R/gtoxFit.R
In pmpsa-hpc/GladiaTOX: R Package for Processing High Content Screening data
Defines functions
gtoxFit
Documented in
gtoxFit
#####################################################################
## This program is distributed in the hope that it will be useful, ##
## but WITHOUT ANY WARRANTY; without even the implied warranty of ##
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ##
## GNU General Public License for more details. ##
#####################################################################
#-------------------------------------------------------------------------------
# gtoxFit: Fit the data
#-------------------------------------------------------------------------------
#' @title Fit the data with the constant, hill, and gain-loss models
#'
#' @description
#' \code{gtoxFit} fits the constant, hill, and gain-loss models to the given
#' data and returns some summary statistics and the fit parameters in a list.
#'
#' @param logc Numeric, log concentration values
#' @param resp Numeric, normalized response values
#' @param bmad Numeric, the baseline median absolute deviation for the entire
#' assay
#' @param force.fit Logical, TRUE indicates to attempt fitting every
#' concentration series
#' @param \dots Any other data to be included in list output.
#'
#' @details
#' By default, \code{gtoxFit} will only attempt to fit concentration series
#' when at least one median value is greater than 3*bmad.
#'
#' @examples
#' logc <- 1:10
#' resp <- sapply(1:10, gtoxHillVal, ga = 5, tp = 50, gw = 0.5)
#' params <- gtoxFit(logc = logc, resp = resp, bmad = 10)
#' plot(resp ~ logc)
#' gtoxAddModel(pars = params, modl = "hill")
#'
#' @return List of summary values and fit parameters for the given data.
#'
#' @seealso \code{\link{gtoxObjCnst}}, \code{\link{gtoxObjHill}},
#' \code{\link{gtoxObjGnls}}, \code{\link{constrOptim}}
#'
#' @importFrom numDeriv hessian
#' @importFrom stats optim constrOptim median mad
#' @importFrom methods is
#' @export
gtoxFit <- function(logc, resp, bmad, force.fit=FALSE, ...) {
## Variable-binding to pass R CMD Check
hill_tp <- hill_ga <- hill_gw <- gnls_ga <- gnls_gw <- gnls_la <- NULL
gnls_lw <- gnls_tp <- hill_tp_sd <- hill_ga_sd <- hill_gw_sd <- NULL
hill_er <- hill_er_sd <- gnls_tp_sd <- gnls_ga_sd <- gnls_gw_sd <- NULL
gnls_la_sd <- gnls_lw_sd <- gnls_er <- gnls_er_sd <- NULL
fenv <- environment()
bmad <- min(bmad)
rmns <- tapply(resp, logc, mean)
rmds <- tapply(resp, logc, median)
mmed <- max(rmds)
mmed_conc <- as.numeric(names(which.max(rmds)))
hprs <- paste0("hill_", c("tp", "ga", "gw", "er"))
hsds <- paste0("hill_", c("tp", "ga", "gw", "er"), "_sd")
gprs <- paste0("gnls_", c("tp", "ga", "gw", "la", "lw", "er"))
gsds <- paste0("gnls_", c("tp", "ga", "gw", "la", "lw", "er"), "_sd")
resp_max <- max(resp)
resp_min <- min(resp)
logc_med <- median(logc)
logc_min <- min(logc)
logc_max <- max(logc)
ncnc <- lu(logc)
npts <- length(resp)
## Meidan number replicates
nrep <- as.numeric(median(tapply(resp, logc, lu)))
