R/ba_mortality_Bengtsson_1978.R

In Silviculturalist/forester: Forest Science and Forestry

#' #' Natural mortality, Bengtsson 1978
#' #'
#' #' @description Natural mortality. Functions based on National Forest Inventory
#' #'  surveys of dead trees during 1973-1975. Dead or wind-felled trees above 5 cm
#' #'  diameter at breast height. Avoided harsh storm damages during 1969. Largest
#' #'  insecurity pertains to which season the substrate in question died.
#' #'
#' #'  A 'roof' was set at a maximum of 0.9% per annum and never let the loss be less than 0.1% per annum.
#' #'
#' #'  The mortality level during the observed period was judged to have been
#' #'  higher than normal so at application the mortality given by the functions
#' #'  was reduced with 40 % in northern Sweden and 25 % in southern Sweden.
#' #'
#' #'  \href{https://lagen.nu/sou/1978:7/sid287.png}{Available Online (Swedish)}
#' #'
#' #' @param standData
#' #'
#' #' @return Proportion of the raw standing volume lost per annum.
#' #' #export
#' #'
#' #' @examples
#' # ba_mortality_thinned_Bengtsson_1978 <- function(standData){
#' #   if(!class(standData)%in%c("standData")){
#' #     stop("Input standData is not a standData object. Please make sure it is the correct class.")
#' #   }
#' #
#' #   #Sites as SI Pine
#' #   si_pine <- forester::SIS_estimate(species = "Pinus sylvestris",
#' #                                     vegetation = standData$siteData$vegetation,
#' #                                     ground_layer = standData$siteData$ground_layer,
#' #                                     latitude = standData$siteData$latitude,
#' #                                     longitude = standData$siteData$longitude,
#' #                                     altitude = standData$siteData$altitude,
#' #                                     aspect_main = standData$siteData$aspect_main,
#' #                                     incline_percent = standData$siteData$incline_percent,
#' #                                     soil_moisture = standData$siteData$soil_moisture,
#' #                                     soil_texture = standData$siteData$soil_texture,
#' #                                     soil_depth = standData$siteData$soil_depth,
#' #                                     lateral_water = standData$siteData$lateral_water,
#' #                                     ditched = standData$siteData$ditched,
#' #                                     climate_code = standData$siteData$climate_code,
#' #                                     county = standData$siteData$county
#' #   )
#' #
#' #   #Main cohort age.
#' #   stand_age <-  standData$standSummary$Main_cohort_age
#' #
#' #   #Recommendation due to grouped regression, according to Heureka manual.
#' #   if(stand_age<30){
#' #     stand_age <- 30
#' #   } else if(stand_age>120){
#' #     stand_age <- 120
#' #   }
#' #
#' #   #mean diameter in stand
#' #   mean_diameter <- standData$standSummary$Mean_diameter
#' #
#' #   #Recommendation due to grouped regression, according to Heureka manual.
#' #   if(mean_diameter<7){
#' #     mean_diameter <- 7
#' #   } else if(mean_diameter>30){
#' #     mean_diameter <- 30
#' #   }
#' #
#' #   #Northern Sweden here "Norrland och Dalarna", p. 270.
#' #   #Counties interpreted to be included see list below.
#' #   northern_sweden <- ifelse(standData$siteData$county %in%  c("Norrbottens lappmark",
#' #                                                               "Norrbottens kustland",
#' #                                                               "Västerbottens lappmark",
#' #                                                               "Västerbottens kustland",
#' #                                                               "Västernorrland - Ångermanlands landskap",
#' #                                                               "Västernorrland - Medelpads landskap",
#' #                                                               "Jämtland - Jämtlands landskap",
#' #                                                               "Jämtland - Härjedalens landskap",
#' #                                                               "Kopparberg - Sälen-Idre",
#' #                                                               "Kopparberg - övriga",
#' #                                                               "Gävleborg - Hälsinglands landskap",
#' #                                                               "Gävleborg - övriga"), 1,0)
#' #
#' #
#' #   if (northern_sweden==1){
#' #     if(standData$standSummary$main_species == "Pinus sylvestris"){
#' #       a <- 0.00437
#' #       b1 <- -0.000847
#' #       b2 <- 0.0000214
#' #       b3 <- 0.000104
#' #       b4 <- -0.000000317
#' #       b5 <- 0
#' #       mai_pine_s_sweden <- 0
#' #
#' #     } else if(standData$standSummary$main_species == "Picea abies"){
#' #       a <- 0.00390
#' #       b <- -0.000610
#' #       b2 <- 0.0000160
#' #       b3 <- 0.000050
#' #       b4 <- 0
#' #       b5 <- 0
#' #       mai_pine_s_sweden <- 0
#' #
#' #     } else if(tree_type(standData$standSummary$main_species)=="Deciduous"){
#' #       a <- 0.01005
#' #       b1 <- -0.000843
#' #       b2 <- 0.0000176
#' #       b3 <- -0.00000174
#' #       b4 <- 0.000000591
#' #       b5 <- 0
#' #       mai_pine_s_sweden <- 0
#' #     }
#' #   } else if(northern_sweden==0){
#' #     if(standData$standSummary$main_species == "Pinus sylvestris"){
#' #       a <- 0.00760
#' #       b1 <- -0.000430
#' #       b2 <- 0
#' #       b3 <- 0.000047
#' #       b4 <- 0
#' #       b5 <- 0.00048
#' #
#' #       mai_pine_s_sweden <- si_to_bonitet_integrated(standData$siteData$SIS_Pinus_sylvestris,
#' #                                                     main_species="Pinus sylvestris",
#' #                                                     vegetation=standData$siteData$vegetation,
#' #                                                     altitude=standData$siteData$vegetation,
#' #                                                     county=standData$siteData$county)
#' #
#' #     } else if(standData$standSummary$main_species == "Picea abies"){
#' #       a <- 0.00330
#' #       b1 <- -0.000130
#' #       b2 <- 0
#' #       b3 <- 0.000043
#' #       b4 <- 0
#' #       b5 <- 0
#' #       mai_pine_s_sweden <- 0
#' #
#' #     } else if(tree_type(standData$standSummary$main_species)=="Deciduous"){
#' #       a <- 0.00460
#' #       b1 <- -0.000200
#' #       b2 <- 0
#' #       b3 <- 0.000046
#' #       b4 <- 0
#' #       b5 <- 0
#' #       mai_pine_s_sweden <-0
#' #
#' #   }
#' #
#' #   }
#' #
#' #   #The mortality level during the observed period was judged to have been higher
#' #   #than normal so at application the mortality given by the functions was
#' #   #reduced with 40 % in northern Sweden and 25 % in southern Sweden.
