Updating to 1.3.0

See News.md for changes.

.Rbuildignore

@@ -9,3 +9,5 @@ man/figures
 ^docs$
 vignettes
 pkgdown
+references.bib
+environmental-modelling-and-software.csl

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: DynACof
 Type: Package
-Title: Dynamic Crop Model to Simulate Coffee Crop Ecophysiology for Monospecific Stands or Agroforestry
-Version: 1.2.0
-Date: 2019-03-14
+Title: A Process-based Model to Study Growth, Yield and Ecosystem Services of Coffee Agroforestry Systems
+Version: 1.3.0
+Date: 2020-02-01
 Authors@R: c(person("Remi", "Vezy",, "[email protected]", c("aut", "cre", "cph"),comment = c(ORCID = "0000-0002-0808-1461")),
     person("Olivier", "Roupsard",, "[email protected]", c("aut", "cph")),
     person("Guerric", "le Maire", role = c("aut", "cph")))
@@ -33,7 +33,7 @@ Imports:
     solartime,
     JuliaCall,
     rstudioapi
-RoxygenNote: 6.1.1
+RoxygenNote: 7.0.0
 Roxygen: list(markdown = TRUE)
 Suggests: 
     knitr,

NEWS.md

@@ -1,3 +1,35 @@
+# DynACof 1.2.1
+
+* Tsoil used for Rm roots now  
+* Remove `MaxTT` from `GDD`  
+* Replace `Tleaf_Coffee` by `TairCanopy` in `DegreeDays_Tcan` and `T_VG` (for `ratioNodestoLAI`) as it should be (see documentation)  
+* Put `CM_Fruit_Cohort_remain` to 0 when harvested  
+* Add option for no harvest at all  
+* `E_Soil` take in priority in surface layer, and then possibly in `W_1`  
+* `LeafWaterPotential` is now fully computed  
+* Rename `LeafWaterPotential` into `PSIL`  
+* Add `PSIL_Tree` computation   
+* Update default metamodels and parameters (revision of article)  
+* Remove `LAI_max` dependence for leaf C demand computation  
+* [DynACof.jl](https://github.com/VEZY/DynACof.jl) related:  
+  * Update dynacof.jl_setup for dev versions  
+  * Update `dynacof.jl_setup` doc + website  
+  * Add Pkg.free when R terminates  
+  * Update the code following modifs in julia version (from 69cd69ba69d210e0479b8749deebc9585b58c1c0 to 7239c93bc2c50eb761de330cf4c43429fe18b4ef)  
+* Runs shade tree model only if `Stocking_Tree > 0.0` and remove overcomplicated shade tree models (keep only one now), following [DynACof.jl](https://github.com/VEZY/DynACof.jl)  
+* Update docs to Roxygen 7.0.0.  
+* Add startup message  
+* Fix several bugs:  
+  * Fix issue in the PENMON implementation  
+  * FileName reading  
+  * Fix format of simulation Table returned by DynACof with several cycles  
+  * Fix error in dynacof_i  
+  * Fix issues in the soil module  
+  * Fix transpiration metamodel bug  
+  * Fix the computation of the overriped fruits (could potentially count the same overriped fruits)  
+  * Fix issue in soil RootWaterExtract_*  
+  * Fix issue with LeafWaterPotential (was computed before T_Coffee)  
+
 # DynACof 1.2.0
 
 * Reformat the code so the shade tree, coffee, soil and energy balance are made by separate functions sequentially  

