#' Fit a Logistic Curve to Growth Data
#'
#' \code{fit_growth_logistic} fits a logistic curve to a tidy growth data set
#' using nonlinear least squares
#'
#' @inheritParams fit_growth
#' @param ... Additional arguments to \code{\link[stats]{nls}}
#'
#' @seealso \url{https://en.wikipedia.org/wiki/Logistic_function}
#' @return A \code{\link{growthcurve}} object
#'
#' @export
#'
#' @examples
#' \dontrun{
#' # Fit the data given in columns Time and OD600
#' fit_growth_logistic(mydata, Time, OD600)}
#'
fit_growth_logistic <- function(df, time, data, ...) {
fit_growth_logistic_(
df = df,
time_col = lazyeval::lazy(time),
data_col = lazyeval::lazy(data),
...
)
}
#' @rdname fit_growth_logistic
#' @inheritParams fit_growth_
#' @importFrom stats coef D
#' @export
#' @examples
#' \dontrun{
#' fit_growth_logistic_(mydata, "Time", "OD600")
#' }
fit_growth_logistic_ <- function(df, time_col, data_col, ...) {
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")
nlsmodel <- stats::nls(
growth_data ~ SSlogis(time_data, Asym, xmid, scal),
...
)
expr_logis <- expression(Asym / (1 + exp((xmid - input) / scal)))
# calculate growth values for a given time point according to the model
yval <- function(x = time_data) {
eval_env(
expr_logis,
Asym = coef(nlsmodel)[["Asym"]],
xmid = coef(nlsmodel)[["xmid"]],
scal = coef(nlsmodel)[["scal"]],
input = x
)
}
growthcurve(
type = "logistic",
model = nlsmodel,
fit = list(
x = time_data,
y = stats::predict(nlsmodel),
residuals = stats::residuals(nlsmodel)
),
f = yval,
parameters = list(
asymptote = coef(nlsmodel)[["Asym"]],
max_rate = list(
time = coef(nlsmodel)[["xmid"]],
value = yval(coef(nlsmodel)[["xmid"]]),
rate = eval_env(
D(expr = expr_logis, name = "input"),
Asym = coef(nlsmodel)[["Asym"]],
xmid = coef(nlsmodel)[["xmid"]],
scal = coef(nlsmodel)[["scal"]],
input = coef(nlsmodel)[["xmid"]]
)
),
augc = calculate_augc(time_data, stats::predict(nlsmodel))
),
df = df,
time_col = as.character(time_col)[1],
data_col = as.character(data_col)[1]
)
}
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