#' #
#' #   if(northern_sweden==1){
#' #   return(
#' #     (a+(b1*mean_diameter) + (b2*(mean_diameter^2)) + (b3*stand_age) + (b4*(stand_age^2)) + (b5*mai_pine_s_sweden))*0.6
#' #   )
#' #   } else {
#' #     return(
#' #     (a+(b1*mean_diameter) + (b2*(mean_diameter^2)) + (b3*stand_age) + (b4*(stand_age^2)) + (b5*mai_pine_s_sweden))*0.75
#' #     )
#' #   }
#' #
#' # }
#'
#'
#' Bengtsson_1978_BA_mortality
#' ba_mortality_thinned_Bengtsson_1978 <- function(mainSpecies,standAge,DBH,county,NormProduktion,floor=0.01,ciel=0.09){
#'    #Recommendation due to grouped regression, according to Heureka manual.
#'   if(standAge<30){
#'     standAge <- 30
#'   } else if(standAge>120){
#'     standAge <- 120
#'   }
#'
#'   #Recommendation due to grouped regression, according to Heureka manual.
#'   if(DBH<7){
#'     DBH <- 7
#'   } else if(DBH>30){
#'     DBH <- 30
#'   }
#'
#'   #Northern Sweden here "Norrland och Dalarna", p. 270.
#'   #Counties interpreted to be included see list below.
#'   northern_sweden <- ifelse(county %in%  c("Norrbottens lappmark",
#'                                                               "Norrbottens kustland",
#'                                                               "Västerbottens lappmark",
#'                                                               "Västerbottens kustland",
#'                                                               "Västernorrland - Ångermanlands landskap",
#'                                                               "Västernorrland - Medelpads landskap",
#'                                                               "Jämtland - Jämtlands landskap",
#'                                                               "Jämtland - Härjedalens landskap",
#'                                                               "Kopparberg - Sälen-Idre",
#'                                                               "Kopparberg - övriga",
#'                                                               "Gävleborg - Hälsinglands landskap",
#'                                                               "Gävleborg - övriga"), 1,0)
#'
#'
#'   if (northern_sweden==1){
#'     if(mainSpecies == "Pinus sylvestris"){
#'       a <- 0.00437
#'       b1 <- -0.000847
#'       b2 <- 0.0000214
#'       b3 <- 0.000104
#'       b4 <- -0.000000317
#'       b5 <- 0
#'       NormProduktion <- 0
#'
#'     } else if(mainSpecies == "Picea abies"){
#'       a <- 0.00390
#'       b <- -0.000610
#'       b2 <- 0.0000160
#'       b3 <- 0.000050
#'       b4 <- 0
#'       b5 <- 0
#'       NormProduktion <- 0
#'
#'     } else if(forester::tree_type(mainSpecies)=="Deciduous"){
#'       a <- 0.01005
#'       b1 <- -0.000843
#'       b2 <- 0.0000176
#'       b3 <- -0.00000174
#'       b4 <- 0.000000591
#'       b5 <- 0
#'       NormProduktion <- 0
#'     }
#'   } else if(northern_sweden==0){
#'     if(mainSpecies == "Pinus sylvestris"){
#'       a <- 0.00760
#'       b1 <- -0.000430
#'       b2 <- 0
#'       b3 <- 0.000047
#'       b4 <- 0
#'       b5 <- 0.00048
#'
#'     } else if(mainSpecies == "Picea abies"){
#'       a <- 0.00330
#'       b1 <- -0.000130
#'       b2 <- 0
#'       b3 <- 0.000043
#'       b4 <- 0
#'       b5 <- 0
#'       NormProduktion <- 0
#'
#'     } else if(forester::tree_type(mainSpecies)=="Deciduous"){
#'       a <- 0.00460
#'       b1 <- -0.000200
#'       b2 <- 0
#'       b3 <- 0.000046
#'       b4 <- 0
#'       b5 <- 0
#'       NormProduktion <-0
#'
#'     }
#'
#'   }
#'
#'   #The mortality level during the observed period was judged to have been higher
#'   #than normal so at application the mortality given by the functions was
#'   #reduced with 40 % in northern Sweden and 25 % in southern Sweden.
#'
#'   if(northern_sweden==1){
#'     return(
#'       (a+(b1*DBH) + (b2*(DBH^2)) + (b3*standAge) + (b4*(standAge^2)) + (b5*NormProduktion))*0.6
#'     )
#'   } else {
#'     return(
#'       (a+(b1*DBH) + (b2*(DBH^2)) + (b3*standAge) + (b4*(standAge^2)) + (b5*NormProduktion))*0.75
#'     )
#'   }
#'
#' }
#'