R/0-Functions.R

@@ -248,7 +248,7 @@ GDD= function(Tmax=NULL,Tmin=NULL,MinTT=5,Round=T,Tmean=NULL){
 #'
 #' @note This function force \eqn{S_0= S_g} when \eqn{S_0= 0} to avoid the production of `NA`'s.
 #'
-#' @return \item{\eqn{Hd/H}}{Daily diffuse fraction of light (\%)}
+#' @return \item{\eqn{Hd/H}}{Daily diffuse fraction of light (%)}
 #'
 #' @references \itemize{
 #'   \item Duffie, J.A. and W.A. Beckman, Solar engineering of thermal processes. 2013: John Wiley & Sons.
@@ -344,7 +344,7 @@ Rad_ext= function(DOY,Latitude,Gsc=Constants()$Gsc){
 #' @param RAD         Incident daily total radiation (\eqn{MJ\ m^{-2} d^{-1}}{MJ m-2 d-1})
 #' @param Tmax        Maximum daily air temperature (celsius degree)
 #' @param Tmin        Minimum daily air temperature (celsius degree)
-#' @param Rh          Average daily relative humidity (`\%`)
+#' @param Rh          Average daily relative humidity (`%`)
 #' @param VPD         Mean daily Vapor Pressure Deficit (\eqn{hPa}), only needed if `Rh` is missing
 #' @param Latitude    Latitude (\eqn{deg})
 #' @param Elevation   Elevation (\eqn{m})
@@ -1026,9 +1026,9 @@ logistic_deriv= function(xi,u_log,s_log){
 #' @param a      Parameter
 #' @param b      Parameter
 #' @param x0     Mid-maturation (logistic function inflexion point)
-#' @param y0     Sucrose content at the beginning (in \%, 1-100)
+#' @param y0     Sucrose content at the beginning (in %, 1-100)
 #'
-#' @return Sucrose content, in \% of fruit total dry mass
+#' @return Sucrose content, in % of fruit total dry mass
 #'
 #' @references Pezzopane et al. (2012) :
 #' Pezzopane, J., et al., Agrometeorological parameters for prediction of the maturation period
@@ -1050,11 +1050,11 @@ Sucrose_cont_perc= function(x,a,b,x0,y0){
 #' @description Computes the percentage of living tissue in the organ according to age
 #'
 #' @param Age_Max Maximum age of the organ (year)
-#' @param P_Start Percentage of living tissue at first age (\% of dry mass)
-#' @param P_End   Percentage of living tissue at last age (\% of dry mass)
+#' @param P_Start Percentage of living tissue at first age (% of dry mass)
+#' @param P_End   Percentage of living tissue at last age (% of dry mass)
 #' @param k       Rate between P_Start and P_End
 #'
-#' @return Living tissue at each age in \% of organ dry mass
+#' @return Living tissue at each age in % of organ dry mass
 #'
 #' @details The percentage of living tissue is computed as follows:
 #'  \deqn{P_{End}+\left((P_{Start}-P_{End})\cdot e^{seq(0,-k,length.out=Age_{Max})}\right)}{

R/1-Meteo.R

@@ -27,15 +27,15 @@
 #'          likely to be depreciated in the near future as the computation has been replaced by a metamodel. It is kept for
 #'          information for the moment.
 #' \tabular{llll}{
-#' \strong{Var}    \tab \strong{unit} \tab \strong{Definition}                        \tab \strong{If missing} \cr
+#' *Var*           \tab *unit*      \tab *Definition*                                 \tab *If missing* \cr
 #' Date            \tab POSIXct     \tab Date in POSIXct format                       \tab Computed from start date parameter, or set a dummy date if missing \cr
 #' year            \tab year        \tab Year of the simulation                       \tab Computed from Date \cr
 #' DOY             \tab day         \tab day of the year                              \tab Computed from Date \cr
 #' Rain            \tab mm          \tab Rainfall                                     \tab Assume no rain \cr
 #' Tair            \tab Celsius     \tab Air temperature (above canopy)               \tab Computed from Tmax and Tmin \cr
 #' Tmax            \tab Celsius     \tab Maximum air temperature during the day       \tab Required (error) \cr
 #' Tmin            \tab Celsius     \tab Minimum air temperature during the day       \tab Required (error) \cr
-#' RH              \tab \%          \tab Relative humidity                            \tab Not used, but prefered over VPD for Rn computation \cr
+#' RH              \tab %           \tab Relative humidity                            \tab Not used, but prefered over VPD for Rn computation \cr
 #' RAD             \tab MJ m-2 d-1  \tab Incident shortwave radiation                 \tab Computed from PAR \cr
 #' Pressure        \tab hPa         \tab Atmospheric pressure                         \tab Computed from VPD, Tair and Elevation, or alternatively from Tair and Elevation. \cr
 #' WindSpeed       \tab m s-1       \tab Wind speed                                   \tab Taken as constant: `Parameters$WindSpeed` \cr

