#' Fit a Parametric Model to Growth Data (using grofit)
#'
#' \code{fit_growth_grofit_parametric} allows you to fit a parametric model to a
#' tidy growth data set using \code{\link[grofit]{gcFitModel}} from the
#' \pkg{grofit} package. Several candidate models are fitted, and the model with
#' the best AIC is returned.
#'
#' @inheritParams fit_growth
#' @param ... Additional arguments for \code{\link[grofit]{gcFitModel}}
#' @return A \code{\link{growthcurve}} object
#'
#' @export
#'
#' @seealso \link{grofit_wrappers}
#' @examples
#' \dontrun{
#' # Fit the data given in columns Time and OD600
#' fit_growth_grofit_parametric(mydata, Time, OD600)}
#'
fit_growth_grofit_parametric <- function(df, time, data, ...) {
fit_growth_grofit_parametric_(
df,
time_col = lazyeval::lazy(time),
data_col = lazyeval::lazy(data),
...
)
}
# Helper function that fits the model type specified by 'type'
fit_growth_grofit_ptype <- function(df, time, data, type, ...) {
stop_without_package("grofit")
ctl <- grofit::grofit.control(model.type = type, suppress.messages = TRUE)
fit_growth_grofit_parametric(df, time = time, data = data, control = ctl,
...)
}
#' @rdname fit_growth_grofit_parametric
#' @export
fit_growth_grofit_logistic <- function(df, time, data, ...) {
fit_growth_grofit_ptype(
df = df,
time = time,
data = data,
type = "logistic",
...
)
}
#' @rdname fit_growth_grofit_parametric
#' @export
fit_growth_grofit_gompertz <- function(df, time, data, ...) {
fit_growth_grofit_ptype(
df = df,
time = time,
data = data,
type = "gompertz",
...
)
}
#' @rdname fit_growth_grofit_parametric
#' @export
fit_growth_grofit_gompertz.exp <- function(df, time, data, ...) {
fit_growth_grofit_ptype(
df = df,
time = time,
data = data,
type = "gompertz.exp",
...
)
}
#' @rdname fit_growth_grofit_parametric
#' @export
fit_growth_grofit_richards <- function(df, time, data, ...) {
fit_growth_grofit_ptype(
df = df,
time = time,
data = data,
type = "richards",
...
)
}
#' @export
#' @inheritParams fit_growth_
#' @rdname fit_growth_grofit_parametric
#' @examples
#' \dontrun{
#' # Fit the data given in columns Time and OD600
#' fit_growth_grofit_parametric_(mydata, time_col = "Time", data_col = "OD600")}
#'
fit_growth_grofit_parametric_ <- function(df, time_col, data_col, ...) {
stop_without_package("grofit")
growth_data <- lazyeval::lazy_eval(data_col, df)
time_data <- lazyeval::lazy_eval(time_col, df)
if (any(is.na(time_data))) stop("NAs in time data")
if (any(is.na(growth_data))) stop("NAs in growth data")
tryCatch(gres <- grofit::gcFitModel(time = time_data,
data = growth_data,
...),
warning = function(w) stop(w))
fit_dydt <- diff(gres$fit.data) / diff(gres$fit.time)
i_max_rate <- which.max(fit_dydt)
yvals <- function(x = time_data) {
f <- switch(gres$model,
logistic = grofit::logistic,
gompertz = grofit::gompertz,
gompertz.exp = grofit::gompertz.exp,
richards = grofit::richards)
y <- f(
time = x,
A = gres$parameters$A[[1]],
mu = gres$parameters$mu[[1]],
lambda = gres$parameters$lambda[[1]]
)
y
}
result <- growthcurve(
type = paste0(c("grofit", gres$model), collapse = "_"),
model = gres$nls,
fit = list(
x = gres$fit.time,
y = gres$fit.data,
residuals = stats::residuals(gres$nls)
),
f = yvals,
parameters = list(
asymptote = gres$parameters$A[[1]],
max_rate = list(
time = gres$fit.time[i_max_rate],
value = gres$fit.data[i_max_rate],
rate = gres$parameters$mu[[1]],
lambda = gres$parameters$lambda[[1]]
),
augc = gres$parameters$integral
),
df = df,
time_col = as.character(time_col)[1],
data_col = as.character(data_col)[1]
)
result$grofit <- gres
class(result) <- c(class(result), "grofit")
result
}
# Helper function that fits the model type specified by 'type'
fit_growth_grofit_ptype_ <- function(df, time_col, data_col, type, ...) {
stop_without_package("grofit")
ctl <- grofit::grofit.control(model.type = type, suppress.messages = TRUE)
fit_growth_grofit_parametric_(df = df, time_col = time_col,
data_col = data_col, control = ctl, ...)
}
#' @rdname fit_growth_grofit_parametric
#' @export
fit_growth_grofit_logistic_ <- function(df, time_col, data_col, ...) {
fit_growth_grofit_ptype_(
df = df,
time_col = time_col,
data_col = data_col,
type = "logistic",
...
)
}
#' @rdname fit_growth_grofit_parametric
#' @export
fit_growth_grofit_gompertz_ <- function(df, time_col, data_col, ...) {
fit_growth_grofit_ptype_(
df = df,
time_col = time_col,
data_col = data_col,
type = "gompertz",
...
)
}
#' @rdname fit_growth_grofit_parametric
#' @export
fit_growth_grofit_gompertz.exp_ <- function(df, time_col, data_col, ...) {
fit_growth_grofit_ptype_(
df = df,
time_col = time_col,
data_col = data_col,
type = "gompertz.exp",
...
)
}
#' @rdname fit_growth_grofit_parametric
#' @export
fit_growth_grofit_richards_ <- function(df, time_col, data_col, ...) {
fit_growth_grofit_ptype_(
df = df,
time_col = time_col,
data_col = data_col,
type = "richards",
...
)
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.