nmed_gtbl <- lw(rmds >= 3 * bmad) # Number of medians above 3 * bmad
## Do not fit anything with less than four concentrations of data.
if (length(rmds) >= 4) {
er_est <- if ((rmad <- mad(resp)) > 0) log(rmad) else log(1e-32)
###----------------------- Fit the Constant Model -----------------------###
cfit <- optim(
er_est,
gtoxObjCnst,
method="Brent",
lower=er_est - 2,
upper=er_est + 2,
control=list(
fnscale=-1,
reltol=1e-4,
maxit=500
),
resp=resp
)
if (!is(cfit, "try-error")) {
cnst <- 1L
cnst_er <- cfit$par
## 2*length(cfit$par) - 2*cfit$value
caic <- 2 - 2*cfit$value
## Calculate the rmse for constant
crme <- sqrt(mean((0 - resp)^2, na.rm=TRUE))
} else {
cnst <- 0L
cnst_er <- NA_real_
caic <- NA_integer_
crme <- NA_real_
}
if (lw(rmds >= 3*bmad) > 0 | force.fit) {
###------------------------ Fit the Hill Model ------------------------###
## Starting parameters for the Hill Model
## cind <- (ceiling(length(meds)/2) + 1):length(meds)
h <- c(
mmed, # top (tp)
mmed_conc - 1, # logAC50 (ga)
1.2, # hill coefficient (gw)
er_est # logSigma (er)
)
if (h[1] == 0) h[1] <- 0.1
hUi <- matrix(
## Generate the bound matrices to constrain the model.
## tp ga gw er
c(
1, 0, 0, 0,
-1, 0, 0, 0,
0, 1, 0, 0,
0, -1, 0, 0,
0, 0, 1, 0,
0, 0, -1, 0),
byrow=TRUE, nrow=6, ncol=4
)
hbnds <- c(
0, -1.2*resp_max, # tp bounds
logc_min - 2, -(logc_max + 0.5), # ga bounds
0.3, -8
) # gw bounds
hCi <- matrix(hbnds, nrow=6, ncol=1)
## Optimize the hill model
hfit <- try(
constrOptim(
h,
gtoxObjHill,
ui=hUi,
ci=hCi,
mu=1e-6,
method="Nelder-Mead",
control=list(
fnscale=-1,
reltol=1e-10,
maxit=6000
),
lconc=logc,
resp=resp
),
silent=TRUE
)
## Generate some summary statistics
if (!is(hfit, "try-error")) { # Hill model fit the data
hill <- 1L
haic <- 8 - 2*hfit$value # 2*length(hfit$par) - 2*hfit$value
mapply(
assign,
c(hprs),
hfit$par,
MoreArgs=list(envir=fenv)
)
## Calculate rmse for hill
hill_modl <- hill_tp/(1 + 10^((hill_ga - logc)*hill_gw))
hrme <- sqrt(mean((hill_modl - resp)^2, na.rm=TRUE))
## Calculate the sd for the hill parameters
hfit$cov <- try(
solve(
-hessian(
gtoxObjHill,
hfit$par,
lconc=logc,
resp=resp
)
),
silent=TRUE
)
if (!is(hfit$cov, "try-error")) { # Could invert hill Hessian
hcov <- 1L
hdiag_sqrt <- suppressWarnings(sqrt(diag(hfit$cov)))
if (any(is.nan(hdiag_sqrt))) {
mapply(
assign,
hsds,
NaN,
MoreArgs=list(envir=fenv)
)
} else {
mapply(
assign,
hsds,
hdiag_sqrt,
MoreArgs=list(envir=fenv)
)
}
} else { # Could not invert hill Hessian
hcov <- 0L
mapply(
assign,
c(hsds),
NA_real_,
MoreArgs=list(envir=fenv)
)
}
} else { # Hill model did not fit the data
hill <- 0L
haic <- NA_real_
hcov <- NA_integer_
hrme <- NA_real_
mapply(
assign,
c(hprs, hsds),
NA_real_,
MoreArgs=list(envir=fenv)
)
}
###--------------------- Fit the Gain-Loss Model ----------------------###
## Starting parameters for the Gain-Loss Model
## cind <- (ceiling(length(meds)/2) + 1):length(meds)
g <- c(
mmed, # top (tp)
mmed_conc - 1, # gain logAC50 (ga)
1.2, # gain hill coefficient (gw)
mmed_conc + 0.1, # loss logAC50 (la)
5, # loss hill coefficient (lw)
er_est # logSigma (er)
)
