Merge pull request #27 from PaulMelloy/dev

update main branch to prerelease version 0.0.0.9003

.Rbuildignore

@@ -9,3 +9,5 @@
 ^pkgdown$
 ^\.github$
 .Rprofile
+^cran-comments\.md$
+codemeta.json

.gitignore

@@ -4,5 +4,4 @@
 .httr-oauth
 .DS_Store
 inst/doc
-docs
 .Rprofile

DESCRIPTION

@@ -1,16 +1,16 @@
 Package: cercospoRa
-Title: Mechanistic Epidemiological Model for Cercospora Leaf Spot of Sugar Beet
-Version: 0.0.0.9002
+Title: Process based Epidemiological Model for Cercospora Leaf Spot of Sugar Beet
+Version: 0.0.0.9003
 Authors@R: c(
     person(given = "Paul",
            family = "Melloy",
-           role = c("aut", "cre", "trl"),
+           role = c("aut", "cre", "trl","cph"),
            email = "[email protected]",
            comment = c(ORCID = "0000-0003-4253-7167",
                        "Translated equations from literature and developed package.")),
     person(given = "Rene",
            family = "Heim",
-           role = c("aut"),
+           role = c("aut", "cph"),
            email = "[email protected]",
            comment = c(ORCID = "0000-0002-0666-2588",
                        "Code review and development of leaf area index model")),
@@ -30,10 +30,10 @@ Authors@R: c(
            family = "Mahlein",
            role = c("ctb"),
            comment = c(ORCID = "0000-0003-1091-3690")))
-Description: This package provides functions to recreate the negative prognosis 
-    epidemiological model for describing when the model can't be certain a 
-    chance Cercospora leaf spot (_Cercospora beticola_) epidemic has not 
-    commenced. The model is based on the work of Wolf and Verreet 
+Description: This package provides functions to estimate sugar beet canopy 
+    closure with remotely sensed LAI and estimate when action might be needed to
+    protect the crop from a Cercospora leaf spot (_Cercospora beticola_) epidemic
+    with a negative prognosis model based on the work of Wolf and Verreet 
     (2005 <https://apsjournals.apsnet.org/doi/abs/10.1094/PHYTO-95-0269>).
 License: MIT + file LICENSE
 Encoding: UTF-8
@@ -59,8 +59,7 @@ VignetteBuilder: knitr
 Remotes: 
     PaulMelloy/epiphytoolR
 Depends: 
-    R (>= 2.10)
+    R (>= 4.0.0)
 LazyData: true
 URL: https://paulmelloy.github.io/cercospoRa/
 BugReports: https://github.com/PaulMelloy/cercospoRa/issues
-

LICENSE

@@ -1,2 +1,2 @@
-YEAR: 2023
+YEAR: 2024
 COPYRIGHT HOLDER: cercospoRa authors

NAMESPACE

@@ -9,4 +9,3 @@ export(read_sb_growth_parameter)
 import(data.table)
 importFrom(Rdpack,reprompt)
 importFrom(data.table,":=")
-importFrom(terra,plot)

NEWS.md

@@ -1,4 +1,6 @@
-# cercospoRa (development version)
+# cercospoRa (development version)  
+
+# cercospoRa 0.0.0.9003
 ## New Features and minor improvements
   - Four functions have been added to deal with spatial heterogeneity:
     - `read_sb_growth_parameter`: read in and format raster images to allow 
@@ -10,11 +12,16 @@
   - Example datasets have been provided to check the functions. 
   It consists of a folder containing two LAI maps computed from UAV images.  
 
+## Features removed  
+  - Removed methods from Racca paper and set them to a new branch 
+  [plus_racca](https://github.com/PaulMelloy/cercospoRa/tree/plus_racca)
+
 ## Documentation fixes  
   - add metadata  
   - Further simplification of `main` and `dev` branches to only the Wolf and 
   Verreet functions.  
-  - add badge
+  - add badge  
+  - spelling and grammar fixes
 
