stage_transitions: Compute what it takes to advance through development stages

In chillR: Statistical Methods for Phenology Analysis in Temperate Fruit Trees

Compute what it takes to advance through development stages

Description

Function to compute the thermal requirements of transitioning through a series of developmental stages.

Usage

stage_transitions(
  observations,
  hourtemps,
  stages,
  models = list(Chill_Portions = Dynamic_Model, GDH = GDH),
  max_steps = length(stages)
)

Arguments

observations	data.frame containing observed developmental dates, e.g. different stages of flower or leaf development. Should contain the columns 'Stage' (containing the names of the development stages), 'Season' (containing the 'development year' the observation belongs to, e.g. budbreak for trees may be considered a stage of the 'dormancy year' that started in the previous calendar year), 'Year' (the calendar year the observation was made), 'JDay' (the Julian Date, a.k.a. day of the year, that the stage was observed).
hourtemps	a list of two elements, with element 'hourtemps' being a dataframe of hourly temperatures (e.g. produced by stack_hourly_temps). This data frame must have a column for Year, a column for JDay (Julian date, or day of the year), a column for Hour and a column for Temp (hourly temperature). The second (optional) element is QC, which is a data.frame indicating completeness of the dataset. This is automatically produced by stack_hourly_temps. This also works if only the 'hourtemps' dataframe is passed to the function.
stages	character vector containing the relevant development stages in their order of occurrence.
models	named list of models that should be applied to the hourly temperature data. These should be functions that take as input a vector of hourly temperatures. This defaults to list(Chill_Portions=Dynamic_Model, GDH=GDH), models that are often used for describing chill and heat accumulation in temperate fruit trees.
max_steps	integer indicating the maximum number of stage steps (i.e. transitions from one step to the next), for which thermal requirements should be calculated. This defaults to length(stages), which is also the maximum value. If only requirements between each stage and the following stage are of interest, this should be set to 1.

Value

data frame with rows for all transitions that occurred during the observed records and the values of the metrics specified in 'models' that accrued between the respective dates. Columns are c('Season','Stage', 'to_Stage','stage_steps') and one column for each thermal metrics.

Author(s)

Eike Luedeling

Examples

hourtemps<-stack_hourly_temps(KA_weather)
observations<-data.frame(Stage=c("V1","V2","V3","V1","V2","V3","V1","V3"),
                        Season=c(2001,2001,2001,2002,2002,2002,2003,2003),
                        Year=c(2001,2001,2001,2002,2002,2002,2003,2003),
                        JDay=c(30,45,60,35,42,55,37,62))
stages<-c("V1","V2","V3") 

stage_transitions(observations,hourtemps,stages)

chillR documentation built on Nov. 28, 2023, 1:09 a.m.