if (g[1] == 0) g[1] <- 0.1
gUi <- matrix(
## Generate the bound matrices to constrain the model.
## tp ga gw la lw er
c(
1, 0, 0, 0, 0, 0,
-1, 0, 0, 0, 0, 0,
0, 1, 0, 0, 0, 0,
0, -1, 0, 0, 0, 0,
0, 0, 1, 0, 0, 0,
0, 0, -1 , 0, 0, 0,
0, 0, 0, 1, 0, 0,
0, 0, 0, -1, 0, 0,
0, 0, 0, 0, 1, 0,
0, 0, 0, 0, -1, 0,
0, -1, 0, 1, 0, 0
),
byrow=TRUE, nrow=11, ncol=6
)
gbnds <- c(
0, -1.2*resp_max, # tp bounds
logc_min - 2, -(logc_max), # ga bounds
0.3, -8, # gw bounds
logc_min - 2, -(logc_max + 2), # la bounds
0.3, -18, # lw bounds
0.25 # ga < la
)
## if (mmed_conc > logc_min) g[7] <- mmed_conc - 0.25
gCi <- matrix(gbnds, nrow=11, ncol=1)
## Optimize the gnls model
gfit <- try(
constrOptim(
g,
gtoxObjGnls,
ui=gUi,
ci=gCi,
mu=1e-6,
method="Nelder-Mead",
control=list(
fnscale=-1,
reltol=1e-10,
maxit=6000
),
lconc=logc,
resp=resp),
silent=TRUE
)
## Generate some summary statistics
if (!is(gfit, "try-error")) { # Gain-loss fit the data
gnls <- 1L
gaic <- 12 - 2*gfit$value # 2*length(gfit$par) - 2*gfit$value
mapply(
assign,
c(gprs),
gfit$par,
MoreArgs=list(envir=fenv)
)
## Calculate rmse for gnls
gnls_gn <- (1/(1 + 10^((gnls_ga - logc)*gnls_gw)))
gnls_ls <- (1/(1 + 10^((logc - gnls_la)*gnls_lw)))
gnls_modl <- gnls_tp * gnls_gn * gnls_ls
grme <- sqrt(mean((gnls_modl - resp)^2, na.rm=TRUE))
## Calculate the sd for the gnls parameters
gfit$cov <- try(
solve(
-hessian(
gtoxObjGnls,
gfit$par,
lconc=logc,
resp=resp
)
),
silent=TRUE
)
if (!is(gfit$cov, "try-error")) { # Could invert gnls Hessian
gcov <- 1L
gdiag_sqrt <- suppressWarnings(sqrt(diag(gfit$cov)))
if (any(is.nan(gdiag_sqrt))) {
mapply(
assign,
gsds,
NaN,
MoreArgs=list(envir=fenv)
)
} else {
mapply(
assign,
gsds,
gdiag_sqrt,
MoreArgs=list(envir=fenv)
)
}
} else { # Could not invert gnls Hessian
gcov <- 0L
mapply(
assign,
c(gsds),
NA_real_,
MoreArgs=list(envir=fenv)
)
}
} else { # Gain-loss did not fit the data
gnls <- 0L
gaic <- NA_real_
gcov <- NA_integer_
grme <- NA_real_
mapply(
assign,
c(gprs, gsds),
NA_real_,
MoreArgs=list(envir=fenv)
)
}
} else { # None of the response values fell outside 3*bmad
hill <- NA_integer_
haic <- NA_real_
hcov <- NA_integer_
hrme <- NA_real_
gnls <- NA_integer_
gaic <- NA_real_
gcov <- NA_integer_
grme <- NA_real_
mapply(
assign,
c(hprs, hsds, gprs, gsds),
NA_real_,
MoreArgs=list(envir=fenv)
)
}
} else { # Data has response data for less than four concentrations.
