R/AQSys.R
In Hutchr/LLSR: Data Analysis of Liquid-Liquid Systems using R
Defines functions
AQSys.plot
AQSys.data
AQSys.default
AQSys
Documented in
AQSys
AQSys.data
AQSys.default
AQSys.plot
if (getRversion() >= "3.5")
utils::globalVariables(
c(
"Series",
"wt",
"wb",
"xlab",
"ylab",
"geom_point",
"geom_line",
"unit",
"element_text",
"element_line",
"element_rect",
"scale_x_continuous",
"scale_y_continuous",
"A",
"B",
"PH",
"TEMP"
)
)
###############################################################################
#' @import rootSolve graphics stats svDialogs ggplot2 svglite
#' @importFrom grDevices dev.off
#' @importFrom grDevices png
# options(warn = 1)
###############################################################################
# Merchuk's Equation to fit Binodal Experimental Data
#' @rdname AQSys
#' @name AQSys
#' @description .
#' @export
#' @seealso \itemize{
#' \item \code{\link{AQSys.default}}
#' \item \code{\link{AQSys.plot}}
#' \item \code{\link{AQSys.LevArmRule}}
#' \item \code{\link{AQSysOthmer}}
#' \item \code{\link{AQSysBancroft}}
#' }
###############################################################################
AQSys <- function(dataSET, ...)
UseMethod("AQSys")
###############################################################################
#' @rdname AQSys
#' @title Merchuk's nonlinear Equation
#' @description Perform a nonlinear regression fit using any of the several
#' mathematical descriptors implemented in order to calculate the equation's
#' parameters.
#' @details The function returns functions parameters after fitting experimental
#' data to the equations listed in AQSysList().
#' @param modelName - Character String specifying the nonlinear empirical
#' equation to fit data.
#' The default method uses Merchuk's equation. Other mathematical descriptors
#' can be listed using AQSysList().
#' @param dataSET - Binodal Experimental data that will be used in the
#' nonlinear fit
#' @param Order Defines how the data is organized in the Worksheet. Use "xy"
#' whether the first column corresponds to the lower phase fraction and "yx"
#' whether the opposite.
# ' @param maxiter - A positive integer specifying the maximum number of
# iterations allowed.
#' @param ... Additional optional arguments. None are used at present.
#' @method AQSys default
#' @export
#' @return A list containing three data.frame variables with all data parsed
#' from the worksheet and parameters calculated
#' through the available mathematical descriptions.
#' @examples
#' # Populating variable dataSET with binodal data
#' dataSET <- peg4kslt[ , 1:2]
#' # Fitting dataSET using Merchuk's function
#' AQSys(dataSET)
#' @references
#' MURUGESAN, T.; PERUMALSAMY, M. Liquid-Liquid Equilibria of
#' Poly(ethylene glycol) 2000 + Sodium Citrate + Water at
#' (25, 30, 35, 40, and 45) C. Journal of Chemical & Engineering Data,
#' v. 50, n. 4, p. 1392-1395, 2005/07/01 2005. ISSN 0021-9568.
#' (\doi{10.1021/je050081k})
#'
#' MERCHUK, J. C.; ANDREWS, B. A.; ASENJO, J. A. Aqueous two-phase systems for
#' protein separation: Studies on phase inversion. Journal of Chromatography B:
#' Biomedical Sciences and Applications, v. 711, n. 1-2, p. 285-293, 1998.
#' ISSN 0378-4347. (\doi{10.1016/s0378-4347(97)00594-x})
#'
#' TANG, X. et al. The study of phase behavior of aqueous two-phase system
#' containing [Cnmim] BF 4 (n=2, 3, 4)+(NH4)2SO4 + H2O at different
#' temperatures. Fluid Phase Equilibria, v. 383, p. 100-107, 2014.
#' ISSN 0378-3812. (\doi{10.1016/j.fluid.2014.09.029})
#'
#' GONZALEZ-TELLO, P. et al. Liquid-Liquid Equilibrium in the System
#' Poly(ethylene glycol) + MgSO4 + H2O at 298 K. Journal of Chemical &
#' Engineering Data, v. 41, n. 6, p. 1333-1336, 1996/01/01 1996.