R/2-main.R

@@ -23,9 +23,10 @@
 #' Default input files are provided with the package as an example parameterization.
 #'
 #' @return Return invisibly a list containing three objects (Parameters, Meteo and Sim):
-#' \itemize{
-#'   \item Sim: A data.frame of the simulation outputs at daily time-step: \tabular{llll}{
-#' \strong{Type}                \tab \strong{Var}             \tab \strong{unit}       \tab \strong{Definition}                                                                \cr
+#'
+#' * Sim: A data.frame of the simulation outputs at daily time-step:
+#' \tabular{llll}{
+#' *Type*                       \tab *Var*                    \tab *unit*              \tab *Definition*                                                                \cr
 #' General                      \tab Cycle                    \tab -                   \tab Plantation cycle ID                                                                \cr
 #'                              \tab Plot_Age                 \tab year                \tab Plantation age (starting at 1)                                                     \cr
 #'                              \tab Plot_Age_num             \tab year (numeric)      \tab Numeric age of plantation                                                          \cr
@@ -134,29 +135,33 @@
 #'                              \tab MThinning_x_Tree         \tab gc m-2 d-1          \tab Mortality due to thining at organ scale
 #'}
 #'
-#'   \item Meteo: A data.frame of the input meteorology, potentially coming from the output of [Meteorology()]: \tabular{llll}{\strong{Var} \tab \strong{unit} \tab \strong{Definition} \tab \strong{If missing} \cr
-#' Date            \tab POSIXct date\tab Date in POSIXct format                       \tab Computed from start date parameter, or set a dummy date if missing\cr
+#' * Meteo: A data.frame of the input meteorology, potentially coming from the output of [Meteorology()]:
+#' \tabular{llll}{
+#' *Var*           \tab *unit*      \tab *Definition*                                 \tab *If missing* \cr
+#' Date            \tab POSIXct     \tab Date in POSIXct format                       \tab Computed from start date parameter, or set a dummy date if missing \cr
 #' year            \tab year        \tab Year of the simulation                       \tab Computed from Date \cr
 #' DOY             \tab day         \tab day of the year                              \tab Computed from Date \cr
 #' Rain            \tab mm          \tab Rainfall                                     \tab Assume no rain \cr
-#' Tair            \tab deg C       \tab Air temperature (above canopy)               \tab Computed from Tmax and Tmin \cr
-#' Tmax            \tab deg C       \tab Maximum air temperature during the day       \tab Required (error) \cr
-#' Tmin            \tab deg C       \tab Minimum air temperature during the day       \tab Required (error) \cr
-#' RH              \tab \%          \tab Relative humidity                            \tab Not used, but prefered over VPD for Rn computation \cr
+#' Tair            \tab Celsius     \tab Air temperature (above canopy)               \tab Computed from Tmax and Tmin \cr
+#' Tmax            \tab Celsius     \tab Maximum air temperature during the day       \tab Required (error) \cr
+#' Tmin            \tab Celsius     \tab Minimum air temperature during the day       \tab Required (error) \cr
+#' RH              \tab %           \tab Relative humidity                            \tab Not used, but prefered over VPD for Rn computation \cr
 #' RAD             \tab MJ m-2 d-1  \tab Incident shortwave radiation                 \tab Computed from PAR \cr
-#' Pressure        \tab hPa         \tab Atmospheric pressure                         \tab Try to compute from VPD, Tair and Elevation, or Tair and Elevation. \cr
-#' WindSpeed       \tab m s-1       \tab Wind speed                                   \tab Try to set it to constant: `Parameters$WindSpeed` \cr
-#' CO2             \tab ppm         \tab Atmospheric CO2 concentration                \tab Try to set it to constant: `Parameters$CO2`\cr
-#' DegreeDays      \tab deg C       \tab Growing degree days                          \tab Computed using [GDD()] \cr
+#' Pressure        \tab hPa         \tab Atmospheric pressure                         \tab Computed from VPD, Tair and Elevation, or alternatively from Tair and Elevation. \cr
+#' WindSpeed       \tab m s-1       \tab Wind speed                                   \tab Taken as constant: `Parameters$WindSpeed` \cr
+#' CO2             \tab ppm         \tab Atmospheric CO2 concentration                \tab Taken as constant: `Parameters$CO2` \cr
+#' DegreeDays      \tab Celsius     \tab Growing degree days                          \tab Computed using [GDD()] \cr
 #' PAR             \tab MJ m-2 d-1  \tab Incident photosynthetically active radiation \tab Computed from RAD \cr
-#' FDiff           \tab Fraction    \tab Diffuse light fraction                       \tab Computed using [Diffuse_d()] using Spitters formula \cr
+#' FDiff           \tab Fraction    \tab Diffuse light fraction                       \tab Computed using [Diffuse_d()] using Spitters et al. (1986) formula \cr
 #' VPD             \tab hPa         \tab Vapor pressure deficit                       \tab Computed from RH \cr
-#' Rn (!=Rn_tot)    \tab MJ m-2 d-1  \tab Net radiation (will soon be depreciated)     \tab Computed using [Rad_net()] with RH, or VPD \cr
+#' Rn              \tab MJ m-2 d-1  \tab Net radiation (will be depreciated)          \tab Computed using [Rad_net()] with RH, or VPD \cr
 #' DaysWithoutRain \tab day         \tab Number of consecutive days with no rainfall  \tab Computed from Rain \cr
-#' Air_Density     \tab kg m-3      \tab Air density of moist air (\eqn{\rho}) above canopy \tab Computed using [bigleaf::air.density()]}
-#'   \item Parameters: A list of the input parameters (see [site()])
+#' Air_Density     \tab kg m-3      \tab Air density of moist air (\eqn{\rho}) above canopy \tab Computed using [bigleaf::air.density()] \cr
+#' ZEN             \tab radian      \tab Solar zenithal angle at noon                 \tab Computed from Date, Latitude, Longitude and Timezone
 #' }
 #'
+#' * Parameters: A list of the input parameters (see [site()])
+#'
 #' @details The user can import a simulation using [base::readRDS()].
 #'          Almost all variables for coffee exist also for shade trees with the suffix
 #'          `_Tree` after the name of the variable, e.g. : LAI = coffee LAI,
@@ -363,7 +368,7 @@ mainfun= function(cy,Direction,Meteo,Parameters){
 #'
 #' @examples
 #'\dontrun{
-#' Making a regular simulation using example data:
+#' # Making a regular simulation using example data:
 #' S= DynACof(Period= as.POSIXct(c("1979-01-01", "1980-12-31")))
 #'
 #' # Value of the maintenance respiration for coffee on day i=100:
@@ -378,7 +383,7 @@ mainfun= function(cy,Direction,Meteo,Parameters){
 #' # New value of the maintenance respiration for coffee:
 #' S$Sim$Rm[i]
 #'
-#' # To re-run DynACof for several days, use a range for `i`:
+#' # To re-run DynACof for several days, use a range for i:
 #' S= dynacof_i(i:(i+10),S)
 #'
 #'}