cnst <- NA_integer_
cnst_er <- NA_real_
caic <- NA_real_
crme <- NA_real_
hill <- NA_integer_
haic <- NA_real_
hcov <- NA_integer_
hrme <- NA_real_
gnls <- NA_integer_
gaic <- NA_real_
gcov <- NA_integer_
grme <- NA_real_
mapply(
assign,
c(hprs, hsds, gprs, gsds),
NA_real_,
MoreArgs=list(envir=fenv)
)
}
out <- list(
resp_max =resp_max,
resp_min =resp_min,
max_mean =max(rmns),
max_mean_conc=as.numeric(names(which.max(rmns))),
max_med =mmed,
max_med_conc =mmed_conc,
logc_max =logc_max,
logc_min =logc_min,
cnst =cnst,
hill =hill,
hcov =hcov,
gnls =gnls,
gcov =gcov,
cnst_er =cnst_er,
cnst_aic =caic,
cnst_rmse =crme,
hill_tp =hill_tp,
hill_tp_sd =hill_tp_sd,
hill_ga =hill_ga,
hill_ga_sd =hill_ga_sd,
hill_gw =hill_gw,
hill_gw_sd =hill_gw_sd,
hill_er =hill_er,
hill_er_sd =hill_er_sd,
hill_aic =haic,
hill_rmse =hrme,
gnls_tp =gnls_tp,
gnls_tp_sd =gnls_tp_sd,
gnls_ga =gnls_ga,
gnls_ga_sd =gnls_ga_sd,
gnls_gw =gnls_gw,
gnls_gw_sd =gnls_gw_sd,
gnls_la =gnls_la,
gnls_la_sd =gnls_la_sd,
gnls_lw =gnls_lw,
gnls_lw_sd =gnls_lw_sd,
gnls_er =gnls_er,
gnls_er_sd =gnls_er_sd,
gnls_aic =gaic,
gnls_rmse =grme,
nconc =ncnc,
npts =npts,
nrep =nrep,
nmed_gtbl =nmed_gtbl,
...
)
out
}
#-------------------------------------------------------------------------------
pmpsa-hpc/GladiaTOX documentation built on Sept. 1, 2023, 5:52 p.m.
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Defines functions gtoxFit
Documented in gtoxFit
#####################################################################
## This program is distributed in the hope that it will be useful, ##
## but WITHOUT ANY WARRANTY; without even the implied warranty of ##
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ##
## GNU General Public License for more details. ##
#####################################################################
#-------------------------------------------------------------------------------
# gtoxFit: Fit the data
#-------------------------------------------------------------------------------
#' @title Fit the data with the constant, hill, and gain-loss models
#'
#' @description
#' \code{gtoxFit} fits the constant, hill, and gain-loss models to the given
#' data and returns some summary statistics and the fit parameters in a list.
#'
#' @param logc Numeric, log concentration values
#' @param resp Numeric, normalized response values
#' @param bmad Numeric, the baseline median absolute deviation for the entire
#' assay
#' @param force.fit Logical, TRUE indicates to attempt fitting every
#' concentration series
#' @param \dots Any other data to be included in list output.
#'
#' @details
#' By default, \code{gtoxFit} will only attempt to fit concentration series
#' when at least one median value is greater than 3*bmad.
#'
#' @examples
#' logc <- 1:10
#' resp <- sapply(1:10, gtoxHillVal, ga = 5, tp = 50, gw = 0.5)
#' params <- gtoxFit(logc = logc, resp = resp, bmad = 10)
#' plot(resp ~ logc)
#' gtoxAddModel(pars = params, modl = "hill")
#'
#' @return List of summary values and fit parameters for the given data.