#' ISSN 0021-9568. (\doi{10.1021/je960075b})
#'
#' CHEN, Y. et al. Liquid-liquid equilibria of aqueous biphasic systems
#' composed of 1-butyl-3-methyl imidazolium tetrafluoroborate+ sucrose/maltose+
#' water. Journal of Chemical & Engineering Data, v. 55, n. 9, p. 3612-3616,
#' 2010. ISSN 0021-9568. (\doi{10.1021/je100212p})
#
# XUEQIAO, X. et al. Measurement and Correlation of the Phase Diagram Data for
# PPG400 + (K3PO4, K2CO3, and K2HPO4) + H2O Aqueous Two-Phase Systems at
# T = 298.15 K. Journal of Chemical & Engineering Data, v. 55, n. 11,
# p. 4741-4745, 2010/11/11 2010. ISSN 0021-9568.
# (\href{https://pubs.acs.org/doi/full/10.1021/je100356s?src=recsys}
# {ACS Publications})
#
# XIE, X. et al. Liquidb-liquid equilibrium of aqueous two-phase systems of
# PPG400 and biodegradable salts at temperatures of (298.15, 308.15, and 318.15)
# K. Journal of Chemical & Engineering Data, v. 55, n. 8, p. 2857-2861, 2010.
# ISSN 0021-9568.
# (\href{https://pubs.acs.org/doi/abs/10.1021/je901019t}{ACS Publications})
AQSys.default <- function(dataSET, modelName = "merchuk", Order="xy", ...) {
# arrange data and guarantee R converted it to numbers but dont switch
# columns to prevent incompatibility with pre-existent functions
dataSET <- toNumeric(dataSET, Order)
# each switch option calls a correspondent equation to fit dataSET
# equations are functions declared in AQSysFormulas.R
if (modelName %in% names(AQSysList(TRUE))) {
ans <- do.call(modelName, list(dataSET))
} else{
AQSys.err("0")
}
# return fitting parameters ans statistical data
return(ans)
}
#
###############################################################################
#' @rdname AQSys.data
#' @title Dataset and Fitted Function plot
#' @description The function returns a plot after fitting a dataset to the
#' mathematical descriptor chosen by the user.
#' @details This version uses the plot function and return a regular orthogonal
#' plot.
#' @method AQSys data
#' @export AQSys.data
#' @export
#'
#' @param dataSET - Binodal Experimental data that will be used in the nonlinear
#' fit. It might hold multiple systems stacked side-by-side. [type:data.frame]
#' @param modelName - Character String specifying the nonlinear empirical
#' equation to fit data. [type:String]
#' The default method uses Merchuk's equation. Other mathematical descriptors
#' can be listed using AQSysList().
#' @param Order Defines how the data is organized in the Worksheet. Use "xy"
#' whether the first column corresponds to the lower phase fraction and "yx"
#' whether the opposite. [type:String]
#' @param xmax Maximum value for the Horizontal axis'
#' value - optional [type:double]
#' @param ymax Maximum value for the Vertical axis'
#' value - optional [type:double]
#' @param ... Additional optional arguments. None are used at present.
#' @return return a data.frame with data fitted using the chosen mathematical
#' descriptor.
#' @examples
#' # Populating variable dataSET with binodal data
#' dataSET <- peg4kslt[ , 1:2]
#' # Fitting dataSET using Merchuk's function
#' data <- AQSys.data(dataSET, Order = "xy")
AQSys.data <- function(dataSET,
modelName = "merchuk",
Order = "xy",
xmax = "",
ymax = "",
...
