lateblight {agricolae}R Documentation

LATEBLIGHT - Simulator for potato late blight Version LB2004

Description

LATEBLIGHT is a mathematical model that simulates the effect of weather, host growth and resistance, and fungicide use on asexual development and growth of Phytophthora infestans on potato foliage.

Usage

lateblight(WS, Cultivar, ApplSys,InocDate, LGR, IniSpor, SR, IE, LP, InMicCol,
MatTime=c('EARLYSEASON','MIDSEASON','LATESEASON'),...)

Arguments

WS

object weather-severity

Cultivar

chr

ApplSys

chr

InocDate

days

LGR

num, see example

IniSpor

num

SR

num, see example

IE

num, Initialization infection

LP

num, latent period

InMicCol

num

MatTime

chr

...

plot graphics parameters

Details

LATEBLIGHT Version LB2004 was created in October 2004 (Andrade-Piedra et al., 2005a, b and c), based on the C-version written by B.E. Ticknor ('BET 21191 modification of cbm8d29.c'), reported by Doster et al. (1990) and described in detail by Fry et al. (1991) (This version is referred as LB1990 by Andrade-Piedra et al. [2005a]). The first version of LATEBLIGHT was developed by Bruhn and Fry (1981) and described in detail by Bruhn et al. (1980).

Value

Ofile

"Date","nday","MicCol","SimSeverity",...

Gfile

"dates","nday","MeanSeverity","StDevSeverity"

Note

All format data for date is yyyy-mm,dd, for example "2000-04-22". change with function as.Date()

Author(s)

Jorge L. Andrade-Piedra (1) (j.andrade@cgar.org), Gregory A. Forbes (1) (g.forbes@cgiar.org), Robert J. Hijmans (2) (rhijmans@ucdavis.edu), William E. Fry (3) (wef1@cornell.edu) Translation from C language into SAS language: G.A. Forbes Modifications: J.L. Andrade-Piedra and R.J. Hijmans Translation from SAS into R: Felipe de Mendiburu (1) (1) International Potato Center, P.O. Box 1558, Lima 12, Peru (2) University of California, One Shields Avenue, Davis, California 95616, USA (3) Cornell University, 351 Plant Science, Ithaca, NY 14853, USA

References

Andrade-Piedra, J. L., Hijmans, R. J., Forbes, G. A., Fry, W. E., and Nelson, R. J. 2005a. Simulation of potato late blight in the Andes. I: Modification and parameterization of the LATEBLIGHT model. Phytopathology 95:1191-1199.
Andrade-Piedra, J. L., Hijmans, R. J., Juarez, H. S., Forbes, G. A., Shtienberg, D., and Fry, W. E. 2005b. Simulation of potato late blight in the Andes. II: Validation of the LATEBLIGHT model. Phytopathology 95:1200-1208.
Andrade-Piedra, J. L., Forbes, G. A., Shtienberg, D., Grunwald, N. J., Chacon, M. G., Taipe, M. V., Hijmans, R. J., and Fry, W. E. 2005c. Qualification of a plant disease simulation model: Performance of the LATEBLIGHT model across a broad range of environments. Phytopathology 95:1412-1422.
Bruhn, J.A., Bruck, R.I., Fry, W.E., Arneson, P.A., and Keokosky, E.V. 1980. User's manual for LATEBLIGHT: a plant disease management game. Cornell University, Department of Plant Pathology, Ithaca, NY, USA. Mimeo 80-1.
Bruhn, J.A., and Fry, W.E. 1981. Analysis of potato late blight epidemiology by simulation modeling. Phytopathology 71:612-616.
Doster, M. A., Milgroom, M. G., and Fry, W. E. 1990. Quantification of factors influencing potato late blight suppression and selection for metalaxyl resistance in Phytophthora infestans - A simulation approach. Phytopathology 80:1190-1198.
Fry, W.E., Milgroom, M.G., Doster, M.A., Bruhn, J.A., and Bruck, R.I. 1991. LATEBLIGHT: a plant disease management game - User Manual. Version 3.1. Microsoft Windows Adaptation by B. E. Ticknor, and P. A. Arneson. Ithaca, Cornell University, Department of Plant Pathology, Ithaca, NY, USA.

See Also

weatherSeverity

Examples

library(agricolae)
f <- system.file("external/weather.csv", package="agricolae")
weather <- read.csv(f,header=FALSE)
f <- system.file("external/severity.csv", package="agricolae")
severity <- read.csv(f)
weather[,1]<-as.Date(weather[,1],format = "%m/%d/%Y")
# Parameters dates
dates<-c("2000-03-25","2000-04-09","2000-04-12","2000-04-16","2000-04-22")
dates<-as.Date(dates)
EmergDate <- as.Date('2000/01/19')
EndEpidDate <- as.Date("2000-04-22")
dates<-as.Date(dates)
NoReadingsH<- 1
RHthreshold <- 90
WS<-weatherSeverity(weather,severity,dates,EmergDate,EndEpidDate,
NoReadingsH,RHthreshold)
# Parameters Lateblight
InocDate<-"2000-03-18"
LGR <- 0.00410
IniSpor <- 0
SR <- 292000000
IE <- 1.0
LP <- 2.82
InMicCol <- 9
Cultivar <- 'NICOLA'
ApplSys <- "NOFUNGICIDE"
main<-"Cultivar: NICOLA"
#--------------------------
model<-lateblight(WS, Cultivar,ApplSys, InocDate, LGR,IniSpor,SR,IE, LP,
MatTime='LATESEASON',InMicCol,main=main,type="l",xlim=c(65,95),lwd=1.5,
xlab="Time (days after emergence)", ylab="Severity (Percentage)")
# reproduce graph
x<- model$Ofile$nday
y<- model$Ofile$SimSeverity
w<- model$Gfile$nday
z<- model$Gfile$MeanSeverity
Min<-model$Gfile$MinObs
Max<-model$Gfile$MaxObs
plot(x,y,type="l",xlim=c(65,95),lwd=1.5,xlab="Time (days after emergence)",
ylab="Severity (Percentage)")
points(w,z,col="blue",cex=1,pch=19)
npoints <- length(w)
for ( i in 1:npoints){
segments(w[i],Min[i],w[i],Max[i],lwd=1.5,col="blue")
}
legend("topleft",c("Disease progress curves","Weather-Severity"),
title="Description",lty=1,pch=c(3,19),col=c("black","blue"))


[Package agricolae version 1.3-5 Index]