combineDraws: Combine Draws From brms Models

In pcvr: Plant Phenotyping and Bayesian Statistics

Combine Draws From brms Models

Description

Helper function for binding draws from several brms models to make a data.frame for use with brms::hypothesis(). This will also check that the draws are comparable using basic model metrics.

Usage

combineDraws(..., message = TRUE)

Arguments

...	Some number of brmsfit objects and/or dataframes of draws (should generally be the same type of model fit to different data)
message	Logical, should messages about possible problems be printed? Default is TRUE. This will warn if models may not have converged, if there are different numbers of draws in the objects, or if models have different formulations.

Value

Returns a dataframe of posterior draws.

Examples

# note that this example will fit several bayesian models and may run for several minutes.

simdf <- growthSim("logistic",
  n = 20, t = 25,
  params = list(
    "A" = c(200, 160, 220, 200, 140, 300),
    "B" = c(13, 11, 10, 9, 16, 12),
    "C" = c(3, 3.5, 3.2, 2.8, 3.3, 2.5)
  )
)
ss_ab <- growthSS(
  model = "logistic", form = y ~ time | id / group,
  sigma = "logistic", df = simdf[simdf$group %in% c("a", "b"), ],
  start = list(
    "A" = 130, "B" = 12, "C" = 3,
    "sigmaA" = 15, "sigmaB" = 10, "sigmaC" = 3
  ), type = "brms"
)

ss_cd <- growthSS(
  model = "logistic", form = y ~ time | id / group,
  sigma = "logistic", df = simdf[simdf$group %in% c("c", "d"), ],
  start = list(
    "A" = 130, "B" = 12, "C" = 3,
    "sigmaA" = 15, "sigmaB" = 10, "sigmaC" = 3
  ), type = "brms"
)

ss_ef <- growthSS(
  model = "logistic", form = y ~ time | id / group,
  sigma = "logistic", df = simdf[simdf$group %in% c("e", "f"), ],
  start = list(
    "A" = 130, "B" = 12, "C" = 3,
    "sigmaA" = 15, "sigmaB" = 10, "sigmaC" = 3
  ), type = "brms"
)
ss_ef2 <- growthSS(
  model = "gompertz", form = y ~ time | id / group,
  sigma = "logistic", df = simdf[simdf$group %in% c("e", "f"), ],
  start = list(
    "A" = 130, "B" = 12, "C" = 3,
    "sigmaA" = 15, "sigmaB" = 10, "sigmaC" = 3
  ), type = "brms"
)


fit_ab <- fitGrowth(ss_ab, chains = 1, cores = 1, iter = 1000)
fit_ab2 <- fitGrowth(ss_ab, chains = 1, cores = 1, iter = 1200)
fit_cd <- fitGrowth(ss_cd, chains = 1, cores = 1, iter = 1000)
fit_ef <- fitGrowth(ss_ef, chains = 1, cores = 1, iter = 1000)
fit_ef2 <- fitGrowth(ss_ef2, chains = 1, cores = 1, iter = 1000)

x <- combineDraws(fit_ab, fit_cd, fit_ef)
draws_ef <- as.data.frame(fit_ef)
draws_ef <- draws_ef[, grepl("^b_", colnames(draws_ef))]
x2 <- combineDraws(fit_ab2, fit_cd, draws_ef)
x3 <- combineDraws(fit_ab, fit_cd, fit_ef2)

pcvr documentation built on April 16, 2025, 5:12 p.m.