R/3-Metamodels.R

@@ -30,7 +30,7 @@
 #'           and transpiration through stomatal conductance. Therefore, we derived metamodels from MAESPA for the
 #'           diffuse (\eqn{K_{dif_{Tree}}}{K_dif_Tree}) and the direct (\eqn{K_{dir_{Tree}}}{K_dir_Tree}) shade tree light
 #'           extinction coefficients, the light use efficiency (LUE, gC MJ-1), the coffee canopy temperature (Tcan, deg Celsius)
-#'           and leaf water potential (MPa), the transpiration (T_\*, mm) and plant sensible heat flux (H_\*). The coffee layer was
+#'           and leaf water potential (MPa), the transpiration (T_x, mm) and plant sensible heat flux (H_x). The coffee layer was
 #'           considered homogeneous enough to compute constant extinction coefficients derived from the MAESPA simulation,
 #'           and the partitioning parameter between soil sensible and latent flux was also adjusted using MAESPA outputs.
 #'           MAESPA is a 3D explicit model for energy, carbon and water fluxes simulation, for further details, see:

R/4-dynacof_julia.R

@@ -16,7 +16,7 @@
 #' If you are using a new version of R, please use the argument `rebuild= TRUE` (see [JuliaCall::julia_setup()]).
 #'
 #' @param ... Parameters are passed down to [JuliaCall::julia_setup()]
-#' @param dev_path the path to the `dev` folder location (*e.g.* "C:/Users/<User>/.julia/dev") if a dev version of `DynACof.jl` has to be used.
+#' @param dev_path the path to the `dev` folder location (*e.g.* "C:/Users/{User}/.julia/dev") if a dev version of `DynACof.jl` has to be used.
 #'
 #' @examples
 #' \dontrun{
@@ -186,7 +186,7 @@ dynacof.jl= function(Period=NULL,WriteIt=FALSE,Inpath=NULL,output_f=".RData",
 #' # Setting up julia + DynACof.jl:
 #' dynacof.jl_setup()
 #'
-#' Making a regular simulation using example data:
+#' # Making a regular simulation using example data:
 #' # First, downloading an example meteorology file:
 #' met_file= tempfile()
 #' m= "https://raw.githubusercontent.com/VEZY/DynACof.jl_inputs/master/meteorology.txt"
@@ -209,7 +209,7 @@ dynacof.jl= function(Period=NULL,WriteIt=FALSE,Inpath=NULL,output_f=".RData",
 #' # New value of the maintenance respiration for coffee:
 #' S$Sim$Rm[i]
 #'
-#' # To re-run DynACof for several days, use a range for `i`:
+#' # To re-run DynACof for several days, use a range for i:
 #' S= dynacof_i(i:(i+10),S)
 #' }
 dynacof_i.jl= function(i,S){