 
 # cercospoRa 0.0.0.9001

R/calc_DIV.R

@@ -1,19 +1,19 @@
 #' Calculate daily infection values
 #'
-#' This function calculates the daily infection values for *Cercospora berticola*
+#' This function calculates the daily infection values for *Cercospora beticola*
 #'  on sugar beet. Functions were adapted from \insertCite{wolf_factors_2005}{cercospoRa}
 #'  and \insertCite{wolf_zum_2001}{cercospoRa}
 #'
 #' @param date_time POSIX_ct, date time the weather recording was taken
-#' @param Tm numeric, temperature, in celcius' at time increment in `date_time`
+#' @param Tm numeric, temperature, in Celsius' at time increment in `date_time`
 #' @param RH numeric, relative humidity (%) at time increment in `date_time`
-#' @param rain numeric, volume of rain in millimeters recorded between time recordings
+#' @param rain numeric, volume of rain in millimetres recorded between time recordings
 #' @param dat data.frame, containing column names "times","temp","rh","rain" with
 #'  each of the respective arguments for input. provided as a convenience
 #'
 #' @return data.table, with probability of infection for each day, between 0 and 1
 #'  Undertaken with two methods by Wolf \insertCite{wolf_factors_2005}{cercospoRa}
-#'  under the `DIV` column and method by Racca et. al \insertCite{racca_cercbet_2007}{cercospoRa}
+#'  under the `DIV` column and method by Racca et al. \insertCite{racca_cercbet_2007}{cercospoRa}
 #'  described in the `DIV_racca` column.
 #' @export
 #' @references \insertAllCited{}
@@ -68,8 +68,8 @@ calc_DIV <- function(date_time, Tm,RH, rain,dat){
           "moist_ind") := list(temperature_index(temp),
                               moisture_index(rh,rain,70))]
 
-  DIV <- dat[, list(DIV = mean(fifelse(test = Tm_index == 0 | moist_ind == 0,
-                                  yes = 0, no = (Tm_index * moist_ind)))),
+  DIV <- dat[, list(DIV = round(mean(fifelse(test = Tm_index == 0 | moist_ind == 0,
+                                  yes = 0, no = Tm_index * moist_ind)),digits = 7)),
              by = c("Year", "Month", "Day")]
 
   return(DIV)

R/calc_c_closure.R

@@ -1,4 +1,8 @@
-#' Calculate growth rate(r) and LAI0 at time t0
+#' Calculate canopy closure date
+#'
+#' @details
+#'  Calculates canopy closure dates from LAI and growth rate parameters
+#'
 #'
 #' @param param_rxt Output of the function \link{calc_r_x0}, which produces a
 #'  list containing parameters that are necessary to calculate `c_closure`.
@@ -12,8 +16,6 @@
 #' @return `c_closure` date at which 90% canopy closure is reached at each location.
 #'
 #' @export
-#'
-#'
 #' @examples
 #' img_dir <- system.file("extdata", "uav_img",package = "cercospoRa")
 #' epidemic_onset_param <-

R/calc_epidemic_onset.R

@@ -1,21 +1,21 @@
 #' Calculate epidemic onset
 #'
-#' @param start posixct, start date in which to begin calculating the epidemic
+#' @param start POSIXct, start date in which to begin calculating the epidemic
 #'  onset, if not specified, the first date in the weather data will be used.
-#' @param end posixct, end date, last date to complete calculating the epidemic
+#' @param end POSIXct, end date, last date to complete calculating the epidemic
 #'  onset, if not specified, the last date in the weather data will be used.
 #' @param c_closure POSIXct formatted date to start the model running the model
 #'  This is usually at canopy closure (Wolf)
 #' @param weather data.table, formatted with `epiphytoolR::format_weather`
 #' @param cultivar_sus character, susceptibility of the cultivar in "R" resistant,
 #'  "S" susceptible, "MR" moderately resistant ect.
 #'
-#' @return `$wolf_date:` If the input weather is conducive for epidemic, the function returns a
-#'  POSIX_ct date when epidemic commences. If no epidemic occurs, a numeric,
-#'  proportion indicating the progress an epidemic is returned
-#'  `racca_percent:` If the input weather is conducive for epidemic, the function returns a
-#'  POSIX_ct date when epidemic commences. If no epidemic occurs, a numeric,
-#'  proportion indicating the progress an epidemic is returned
+#' @return `$wolf_date:` If the input weather is conducive for epidemic, the
+#'  function returns a POSIX_ct date when epidemic commences. If no epidemic
+#'  occurs, a numeric, proportion indicating the progress an epidemic is returned
+#'  `racca_percent:` If the input weather is conducive for epidemic, the function
+#'  returns a POSIX_ct date when epidemic commences. If no epidemic occurs, a
+#'  numeric, proportion indicating the progress an epidemic is returned
 #' @export
 #'
 #' @examples

R/calc_epidemic_onset_from_image.R

@@ -1,15 +1,14 @@
 #' Calculate epidemic onset from image
 #'
-#' @param start posixct, start date in which to begin calculating the epidemic
+#' @param start POSIXct, start date in which to begin calculating the epidemic
 #'  onset, if not specified, the first date in the weather data will be used.
-#' @param end posixct, end date, last date to complete calculating the epidemic
+#' @param end POSIXct, end date, last date to complete calculating the epidemic
 #'  onset, if not specified, the last date in the weather data will be used.
 #' @param c_closure map of canopy closure dates formatted as number of days since
 #' 1970-01-01. It defines the date to start running the model (Wolf)
 #' @param weather data.table, formatted with `epiphytoolR::format_weather`
 #' @param cultivar_sus character, susceptibility of the cultivar in "R" resistant,
 #'  "S" susceptible, "MR" moderately resistant ect.
-#' @importFrom terra plot
 #' @return `$wolf_date:` If the input weather is conducive for epidemic, the function returns a
 #'  POSIX_ct date when epidemic commences. If no epidemic occurs, a numeric,
 #'  proportion indicating the progress an epidemic is returned

