assign_observed_data: Observed Data Preparation
In phenModel: Insect Phenology Model Evaluation Based on Daily Temperatures

Description Usage Arguments Details Value Author(s) See Also Examples

Prepares observed data for plotting with model evaluation.

1	assign_observed_data(obj, eggs = NA, larvae = NA, pupae = NA, adults)

`obj`	an object generated from `phen_model`
`eggs`	vector of days in which eggs were observed
`larvae`	vector of days in which larvae were observed
`pupae`	vector of days in which pupae were observed
`adults`	vector of days in which adults were observed

Reads in the data and returns an object ready to be passed to plot_phen_model for plotting. Uses a simple probability checking to determine whether the observations for the adults category belong to the post-diapause, ovipositing or adult emergence stage, based on normal distributions.

Returns a data.frame with five columns, one for each stage (post-diapause, eggs, larvae, pupae and adults).

Rafael de Andrade Moral (rafael.deandrademoral@mu.ie) and Rowan Fealy

phen_model, plot_phen_model

data(casement9596)
casement1995 <- data.frame(casement9596, 
                           with(casement9596, 
                                get_total_info(Tmax, Tmin, Tbase = 7, Lat, day)))

## loading fitted parameters
data(pvulg_budburst_parameters)
data(pvulg_weibull_parameters)
data(pvulg_lactin_parameters)

## evaluating model
quantiles_seq <- seq(.001, .95, .001)

phen95 <- phen_model(Tmean = "Tmean",
                     thermal_units = "thermal_units",
                     chill_days = "chill_days",
                     day_length = "day_length",
                     bud_pars = pvulg_budburst_parameters,
                     weib_pars = pvulg_weibull_parameters,
                     lactin_pars = pvulg_lactin_parameters,
                     max_day_length = 14.92,
                     pop_quantiles = quantiles_seq,
                     data = casement1995)

phen95_gen2 <- phen_model_gen2(Tmean = "Tmean",
                               day_length = "day_length",
                               bud_pars = pvulg_budburst_parameters,
                               weib_pars = pvulg_weibull_parameters,
                               lactin_pars = pvulg_lactin_parameters,
                               sex_mat_day = phen95["0.05","sexual_maturation_day"],
                               pop_quantiles = .05,
                               data = casement1995)

## adding observed points
made_up_data <- assign_observed_data(obj = phen95,
                                     eggs = c(182,184,204,227,233,242),
                                     larvae = c(204,227,233,242,249),
                                     adults = c(204,212,220,221,222,224,227,233,242,269,283,298,
                                                305,310,311,312,313,314,315,316,317,318,
                                                319,320,321,322,323,334,325,326,327,328,
                                                329,330,331,332))

plot_phen_model(obj = phen95, obj_gen2 = phen95_gen2,
                observed_data = made_up_data)