#'
#' @seealso \code{\link{gtoxObjCnst}}, \code{\link{gtoxObjHill}},
#' \code{\link{gtoxObjGnls}}, \code{\link{constrOptim}}
#'
#' @importFrom numDeriv hessian
#' @importFrom stats optim constrOptim median mad
#' @importFrom methods is
#' @export
gtoxFit <- function(logc, resp, bmad, force.fit=FALSE, ...) {
## Variable-binding to pass R CMD Check
hill_tp <- hill_ga <- hill_gw <- gnls_ga <- gnls_gw <- gnls_la <- NULL
gnls_lw <- gnls_tp <- hill_tp_sd <- hill_ga_sd <- hill_gw_sd <- NULL
hill_er <- hill_er_sd <- gnls_tp_sd <- gnls_ga_sd <- gnls_gw_sd <- NULL
gnls_la_sd <- gnls_lw_sd <- gnls_er <- gnls_er_sd <- NULL
fenv <- environment()
bmad <- min(bmad)
rmns <- tapply(resp, logc, mean)
rmds <- tapply(resp, logc, median)
mmed <- max(rmds)
mmed_conc <- as.numeric(names(which.max(rmds)))
hprs <- paste0("hill_", c("tp", "ga", "gw", "er"))
hsds <- paste0("hill_", c("tp", "ga", "gw", "er"), "_sd")
gprs <- paste0("gnls_", c("tp", "ga", "gw", "la", "lw", "er"))
gsds <- paste0("gnls_", c("tp", "ga", "gw", "la", "lw", "er"), "_sd")
resp_max <- max(resp)
resp_min <- min(resp)
logc_med <- median(logc)
logc_min <- min(logc)
logc_max <- max(logc)
ncnc <- lu(logc)
npts <- length(resp)
## Meidan number replicates
nrep <- as.numeric(median(tapply(resp, logc, lu)))
nmed_gtbl <- lw(rmds >= 3 * bmad) # Number of medians above 3 * bmad
## Do not fit anything with less than four concentrations of data.
if (length(rmds) >= 4) {
er_est <- if ((rmad <- mad(resp)) > 0) log(rmad) else log(1e-32)
###----------------------- Fit the Constant Model -----------------------###
cfit <- optim(
er_est,
gtoxObjCnst,
method="Brent",
lower=er_est - 2,
upper=er_est + 2,
control=list(
fnscale=-1,
reltol=1e-4,
maxit=500
),
resp=resp
)
if (!is(cfit, "try-error")) {
cnst <- 1L
cnst_er <- cfit$par
## 2*length(cfit$par) - 2*cfit$value
caic <- 2 - 2*cfit$value
## Calculate the rmse for constant
crme <- sqrt(mean((0 - resp)^2, na.rm=TRUE))
} else {
cnst <- 0L
cnst_er <- NA_real_
caic <- NA_integer_
crme <- NA_real_
}
if (lw(rmds >= 3*bmad) > 0 | force.fit) {
###------------------------ Fit the Hill Model ------------------------###
## Starting parameters for the Hill Model
## cind <- (ceiling(length(meds)/2) + 1):length(meds)
h <- c(
mmed, # top (tp)
mmed_conc - 1, # logAC50 (ga)
1.2, # hill coefficient (gw)
er_est # logSigma (er)
)