) {
# guarantee all lines are valid (non-na and numeric)
dataSET <- toNumeric(dataSET, Order)
# Calculate aesthetically better xmax and ymax
if ((xmax == "") |
((xmax > 1) &
(max(dataSET[1]) <= 1)) |
((xmax > 100) &
(max(dataSET[1]) <= 100) &
(max(dataSET[1]) >= 10)) |
(xmax < round(max(dataSET[1]) / 0.92, 1))) {
xmax <- ceiling(round(max(dataSET[1]) / 0.92, 1)/5)*5
}
if ((ymax == "") |
((ymax > 1) &
(max(dataSET[2]) <= 1)) |
((ymax > 100) &
(max(dataSET[2]) <= 100) &
(max(dataSET[2]) >= 1)) |
(ymax < round(max(dataSET[2]) / 0.92, 1))) {
ymax <- ceiling(round(max(dataSET[2]) / 0.92, 1)/5)*5
}
# Select which model will be used to generate the plot. Function return list
# of plots and respective number of parameters
models_npars <- AQSysList(TRUE)
# choose model based in the user choice or standard value
Fn <- ifelse(modelName %in% names(models_npars),
AQSys.mathDesc(modelName), AQSys.err("0"))
# calculate coefficients using the non-linear regression
CoefSET <- summary(AQSys(dataSET, modelName))$coefficients[, 1]
#
Xs <- as.data.frame(ifelse((xmax != max(dataSET[1])),
rbind(dataSET[1], xmax), dataSET[1]))
rawdt <- setNames(data.frame(Xs, Fn(CoefSET, Xs)), c("XC", "YC"))
#
return(rawdt)
}
###############################################################################
#' @rdname AQSys.plot
#' @title Dataset and Fitted Function plot
#' @description The function returns a plot after fitting a dataset to the
#' mathematical descriptor chosen by the user.
#' @details This version uses the plot function and return a regular orthogonal
#' plot.
#' @method AQSys plot
#' @export AQSys.plot
#' @export
#' @param dataSET - Binodal Experimental data that will be used in the nonlinear
#' fit. It might hold multiple systems stacked side-by-side. [type:data.frame]
#' @param xlbl Plot's Horizontal axis label.
#' @param ylbl Plot's Vertical axis label.
#' @param main Legacy from plot package. For more details,
#' see \code{\link{plot.default}}
#' @param col Legacy from plot package. For more details,
#' see \code{\link{plot.default}}
#' @param type Legacy from plot package. For more details,
#' see \code{\link{plot.default}}
#' @param cex Legacy from plot package. For more details,
#' see \code{\link{plot.default}}
#' @param cexlab Legacy from plot package. For more details,
#' see \code{\link{plot.default}}
#' @param cexaxis Legacy from plot package. For more details,
#' see \code{\link{plot.default}}
#' @param cexmain Legacy from plot package. For more details,
#' see \code{\link{plot.default}}
#' @param cexsub Legacy from plot package. For more details,
#' see \code{\link{plot.default}}
#' @param modelName - Character String specifying the nonlinear empirical
#' equation to fit data. The default method uses
#' Merchuk's equation. Other possibilities can be seen in AQSysList().
#'
#' @param NP Number of points used to build the fitted curve.
#' Default is 100. [type:Integer]
#' @param xmax Maximum value for the Horizontal axis' value
#' @param ymax Maximum value for the Vertical axis' value
#' @param Order Defines how the data is organized in the Worksheet.
#' Use "xy" whether the first column corresponds to the lower phase fraction
#' and "yx" whether the opposite.
#' @param save Save the generated plot in the disk using path and filename
#' provided by the user. [type:Boulean]
#' @param HR Adjust Plot's text to be compatible with High Resolution
#' size [type:Boulean]
#' @param filename Filename provided by the user to save a given
#' plot. [type:String]
#' @param wdir The directory in which the plot file will be
#' saved. [type:String]
#' @param silent save plot file without actually showing it to the
#' user. [type:Boulean]
#' @param ... Additional optional arguments. None are used at present.
#'
#' @return A plot containing the experimental data, the correspondent curve for
#' the binodal in study and the curve's raw XY data.
#' @examples
#' #Populating variable dataSET with binodal data
#' dataSET <- peg4kslt[, 1:2]
#' # Plot dataSET using Merchuk's function
#' #
#' AQSys.plot(dataSET)
#' #
AQSys.plot <- function(dataSET,
xlbl = "",
ylbl = "",
main = NULL,
col = "blue",
type = "p",
cex = 1,
cexlab = 1,
cexaxis = 1,
cexmain = 1,
cexsub = 1,
modelName = "merchuk",
NP = 100,
xmax = "",
ymax = "",
Order = "xy",
save = FALSE,
HR = FALSE,
filename = NULL,
wdir = NULL,
silent = FALSE,
...
