In walmes/RDASC: Reproducible Data Analysis of Cientific Cooperations

#' @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"