if (h[1] == 0) h[1] <- 0.1
hUi <- matrix(
## Generate the bound matrices to constrain the model.
## tp ga gw er
c(
1, 0, 0, 0,
-1, 0, 0, 0,
0, 1, 0, 0,
0, -1, 0, 0,
0, 0, 1, 0,
0, 0, -1, 0),
byrow=TRUE, nrow=6, ncol=4
)
hbnds <- c(
0, -1.2*resp_max, # tp bounds
logc_min - 2, -(logc_max + 0.5), # ga bounds
0.3, -8
) # gw bounds
hCi <- matrix(hbnds, nrow=6, ncol=1)
## Optimize the hill model
hfit <- try(
constrOptim(
h,
gtoxObjHill,
ui=hUi,
ci=hCi,
mu=1e-6,
method="Nelder-Mead",
control=list(
fnscale=-1,
reltol=1e-10,
maxit=6000
),
lconc=logc,
resp=resp
),
silent=TRUE
)
## Generate some summary statistics
if (!is(hfit, "try-error")) { # Hill model fit the data
hill <- 1L
haic <- 8 - 2*hfit$value # 2*length(hfit$par) - 2*hfit$value
mapply(
assign,
c(hprs),
hfit$par,
MoreArgs=list(envir=fenv)
)
## Calculate rmse for hill
hill_modl <- hill_tp/(1 + 10^((hill_ga - logc)*hill_gw))
hrme <- sqrt(mean((hill_modl - resp)^2, na.rm=TRUE))
## Calculate the sd for the hill parameters
hfit$cov <- try(
solve(
-hessian(
gtoxObjHill,
hfit$par,
lconc=logc,
resp=resp
)
),
silent=TRUE
)
if (!is(hfit$cov, "try-error")) { # Could invert hill Hessian
hcov <- 1L
hdiag_sqrt <- suppressWarnings(sqrt(diag(hfit$cov)))
if (any(is.nan(hdiag_sqrt))) {
mapply(
assign,
hsds,
NaN,
MoreArgs=list(envir=fenv)
)
} else {
mapply(
assign,
hsds,
hdiag_sqrt,
MoreArgs=list(envir=fenv)
)
}
} else { # Could not invert hill Hessian
hcov <- 0L
mapply(
assign,
c(hsds),
NA_real_,
MoreArgs=list(envir=fenv)
)
}
} else { # Hill model did not fit the data
hill <- 0L
haic <- NA_real_
hcov <- NA_integer_
hrme <- NA_real_
mapply(
assign,
c(hprs, hsds),
NA_real_,
MoreArgs=list(envir=fenv)
)
}
###--------------------- Fit the Gain-Loss Model ----------------------###
## Starting parameters for the Gain-Loss Model
## cind <- (ceiling(length(meds)/2) + 1):length(meds)
g <- c(
mmed, # top (tp)
mmed_conc - 1, # gain logAC50 (ga)
1.2, # gain hill coefficient (gw)
mmed_conc + 0.1, # loss logAC50 (la)
5, # loss hill coefficient (lw)
er_est # logSigma (er)
)
if (g[1] == 0) g[1] <- 0.1
gUi <- matrix(
## Generate the bound matrices to constrain the model.
## tp ga gw la lw er
c(
1, 0, 0, 0, 0, 0,
-1, 0, 0, 0, 0, 0,
0, 1, 0, 0, 0, 0,
0, -1, 0, 0, 0, 0,
0, 0, 1, 0, 0, 0,
0, 0, -1 , 0, 0, 0,
0, 0, 0, 1, 0, 0,
0, 0, 0, -1, 0, 0,
0, 0, 0, 0, 1, 0,
0, 0, 0, 0, -1, 0,
0, -1, 0, 1, 0, 0
),
byrow=TRUE, nrow=11, ncol=6
)
gbnds <- c(
0, -1.2*resp_max, # tp bounds
logc_min - 2, -(logc_max), # ga bounds
0.3, -8, # gw bounds
logc_min - 2, -(logc_max + 2), # la bounds
0.3, -18, # lw bounds
0.25 # ga < la
)
## if (mmed_conc > logc_min) g[7] <- mmed_conc - 0.25
gCi <- matrix(gbnds, nrow=11, ncol=1)
## Optimize the gnls model
gfit <- try(
constrOptim(
g,
gtoxObjGnls,
ui=gUi,
ci=gCi,
mu=1e-6,
method="Nelder-Mead",
control=list(
fnscale=-1,
reltol=1e-10,
maxit=6000
),
lconc=logc,
resp=resp),