)
{
#
plot_image = NULL
# verify and adjust data.frame names
if (xlbl == "") {
xlbl <- names(dataSET)[1]
}
if (ylbl == "") {
ylbl <- names(dataSET)[2]
}
# guarantee all lines are valid (non-na and numeric)
dataSET <- toNumeric(dataSET, Order)
# Calculate aesthetically better xmax and ymax
if ((xmax == "") |
((xmax > 1) &
(max(dataSET[1]) <= 1)) |
((xmax > 100) &
(max(dataSET[1]) <= 100) &
(max(dataSET[1]) >= 10)) |
(xmax < round(max(dataSET[1]) / 0.92, 1))) {
xmax <- ceiling(round(max(dataSET[1]) / 0.92, 1)/5)*5
}
if ((ymax == "") |
((ymax > 1) &
(max(dataSET[2]) <= 1)) |
((ymax > 100) &
(max(dataSET[2]) <= 100) &
(max(dataSET[2]) >= 1)) |
(ymax < round(max(dataSET[2]) / 0.92, 1))) {
ymax <- ceiling(round(max(dataSET[2]) / 0.92, 1)/5)*5
}
# If save=TRUE adjust variables and parameters to save plot
wdir <- saveConfig(save, HR, filename, wdir, silent)
# Select which model will be used to generate the plot. Function return
# list of plots and respective number of parameters
models_npars <- AQSysList(TRUE)
# choose model based in the user choice or standard value
Fn <- ifelse(modelName %in% names(models_npars), AQSys.mathDesc(modelName),
AQSys.err("0"))
# calculate coefficients using the non-linear regression
CoefSET <- summary(AQSys(dataSET, modelName))$coefficients[, 1]
# plot phase diagram using experimental data and with previously calculated
# parameters
plot_image <- ggplot(data = dataSET, aes_string(x = "XC", y = "YC")) +
geom_point(shape = 8, size = 2) +
theme_light() + xlab(paste(xlbl, "(%, m/m)")) +
ylab(paste(ylbl, "(%, m/m)")) +
theme(
validate = FALSE,
plot.margin = unit(c(1, 1, 1, 1), "cm"),
text = element_text(size = 16),
legend.position = "top",
axis.title.y = element_text(vjust = 5),
axis.title.x = element_text(vjust = -2),
panel.grid.major = element_line(size = .70, colour = "black"),
panel.grid.minor = element_line(size = .70),
panel.border = element_rect(size = .5, colour = "white"),
axis.text.x = element_text(size = 15),
axis.text.y = element_text(size = 15),
axis.line = element_line(colour = 'black', size = 1.25),
legend.title = element_text(
colour = "black",
size = 12,
face = "bold",
angle = 0
),
legend.text = element_text(
colour = "black",
size = 12,
face = "plain"
)
) +
scale_y_continuous(
expand = c(0, 0),
limits = c(-0.5, ymax),
breaks = seq(0, ymax, by = 5),
labels = seq(0, ymax, by = 5)
) +
scale_x_continuous(
expand = c(0, 0),
limits = c(0, xmax),
breaks = seq(0, ymax, by = xmax / 10),
labels = seq(0, ymax, by = xmax / 10)
)
#
# add curve generated using regression parameters
Xs <- as.data.frame(ifelse((xmax != max(dataSET[1])),
rbind(dataSET[1], xmax), dataSET[1]))
rawdt <- setNames(data.frame(Xs, Fn(CoefSET, Xs)), c("XC", "YC"))
#
plot_image <-
plot_image + geom_line(
data = rawdt,
aes_string(x = "XC", y = "YC"),
color = "red",
linetype = "solid",
size = 1
)
#
if (save == TRUE) {
ggsave(
filename = wdir,
plot = plot_image,
width = 21.14 / 2,
height = 14.39 / 2
)
}
# make available data from fitted curve to user. Function returns it
# silently but user can get data using simple assign '<-'
if (silent == FALSE) {
print(plot_image)
invisible(rawdt)
} else {
invisible(plot_image)
}
}
###############################################################################
Hutchr/LLSR documentation built on May 31, 2022, 11:56 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions AQSys.plot AQSys.data AQSys.default AQSys
Documented in AQSys AQSys.data AQSys.default AQSys.plot
if (getRversion() >= "3.5")
utils::globalVariables(
c(
"Series",
"wt",
"wb",
"xlab",
"ylab",
"geom_point",
"geom_line",
"unit",
"element_text",
"element_line",
"element_rect",
"scale_x_continuous",
"scale_y_continuous",
"A",
"B",
"PH",
"TEMP"
)
)
###############################################################################
#' @import rootSolve graphics stats svDialogs ggplot2 svglite
#' @importFrom grDevices dev.off
#' @importFrom grDevices png
# options(warn = 1)
###############################################################################
# Merchuk's Equation to fit Binodal Experimental Data
#' @rdname AQSys
#' @name AQSys
#' @description .
