assign_observed_data {phenModel}

Observed Data Preparation

Description

Prepares observed data for plotting with model evaluation.

Usage

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

Arguments

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

Details

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.

Value

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

Author(s)

Rafael de Andrade Moral ([e-mail]) and Rowan Fealy

See Also

phen_model, plot_phen_model

Examples

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)