diff --git a/.Rbuildignore b/.Rbuildignore
new file mode 100644
index 0000000..91114bf
--- /dev/null
+++ b/.Rbuildignore
@@ -0,0 +1,2 @@
+^.*\.Rproj$
+^\.Rproj\.user$
diff --git a/DESCRIPTION b/DESCRIPTION
index 84dd5fe..0a8f29d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,13 +1,21 @@
Package: arbintools
Title: Matt Lacey's Arbin Importing and Plotting Functions
-Version: 0.0.0.9000
-Authors@R: person("Matt", "Lacey", email = "matthew.lacey@kemi.uu.se", role = c("aut", "cre"))
+Version: 0.1.0
+Authors@R:
+ c(person(given = "Matt",
+ family = "Lacey",
+ role = c("aut", "cre"),
+ email = "matthew.lacey@kemi.uu.se"),
+ person(given = "Jim",
+ family = "Benson",
+ role = "ctb",
+ email = "james.benson@gatech.edu"))
Description: A set of functions to handle importation and common plotting tasks for data obtained with Arbin battery cycling instruments using the MITS Pro software.
Depends:
R (>= 3.2.0)
License: CC0
LazyData: true
-RoxygenNote: 5.0.1
+RoxygenNote: 6.0.1
Imports: dplyr,
ggplot2,
reshape2,
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000..9cecc1d
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,674 @@
+ GNU GENERAL PUBLIC LICENSE
+ Version 3, 29 June 2007
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+APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+ 16. Limitation of Liability.
+
+ IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+ 17. Interpretation of Sections 15 and 16.
+
+ If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+ END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+ {one line to give the program's name and a brief idea of what it does.}
+ Copyright (C) {year} {name of author}
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ 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.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see .
+
+Also add information on how to contact you by electronic and paper mail.
+
+ If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+ {project} Copyright (C) {year} {fullname}
+ This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License. Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+ You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+.
+
+ The GNU General Public License does not permit incorporating your program
+into proprietary programs. If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library. If this is what you want to do, use the GNU Lesser General
+Public License instead of this License. But first, please read
+.
diff --git a/NAMESPACE b/NAMESPACE
index 8423ad4..a6808c5 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,7 +1,13 @@
# Generated by roxygen2: do not edit by hand
export(arbin_Qplot)
+export(arbin_dQdV)
+export(arbin_dQdV_multi)
export(arbin_import)
+export(arbin_import_folder)
+export(arbin_import_folder_check)
export(arbin_import_raw)
export(arbin_plotvp)
+export(arbin_plotvp_multi)
export(arbin_quickplot)
+export(multiplot)
diff --git a/R/import_functions.R b/R/import_functions.R
index ecef310..b8772f3 100644
--- a/R/import_functions.R
+++ b/R/import_functions.R
@@ -1,7 +1,7 @@
### Importing functions
#' arbin_import
-#'
+#'
#' This function takes an exported data file in Microsoft Excel format,
#' discards or includes certain data depending on the options chosen in the function,
#' and returns a list of two data frames: the complete raw data and an aggregated
@@ -12,64 +12,59 @@
#' @param energy Defaults to TRUE. Includes the (dis)charge energy variables from the data file if TRUE.
#' @param cycles Defaults to 100. Determines the maximum number of cycles to be considered when
#' aggregating the statistics dataset.
-#' @param mass Defaults to NULL. If an active material mass is specified - in MILLIGRAMS - the
-#' capacities in the raw and statistics data frames will be converted to mAh/g.
+#' @param mass Defaults to NULL. If an active material mass is specified - in MILLIGRAMS, mg - it is stored
+#' in the norm parameter for normalization options during plotting.
+#' @param area Defaults to NULL. If an electrode area is specified - in SQUARE CENTIMETERS, cm^2 - it is stored
+#' in the norm parameter for normalization options during plotting.
+#' @param vol Defaults to NULL. If an active material volume is specified - in CUBIC CENTIMETERS, cm^3 - it is stored
+#' in the norm parameter for normalization options during plotting.
#' @param meanE Defaults to FALSE. Will calculate a statistic for average charge and discharge voltage
#' if set to TRUE.