#' @export
#' @seealso \itemize{
#' \item \code{\link{AQSys.default}}
#' \item \code{\link{AQSys.plot}}
#' \item \code{\link{AQSys.LevArmRule}}
#' \item \code{\link{AQSysOthmer}}
#' \item \code{\link{AQSysBancroft}}
#' }
###############################################################################
AQSys <- function(dataSET, ...)
UseMethod("AQSys")
###############################################################################
#' @rdname AQSys
#' @title Merchuk's nonlinear Equation
#' @description Perform a nonlinear regression fit using any of the several
#' mathematical descriptors implemented in order to calculate the equation's
#' parameters.
#' @details The function returns functions parameters after fitting experimental
#' data to the equations listed in AQSysList().
#' @param modelName - Character String specifying the nonlinear empirical
#' equation to fit data.
#' The default method uses Merchuk's equation. Other mathematical descriptors
#' can be listed using AQSysList().
#' @param dataSET - Binodal Experimental data that will be used in the
#' nonlinear fit
#' @param Order Defines how the data is organized in the Worksheet. Use "xy"
#' whether the first column corresponds to the lower phase fraction and "yx"
#' whether the opposite.
# ' @param maxiter - A positive integer specifying the maximum number of
# iterations allowed.
#' @param ... Additional optional arguments. None are used at present.
#' @method AQSys default
#' @export
#' @return A list containing three data.frame variables with all data parsed
#' from the worksheet and parameters calculated
#' through the available mathematical descriptions.
#' @examples
#' # Populating variable dataSET with binodal data
#' dataSET <- peg4kslt[ , 1:2]
#' # Fitting dataSET using Merchuk's function
#' AQSys(dataSET)
#' @references
#' MURUGESAN, T.; PERUMALSAMY, M. Liquid-Liquid Equilibria of
#' Poly(ethylene glycol) 2000 + Sodium Citrate + Water at
#' (25, 30, 35, 40, and 45) C. Journal of Chemical & Engineering Data,
#' v. 50, n. 4, p. 1392-1395, 2005/07/01 2005. ISSN 0021-9568.
#' (\doi{10.1021/je050081k})
#'
#' MERCHUK, J. C.; ANDREWS, B. A.; ASENJO, J. A. Aqueous two-phase systems for
#' protein separation: Studies on phase inversion. Journal of Chromatography B:
#' Biomedical Sciences and Applications, v. 711, n. 1-2, p. 285-293, 1998.
#' ISSN 0378-4347. (\doi{10.1016/s0378-4347(97)00594-x})
#'
#' TANG, X. et al. The study of phase behavior of aqueous two-phase system
#' containing [Cnmim] BF 4 (n=2, 3, 4)+(NH4)2SO4 + H2O at different
#' temperatures. Fluid Phase Equilibria, v. 383, p. 100-107, 2014.
#' ISSN 0378-3812. (\doi{10.1016/j.fluid.2014.09.029})
#'
#' GONZALEZ-TELLO, P. et al. Liquid-Liquid Equilibrium in the System
#' Poly(ethylene glycol) + MgSO4 + H2O at 298 K. Journal of Chemical &
#' Engineering Data, v. 41, n. 6, p. 1333-1336, 1996/01/01 1996.
