Calculate daily infection values — calc

This function calculates the daily infection values for Cercospora berticola on sugar beet. Functions were adapted from (Wolf and Verreet 2005) and (Wolf et al. 2001)

Usage

calc_DIV(date_time, Tm, RH, rain, dat)

Arguments

date_time: POSIX_ct, date time the weather recording was taken
Tm: numeric, temperature, in celcius' at time increment in date_time
RH: numeric, relative humidity (%) at time increment in date_time
rain: numeric, volume of rain in millimeters recorded between time recordings
dat: data.frame, containing column names "times","temp","rh","rain" with each of the respective arguments for input. provided as a convenience

Value

data.table, with probability of infection for each day, between 0 and 1 Undertaken with two methods by Wolf (Wolf and Verreet 2005)

under the DIV column and method by Racca et. al (Racca and Jörg 2007)

described in the DIV_racca column.

References

Racca P, Jörg E (2007). “CERCBET 3 – a forecaster for epidemic development of Cercospora beticola*.” EPPO Bulletin, 37(2), 344--349. ISSN 1365-2338, doi:10.1111/j.1365-2338.2007.01136.x , _ eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-2338.2007.01136.x, https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-2338.2007.01136.x.

Wolf PFJ, Heindl M, Verreet JA (2001). “Zum Einfluss des Bestandesklimas auf die Prädisposition der Zuckerrübe gegenüber Infektionen von Cercospora beticola (Sacc.) / Influence of sugar beet leaf mass development on predisposition of the crop to Cercospora beticola (Sacc.).” Zeitschrift für Pflanzenkrankheiten und Pflanzenschutz / Journal of Plant Diseases and Protection, 108(6), 578--592. ISSN 0340-8159, Publisher: Verlag Eugen Ulmer KG, https://www.jstor.org/stable/43215404.

Wolf PFJ, Verreet JA (2005). “Factors Affecting the Onset of Cercospora Leaf Spot Epidemics in Sugar Beet and Establishment of Disease-Monitoring Thresholds.” Phytopathology®, 95(3), 269--274. ISSN 0031-949X, doi:10.1094/PHYTO-95-0269 , Publisher: Scientific Societies, https://apsjournals.apsnet.org/doi/abs/10.1094/PHYTO-95-0269.

Examples

date_t <- Sys.time() + seq(0, 179 * 60 * 10, (60 * 10))
Tm <- rnorm(180,20,10)
RH <- runif(180,min = 40,90)
rain <- rbinom(180,1,0.1) * runif(180,0.1,20)

DIV1 <- calc_DIV(
date_time = date_t,
Tm = Tm,
RH = RH,
rain = rain
)