Residuals from a fitted wisp model — residuals.wisp • wispack

Returns the residual summary statistics (mean, sd, variance, by group) computed by analyze_residuals and stored on the fitted model, either for raw residuals or log-residuals.

Usage

# S3 method for class 'wisp'
residuals(object, type = c("raw", "log"), ...)

Arguments

object: List, output of the wisp function (an object of class "wisp").
type: Character string, one of "raw" (default) or "log", specifying whether to return the summary statistics for raw residuals (object$stats$residuals) or log-residuals (object$stats$residuals.log).
...: Ignored; present only for S3 method consistency with residuals.

Value

A data frame of residual summary statistics by group (columns group, mean, sd, variance), or an error if statistical analysis was never run on this model (e.g. it was fit with fit_only = TRUE).

Examples

set.seed(1)
grid <- expand.grid(bin = 1:20, age = c(12, 18), ran = c("r1", "r2"), rep = 1:6)
base_rate <- ifelse(grid$bin <= 10, 3, 9)
age_effect <- ifelse(grid$age == 18, 1.5, 1)
grid$count <- rpois(nrow(grid), base_rate * age_effect)
countdata <- data.frame(
  bin = grid$bin, count = grid$count, age = grid$age, ran = grid$ran,
  species = "demoGene", context = "demoContext"
)
model <- wisp(
  countdata,
  variables      = list(timeseries = "age"),
  model.settings = list(LRO_cost = "none"),
  plot.settings  = list(print.plots = FALSE),
  MCMC.settings  = list(MCMC.steps = 100, MCMC.burnin = 20),
  bootstraps.num = 10,
  max.fork       = 1,
  verbose        = FALSE
)
residuals(model)
#>                  group     mean       sd variance
#> 1                  all 3.725845 7.988364 63.81396
#> 2         ran_lvl_none 4.033232 6.461292 41.74830
#> 3           ran_lvl_r1 4.637785 9.219901 85.00657
#> 4           ran_lvl_r2 2.506519 8.092267 65.48478
#> 5        treatment_ref 3.223797 6.423804 41.26526
#> 6         treatment_18 4.227894 9.323712 86.93161
#> 7 demoContext_demoGene 3.725845 7.988364 63.81396
residuals(model, type = "log")
#>                  group       mean        sd   variance
#> 1                  all 0.10081184 0.2049539 0.04200609
#> 2         ran_lvl_none 0.10238083 0.1616210 0.02612136
#> 3           ran_lvl_r1 0.10026499 0.2129685 0.04535560
#> 4           ran_lvl_r2 0.09978970 0.2380999 0.05669157
#> 5        treatment_ref 0.10734713 0.2110623 0.04454727
#> 6         treatment_18 0.09427655 0.2002249 0.04009001
#> 7 demoContext_demoGene 0.10081184 0.2049539 0.04200609