#' ISSN 0021-9568. (\doi{10.1021/je960075b})
#'
#' CHEN, Y. et al. Liquid-liquid equilibria of aqueous biphasic systems
#' composed of 1-butyl-3-methyl imidazolium tetrafluoroborate+ sucrose/maltose+
#' water. Journal of Chemical & Engineering Data, v. 55, n. 9, p. 3612-3616,
#' 2010. ISSN 0021-9568. (\doi{10.1021/je100212p})
#
# XUEQIAO, X. et al. Measurement and Correlation of the Phase Diagram Data for
# PPG400 + (K3PO4, K2CO3, and K2HPO4) + H2O Aqueous Two-Phase Systems at
# T = 298.15 K. Journal of Chemical & Engineering Data, v. 55, n. 11,
# p. 4741-4745, 2010/11/11 2010. ISSN 0021-9568.
# (\href{https://pubs.acs.org/doi/full/10.1021/je100356s?src=recsys}
# {ACS Publications})
#
# XIE, X. et al. Liquidb-liquid equilibrium of aqueous two-phase systems of
# PPG400 and biodegradable salts at temperatures of (298.15, 308.15, and 318.15)
# K. Journal of Chemical & Engineering Data, v. 55, n. 8, p. 2857-2861, 2010.
# ISSN 0021-9568.
# (\href{https://pubs.acs.org/doi/abs/10.1021/je901019t}{ACS Publications})
AQSys.default <- function(dataSET, modelName = "merchuk", Order="xy", ...) {
# arrange data and guarantee R converted it to numbers but dont switch
# columns to prevent incompatibility with pre-existent functions
dataSET <- toNumeric(dataSET, Order)
# each switch option calls a correspondent equation to fit dataSET
# equations are functions declared in AQSysFormulas.R
if (modelName %in% names(AQSysList(TRUE))) {
ans <- do.call(modelName, list(dataSET))
} else{
AQSys.err("0")
}
# return fitting parameters ans statistical data
return(ans)
}
#
###############################################################################
#' @rdname AQSys.data
#' @title Dataset and Fitted Function plot
#' @description The function returns a plot after fitting a dataset to the
#' mathematical descriptor chosen by the user.
#' @details This version uses the plot function and return a regular orthogonal
#' plot.
#' @method AQSys data
#' @export AQSys.data
#' @export
#'
#' @param dataSET - Binodal Experimental data that will be used in the nonlinear
#' fit. It might hold multiple systems stacked side-by-side. [type:data.frame]
#' @param modelName - Character String specifying the nonlinear empirical
#' equation to fit data. [type:String]
#' The default method uses Merchuk's equation. Other mathematical descriptors
#' can be listed using AQSysList().
#' @param Order Defines how the data is organized in the Worksheet. Use "xy"
#' whether the first column corresponds to the lower phase fraction and "yx"
#' whether the opposite. [type:String]
#' @param xmax Maximum value for the Horizontal axis'
#' value - optional [type:double]
#' @param ymax Maximum value for the Vertical axis'
#' value - optional [type:double]
#' @param ... Additional optional arguments. None are used at present.
#' @return return a data.frame with data fitted using the chosen mathematical
#' descriptor.
#' @examples
#' # Populating variable dataSET with binodal data
#' dataSET <- peg4kslt[ , 1:2]
#' # Fitting dataSET using Merchuk's function
#' data <- AQSys.data(dataSET, Order = "xy")
AQSys.data <- function(dataSET,
modelName = "merchuk",
Order = "xy",
xmax = "",
ymax = "",
...