R/calc_r_x0.R

@@ -1,18 +1,24 @@
-#' Calculate growth rate(r) and LAI0 at time t0
+#' Calculate growth rate and LAI at t0
 #'
-#' @param param_r Output of the function \link[cercospoRa]{read_sb_growth_parameter}, which
-#'  produces a list containing the LAI images and the associated dates
+#' @details
+#' Fits a non-linear model to remotely sensed LAI values and estimates the leaf
+#' area index (LAI) and growth rate _r_ at the start of the time window _t0_.
+#'
+#'
+#' @param param_r Output of the function \link[cercospoRa]{read_sb_growth_parameter},
+#'  which produces a list containing the LAI images and the associated dates
 #' @param min_r minimum growth rate for sugar beet. Default `min_r` is fixed to
-#'  0.02 to ensure that the growth rate at the inflexion point of the sigmiod is
+#'  0.02 to ensure that the growth rate at the inflexion point of the sigmoid is
 #'  at least 1 unit of LAI per month.
-#' @param max_r manimum growth rate for sugar beet. Default `max_r` is fixed to
+#' @param max_r maximum growth rate for sugar beet. Default `max_r` is fixed to
 #'  0.05 to ensure that the growth rate at the inflexion point of the sigmoid is
 #'  at most 2.5 units of LAI per month.
-#' @param k carrying capaciy, which is the maximum LAI that can be attained.
+#' @param k carrying capacity, which is the maximum LAI that can be attained.
 #'  This value can be cultivar-dependent. The default is fixed to 6
 #'
-#' @return `param_rxt:` list containing parameters that are necessary to calculate `c_closure`. These parameters are `r`, the
-#' growth rate, `x0`, the initial LAI value, and `t0`, the initial date.
+#' @return `param_rxt:` list containing parameters that are necessary to calculate
+#' `c_closure`. These parameters are `r`, the growth rate, `x0`, the initial LAI
+#'  value, and `t0`, the initial date.
 #'
 #' @export
 #'
@@ -55,7 +61,7 @@ calc_r_x0 <- function(param_r,
 #' Fit non-linear model to raster layers
 #'
 #' @param xyi Spatrast stack
-#' @param k carrying capaciy, which is the maximum LAI that can be attained.
+#' @param k carrying capacity, which is the maximum LAI that can be attained.
 #'  This value can be cultivar-dependent. The default is fixed to 6
 #' @param tm numeric, form of dates from each raster layer in `xyi`
 #' @param t0 numeric, form of date from first raster layer in `xyi`

R/latent_period.R

@@ -12,6 +12,7 @@
 #' @return numeric, Latent period for a given hour. `ref = "jarroudi"` returns
 #'  latent period in days.
 #' @references \insertRef{wolf_factors_2005}{cercospoRa}; equation 4
+#'
 #'  \insertRef{el_jarroudi_weather-based_2021}{cercospoRa}; equation 1
 latent_period <- function(Tm, ref = "wolf"){
   if(ref == "wolf"){

README.md

@@ -5,8 +5,18 @@
 <!-- badges: end -->
 <br>
 
-`cercospoRa` is a mechanistic epidemiological model for estimating epidemics of 
-_Cercospora beticola_ in sugar beet farms, available as an R package.  
+This R package, `cercospoRa`, takes steps to automate the epidemiological 
+modelling of Cercospora leaf spot epidemics in _Cercospora beticola_ in sugar 
+beet farms, available as an R package.
+The package contains functions to use remotely sensed spatially explicit empirical
+data to estimate leaf area index (LAI) when the crop canopy closes. 
+Crop canopy closure is a key variable in modelling the estimating when growers 
+will need to be vigilant and protect their crop with fungicides to prevent a 
+yield limiting cercospora leaf spot epidemic.  
+
+`cercospoRa` uses functions described by Wolf and Verreet (2005) "Factors 
+Affecting the Onset of Cercospora Leaf Spot Epidemics in Sugar Beet and 
+Establishment of Disease-Monitoring Thresholds" _Phytopathology_  
 