silent=TRUE
)
## Generate some summary statistics
if (!is(gfit, "try-error")) { # Gain-loss fit the data
gnls <- 1L
gaic <- 12 - 2*gfit$value # 2*length(gfit$par) - 2*gfit$value
mapply(
assign,
c(gprs),
gfit$par,
MoreArgs=list(envir=fenv)
)
## Calculate rmse for gnls
gnls_gn <- (1/(1 + 10^((gnls_ga - logc)*gnls_gw)))
gnls_ls <- (1/(1 + 10^((logc - gnls_la)*gnls_lw)))
gnls_modl <- gnls_tp * gnls_gn * gnls_ls
grme <- sqrt(mean((gnls_modl - resp)^2, na.rm=TRUE))
## Calculate the sd for the gnls parameters
gfit$cov <- try(
solve(
-hessian(
gtoxObjGnls,
gfit$par,
lconc=logc,
resp=resp
)
),
silent=TRUE
)
if (!is(gfit$cov, "try-error")) { # Could invert gnls Hessian
gcov <- 1L
gdiag_sqrt <- suppressWarnings(sqrt(diag(gfit$cov)))
if (any(is.nan(gdiag_sqrt))) {
mapply(
assign,
gsds,
NaN,
MoreArgs=list(envir=fenv)
)
} else {
mapply(
assign,
gsds,
gdiag_sqrt,
MoreArgs=list(envir=fenv)
)
}
} else { # Could not invert gnls Hessian
gcov <- 0L
mapply(
assign,
c(gsds),
NA_real_,
MoreArgs=list(envir=fenv)
)
}
} else { # Gain-loss did not fit the data
gnls <- 0L
gaic <- NA_real_
gcov <- NA_integer_
grme <- NA_real_
mapply(
assign,
c(gprs, gsds),
NA_real_,
MoreArgs=list(envir=fenv)
)
}
} else { # None of the response values fell outside 3*bmad
hill <- NA_integer_
haic <- NA_real_
hcov <- NA_integer_
hrme <- NA_real_
gnls <- NA_integer_
gaic <- NA_real_
gcov <- NA_integer_
grme <- NA_real_
mapply(
assign,
c(hprs, hsds, gprs, gsds),
NA_real_,
MoreArgs=list(envir=fenv)
)
}
} else { # Data has response data for less than four concentrations.
cnst <- NA_integer_
cnst_er <- NA_real_
caic <- NA_real_
crme <- NA_real_
hill <- NA_integer_
haic <- NA_real_
hcov <- NA_integer_
hrme <- NA_real_
gnls <- NA_integer_
gaic <- NA_real_
gcov <- NA_integer_
grme <- NA_real_
mapply(
assign,
c(hprs, hsds, gprs, gsds),
NA_real_,
MoreArgs=list(envir=fenv)
)
}
out <- list(
resp_max =resp_max,
resp_min =resp_min,
max_mean =max(rmns),
max_mean_conc=as.numeric(names(which.max(rmns))),
max_med =mmed,
max_med_conc =mmed_conc,
logc_max =logc_max,
logc_min =logc_min,
cnst =cnst,
hill =hill,
hcov =hcov,
gnls =gnls,
gcov =gcov,
cnst_er =cnst_er,
cnst_aic =caic,
cnst_rmse =crme,
hill_tp =hill_tp,
hill_tp_sd =hill_tp_sd,
hill_ga =hill_ga,
hill_ga_sd =hill_ga_sd,
hill_gw =hill_gw,
hill_gw_sd =hill_gw_sd,
hill_er =hill_er,
hill_er_sd =hill_er_sd,
hill_aic =haic,
hill_rmse =hrme,
gnls_tp =gnls_tp,
gnls_tp_sd =gnls_tp_sd,
gnls_ga =gnls_ga,
gnls_ga_sd =gnls_ga_sd,
gnls_gw =gnls_gw,
gnls_gw_sd =gnls_gw_sd,
gnls_la =gnls_la,
gnls_la_sd =gnls_la_sd,
gnls_lw =gnls_lw,
gnls_lw_sd =gnls_lw_sd,
gnls_er =gnls_er,
gnls_er_sd =gnls_er_sd,
gnls_aic =gaic,
gnls_rmse =grme,
nconc =ncnc,
npts =npts,
nrep =nrep,
nmed_gtbl =nmed_gtbl,
...
)
out
}
#-------------------------------------------------------------------------------
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