) {
# guarantee all lines are valid (non-na and numeric)
dataSET <- toNumeric(dataSET, Order)
# Calculate aesthetically better xmax and ymax
if ((xmax == "") |
((xmax > 1) &
(max(dataSET[1]) <= 1)) |
((xmax > 100) &
(max(dataSET[1]) <= 100) &
(max(dataSET[1]) >= 10)) |
(xmax < round(max(dataSET[1]) / 0.92, 1))) {
xmax <- ceiling(round(max(dataSET[1]) / 0.92, 1)/5)*5
}
if ((ymax == "") |
((ymax > 1) &
(max(dataSET[2]) <= 1)) |
((ymax > 100) &
(max(dataSET[2]) <= 100) &
(max(dataSET[2]) >= 1)) |
(ymax < round(max(dataSET[2]) / 0.92, 1))) {
ymax <- ceiling(round(max(dataSET[2]) / 0.92, 1)/5)*5
}
# Select which model will be used to generate the plot. Function return list
# of plots and respective number of parameters
models_npars <- AQSysList(TRUE)
# choose model based in the user choice or standard value
Fn <- ifelse(modelName %in% names(models_npars),
AQSys.mathDesc(modelName), AQSys.err("0"))
# calculate coefficients using the non-linear regression
CoefSET <- summary(AQSys(dataSET, modelName))$coefficients[, 1]
#
Xs <- as.data.frame(ifelse((xmax != max(dataSET[1])),
rbind(dataSET[1], xmax), dataSET[1]))
rawdt <- setNames(data.frame(Xs, Fn(CoefSET, Xs)), c("XC", "YC"))
#
return(rawdt)
}
###############################################################################
#' @rdname AQSys.plot
#' @title Dataset and Fitted Function plot
#' @description The function returns a plot after fitting a dataset to the
#' mathematical descriptor chosen by the user.
#' @details This version uses the plot function and return a regular orthogonal
#' plot.
#' @method AQSys plot
#' @export AQSys.plot
#' @export
#' @param dataSET - Binodal Experimental data that will be used in the nonlinear
#' fit. It might hold multiple systems stacked side-by-side. [type:data.frame]
#' @param xlbl Plot's Horizontal axis label.
#' @param ylbl Plot's Vertical axis label.
#' @param main Legacy from plot package. For more details,
#' see \code{\link{plot.default}}
#' @param col Legacy from plot package. For more details,
#' see \code{\link{plot.default}}
#' @param type Legacy from plot package. For more details,
#' see \code{\link{plot.default}}
#' @param cex Legacy from plot package. For more details,
#' see \code{\link{plot.default}}
#' @param cexlab Legacy from plot package. For more details,
#' see \code{\link{plot.default}}
#' @param cexaxis Legacy from plot package. For more details,
#' see \code{\link{plot.default}}
#' @param cexmain Legacy from plot package. For more details,
#' see \code{\link{plot.default}}
#' @param cexsub Legacy from plot package. For more details,
#' see \code{\link{plot.default}}
#' @param modelName - Character String specifying the nonlinear empirical
#' equation to fit data. The default method uses
#' Merchuk's equation. Other possibilities can be seen in AQSysList().
#'
#' @param NP Number of points used to build the fitted curve.
#' Default is 100. [type:Integer]
#' @param xmax Maximum value for the Horizontal axis' value
#' @param ymax Maximum value for the Vertical axis' value
#' @param Order Defines how the data is organized in the Worksheet.
#' Use "xy" whether the first column corresponds to the lower phase fraction
#' and "yx" whether the opposite.
#' @param save Save the generated plot in the disk using path and filename
#' provided by the user. [type:Boulean]
#' @param HR Adjust Plot's text to be compatible with High Resolution
#' size [type:Boulean]
#' @param filename Filename provided by the user to save a given
#' plot. [type:String]
#' @param wdir The directory in which the plot file will be
#' saved. [type:String]
#' @param silent save plot file without actually showing it to the
#' user. [type:Boulean]
#' @param ... Additional optional arguments. None are used at present.
#'
#' @return A plot containing the experimental data, the correspondent curve for
#' the binodal in study and the curve's raw XY data.
#' @examples
#' #Populating variable dataSET with binodal data
#' dataSET <- peg4kslt[, 1:2]
#' # Plot dataSET using Merchuk's function
#' #
#' AQSys.plot(dataSET)
#' #
AQSys.plot <- function(dataSET,
xlbl = "",
ylbl = "",
main = NULL,
col = "blue",
type = "p",
cex = 1,
cexlab = 1,
cexaxis = 1,
cexmain = 1,
cexsub = 1,
modelName = "merchuk",
NP = 100,
xmax = "",
ymax = "",
Order = "xy",
save = FALSE,
HR = FALSE,
filename = NULL,
wdir = NULL,
silent = FALSE,
...