 <br>  
 
@@ -28,14 +38,15 @@ remotes::install_github(repo = "PaulMelloy/cercospoRa")
 ## Getting started  
 ### Format weather data  
 ```r
+library(data.table)
 library(epiphytoolR)
 library(cercospoRa)
 
 # Inspect raw weather station data
 head(cercospoRa::weathr)
 ```
 
-`weathr` is a data.table containing weather data recorded at a sugar beet field 
+`weathr` is a `data.table` containing weather data recorded at a sugar beet field 
 trial observing the spread and severity of *C. beticola*.
 
 ```r
@@ -97,8 +108,8 @@ calc_epidemic_onset(c_closure = as.POSIXct("2022-07-01"),
                     cultivar_sus = 5)                    
 
 ```
-This returns a `POSIXct` date for the onset of an epidemic for the susceptible and
-more resistant cultivar.
+This returns a `POSIXct` date for the onset of an epidemic for the susceptible 
+and more resistant cultivar.
 If the input weather data does not provide a window where a epidemic onset date 
 is met, the proportional progress towards an epidemic is returned.
 
@@ -116,22 +127,25 @@ This produces a `data.table` detailing the daily infection value for each day us
 the method described in Wolf and Verreet (2005). 
 
 **Note:** Missing humidity values do not prevent the model from running and these
-days are assumed to not progress the model. The Racca and Jörg model returns `NA` values 
-and the Wolf model returns `0` as seen in the `calc_DIV(dat = bris_formated)` function 
-output.  
+days are assumed to not progress the model. The Racca and Jörg model returns `NA` 
+values and the Wolf model returns `0`.  
 
 <br>  
 
 ## Notes for contributors  
 The `main` branch is the production branch and only provides functions to recreate
 the model described in Wolf and Verreet (2005) as explained in the paper. 
-The `main` branch is locked, please contribute to the `dev` branch.
-The `dev` (development) branch also includes functions to recreate other *C. beticola*
-mechanistic models published by Racca and Jörg (2007) and auxiliary functions which
-might be helpful for future versions.  
+The `main` branch is locked, please contribute to the `dev` branch.  
+The `plus_racca` (development) branch also includes functions to recreate other 
+*C. beticola* mechanistic models published by Racca and Jörg (2007) and auxiliary 
+functions which might be helpful for future versions.  
 
 <br>  
 
 ## References  
-Wolf, P. F., & Verreet, J. A. (2005). Factors Affecting the Onset of Cercospora Leaf Spot Epidemics in Sugar Beet and Establishment of Disease-Monitoring Thresholds. *Phytopathology*, 95(3), 269-274.  
-Racca, P., and Jörg, E. (2007). CERCBET 3 – a forecaster for epidemic development of *Cercospora beticola*. *EPPO Bulletin*, 37(2), 344-349.  
+Wolf, P. F., & Verreet, J. A. (2005). Factors Affecting the Onset of Cercospora 
+Leaf Spot Epidemics in Sugar Beet and Establishment of Disease-Monitoring 
+Thresholds. *Phytopathology*, 95(3), 269-274.  
+
+Racca, P., and Jörg, E. (2007). CERCBET 3 – a forecaster for epidemic development 
+of *Cercospora beticola*. *EPPO Bulletin*, 37(2), 344-349.  

codemeta.json

@@ -1,7 +1,7 @@
 {
   "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
   "@type": "SoftwareSourceCode",
-  "@id": "https://github.com/PaulMelloy/cercospoRa",
+  "@id": "https://paulmelloy.github.io/cercospoRa/",
   "identifier": "cercospoRa",
   "description": "This package provides functions to recreate the negative prognosis epidemiological model for describing when the model can't be certain a chance Cercospora leaf spot (_Cercospora beticola_) epidemic has not commenced. The model is based on the work of Wolf and Verreet (2005 <https://apsjournals.apsnet.org/doi/abs/10.1094/PHYTO-95-0269>).",
   "name": "cercospoRa: Mechanistic Epidemiological Model for Cercospora Leaf Spot of Sugar Beet",
@@ -219,7 +219,9 @@
     },
     "SystemRequirements": null
   },
-  "fileSize": "2515.082KB",
+  "fileSize": "2515.167KB",
   "relatedLink": "https://paulmelloy.github.io/cercospoRa/",
-  "releaseNotes": "https://github.com/PaulMelloy/cercospoRa/blob/master/NEWS.md"
+  "releaseNotes": "https://github.com/PaulMelloy/cercospoRa/blob/master/NEWS.md",
+  "readme": "https://github.com/PaulMelloy/cercospoRa/blob/main/README.md",
+  "developmentStatus": "https://www.repostatus.org/#active"
 }

cran-comments.md

@@ -0,0 +1,5 @@
+## R CMD check results
+
+0 errors | 0 warnings | 1 note
+
+* This is a new release.