kinfit <- function(kindata, kinmodels = c("SFO"), parent.0.user = NA, start.SFO = list(parent.0 = NA, k = NA), start.FOMC = list(parent.0 = NA, alpha = NA, beta = NA), start.DFOP = list(parent.0 = NA, k1 = NA, k2 = NA, g = NA), start.HS = list(parent.0 = NA, k1 = NA, k2 = NA, tb = NA), algorithm = "port") { kindata <- subset(kindata, !is.na(kindata$parent)) kinfits <- list() if (!is.na(parent.0.user)) { start.SFO$parent.0 = parent.0.user start.FOMC$parent.0 = parent.0.user } lmlogged = lm(log(parent) ~ t, data = kindata) for (kinmodel in kinmodels) { if (kinmodel == "SFO") { if (is.na(start.SFO$parent.0)) { start.SFO$parent.0 = max(kindata$parent) } if (is.na(start.SFO$k)) { start.SFO$k = - coef(lmlogged)[["t"]] } kinfits[[kinmodel]] = try( nls(parent ~ SFO(t, parent.0, k), data = kindata, model = TRUE, start = start.SFO, algorithm = algorithm), silent=TRUE) } k.est = ifelse(is.na(coef(kinfits$SFO)[["k"]]), -coef(lmlogged)[["t"]], coef(kinfits$SFO)[["k"]]) if (kinmodel == "FOMC") { if (is.na(start.FOMC$parent.0)) { start.FOMC$parent.0 = max(kindata$parent) } if (is.na(start.FOMC$alpha)) { start.FOMC$alpha = 1 } if (is.na(start.FOMC$beta)) { start.FOMC$beta = start.FOMC$alpha / k.est } kinfits[[kinmodel]] = try( nls(parent ~ FOMC(t, parent.0, alpha, beta), data = kindata, model = TRUE, start = start.FOMC, algorithm = algorithm), silent=TRUE) } if (kinmodel == "DFOP") { if (is.na(start.DFOP$parent.0)) { start.DFOP$parent.0 = max(kindata$parent) } if (is.na(start.DFOP$k1)) { start.DFOP$k1 = k.est * 2 } if (is.na(start.DFOP$k2)) { start.DFOP$k2 = k.est / 2 } if (is.na(start.DFOP$g)) { start.DFOP$g = 0.5 } kinfits[[kinmodel]] = try( nls(parent ~ DFOP(t, parent.0, k1, k2, g), data = kindata, model = TRUE, start = start.DFOP, algorithm = algorithm), silent=TRUE) } if (kinmodel == "HS") { if (is.na(start.HS$parent.0)) { start.HS$parent.0 = max(kindata$parent) } if (is.na(start.HS$k1)) { start.HS$k1 = k.est } if (is.na(start.HS$k2)) { start.HS$k2 = k.est / 10 } if (is.na(start.HS$tb)) { start.HS$tb = 0.05 * max(kindata$t) } kinfits[[kinmodel]] = try( nls(parent ~ HS(t, parent.0, k1, k2, tb), data = kindata, model = TRUE, start = start.HS, algorithm = algorithm), silent=TRUE) } } return(kinfits) }