)
{
#
plot_image = NULL
# verify and adjust data.frame names
if (xlbl == "") {
xlbl <- names(dataSET)[1]
}
if (ylbl == "") {
ylbl <- names(dataSET)[2]
}
# guarantee all lines are valid (non-na and numeric)
dataSET <- toNumeric(dataSET, Order)
# Calculate aesthetically better xmax and ymax
if ((xmax == "") |
((xmax > 1) &
(max(dataSET[1]) <= 1)) |
((xmax > 100) &
(max(dataSET[1]) <= 100) &
(max(dataSET[1]) >= 10)) |
(xmax < round(max(dataSET[1]) / 0.92, 1))) {
xmax <- ceiling(round(max(dataSET[1]) / 0.92, 1)/5)*5
}
if ((ymax == "") |
((ymax > 1) &
(max(dataSET[2]) <= 1)) |
((ymax > 100) &
(max(dataSET[2]) <= 100) &
(max(dataSET[2]) >= 1)) |
(ymax < round(max(dataSET[2]) / 0.92, 1))) {
ymax <- ceiling(round(max(dataSET[2]) / 0.92, 1)/5)*5
}
# If save=TRUE adjust variables and parameters to save plot
wdir <- saveConfig(save, HR, filename, wdir, silent)
# Select which model will be used to generate the plot. Function return
# list of plots and respective number of parameters
models_npars <- AQSysList(TRUE)
# choose model based in the user choice or standard value
Fn <- ifelse(modelName %in% names(models_npars), AQSys.mathDesc(modelName),
AQSys.err("0"))
# calculate coefficients using the non-linear regression
CoefSET <- summary(AQSys(dataSET, modelName))$coefficients[, 1]
# plot phase diagram using experimental data and with previously calculated
# parameters
plot_image <- ggplot(data = dataSET, aes_string(x = "XC", y = "YC")) +
geom_point(shape = 8, size = 2) +
theme_light() + xlab(paste(xlbl, "(%, m/m)")) +
ylab(paste(ylbl, "(%, m/m)")) +
theme(
validate = FALSE,
plot.margin = unit(c(1, 1, 1, 1), "cm"),
text = element_text(size = 16),
legend.position = "top",
axis.title.y = element_text(vjust = 5),
axis.title.x = element_text(vjust = -2),
panel.grid.major = element_line(size = .70, colour = "black"),
panel.grid.minor = element_line(size = .70),
panel.border = element_rect(size = .5, colour = "white"),
axis.text.x = element_text(size = 15),
axis.text.y = element_text(size = 15),
axis.line = element_line(colour = 'black', size = 1.25),
legend.title = element_text(
colour = "black",
size = 12,
face = "bold",
angle = 0
),
legend.text = element_text(
colour = "black",
size = 12,
face = "plain"
)
) +
scale_y_continuous(
expand = c(0, 0),
limits = c(-0.5, ymax),
breaks = seq(0, ymax, by = 5),
labels = seq(0, ymax, by = 5)
) +
scale_x_continuous(
expand = c(0, 0),
limits = c(0, xmax),
breaks = seq(0, ymax, by = xmax / 10),
labels = seq(0, ymax, by = xmax / 10)
)
#
# add curve generated using regression parameters
Xs <- as.data.frame(ifelse((xmax != max(dataSET[1])),
rbind(dataSET[1], xmax), dataSET[1]))
rawdt <- setNames(data.frame(Xs, Fn(CoefSET, Xs)), c("XC", "YC"))
#
plot_image <-
plot_image + geom_line(
data = rawdt,
aes_string(x = "XC", y = "YC"),
color = "red",
linetype = "solid",
size = 1
)
#
if (save == TRUE) {
ggsave(
filename = wdir,
plot = plot_image,
width = 21.14 / 2,
height = 14.39 / 2
)
}
# make available data from fitted curve to user. Function returns it
# silently but user can get data using simple assign '<-'
if (silent == FALSE) {
print(plot_image)
invisible(rawdt)
} else {
invisible(plot_image)
}
}
###############################################################################
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.