#' @keywords
#' @export
-#' @examples
+#' @examples
#' mydataset <- arbin_import("dataset.xlsx")
-#' mydataset <- arbin_import("dataset.xlsx", step.time = FALSE, cycles = 200, mass = 2.55)
+#' mydataset <- arbin_import("dataset.xlsx", step.time = FALSE, cycles = 200, mass = 2.55, area=1.267)
+#' Batch import of multiple cells from list, useful for Qplot, plotvp_multi, dQdV_multi, etc.
+#' l=lapply(1:length(cellfile),function(x) arbinimport(cellfile[x],cycles=100,mass=mass[x]))
-arbin_import <- function(file, step.time = TRUE, energy = TRUE, cycles = 100, mass = NULL, meanE = FALSE) {
-
+arbin_import<-function (file, step.time = TRUE, energy = TRUE, cycles = 100, mass = NULL, area = NULL ,
+ vol = NULL, meanE = FALSE)
+ {
require(readxl)
-
- # All the "Channel*" sheets are read in. This function needs the readxl package.
- l <- lapply(grep("Channel*", excel_sheets(file), value = TRUE),
+
+ # All the "Channel*" sheets are read in, excludes plot sheets. This function needs the readxl package.
+ l <- lapply(grep("Channel_\\d", excel_sheets(file), value = TRUE),
read_excel, path = file)
-
+
# The list from the previous step is unlisted into a single data frame
l <- do.call(rbind, l)
-
+
# A new data frame for raw data is created using selected parts of the data.
x <- data.frame(t = l$`Test_Time(s)`, # time (s)
step.n = l$Step_Index, # step number
cyc.n = l$Cycle_Index, # cycle number
I = l$`Current(A)`, # current (A)
E = l$`Voltage(V)`, # voltage (E)
- Q.c = l$`Charge_Capacity(Ah)`, # charge capacity (Ah)
+ Q.c = l$`Charge_Capacity(Ah)`, # charge capacity (Ah)
Q.d = l$`Discharge_Capacity(Ah)` # discharge capacity (Ah)
)
-
+
# Step time is included if specified.
if(step.time == TRUE) {
x$step.t <- l$`Step_Time(s)` # step time (s)
}
-
+
# (Dis)charge energy is included if specified.
if(energy == TRUE) {
x$En.d <- l$`Discharge_Energy(Wh)` # discharge energy (Wh)
x$En.c <- l$`Charge_Energy(Wh)` # charge energy (Wh)
}
-
- # Capacities are converted to mAh/g if active mass is specified.
- if(!is.null(mass) == TRUE) {
- x$Q.c <- x$Q.c * (1E6/mass)
- x$Q.d <- x$Q.d * (1E6/mass)
- }
-
- # Energies, if present, are converted to Wh/kg if active mass is specified.
- if(!is.null(mass) == TRUE & energy == TRUE) {
- x$En.d <- x$En.d * (1E6/mass)
- x$En.c <- x$En.c * (1E6/mass)
- }
-
+
# Number of cycles to be included defaults to 100. In any case, the data is checked
# and incomplete last cycles are discarded.
cycles <- ifelse(max(x$cyc.n >= cycles), cycles, max(x$cyc.n) - 1)
-
+
# Data frame of aggregated statistics is constructed.
stats <- data.frame(
cyc.n = c(1:cycles),
@@ -77,26 +72,28 @@ arbin_import <- function(file, step.time = TRUE, energy = TRUE, cycles = 100, ma
Q.d = sapply(c(1:cycles), function(i) tail(x$Q.d[x$cyc.n == i], 1)),
CE = sapply(c(1:cycles), function(i) tail(x$Q.d[x$cyc.n == i], 1) / tail(x$Q.c[x$cyc.n == i], 1))
)
-
+
# Energy is included if specified.
if(energy == TRUE) {
stats$EE <- sapply(c(1:cycles), function(i) tail(x$En.d[x$cyc.n == i], 1) / tail(x$En.c[x$cyc.n == i], 1))
}
-
+
# Mean voltages are included if specified.
if(meanE == TRUE) {
stats$meanE.d <- sapply(c(1:cycles), function(i) mean(x$E[x$cyc.n == i & x$I < 0], 1))
stats$meanE.c <- sapply(c(1:cycles), function(i) mean(x$E[x$cyc.n == i & x$I > 0], 1))
}
-
- # Raw and statistics data frames are returned as a list.
- out <- list(raw = x, stats = stats)
+#Save information for normalization into list.
+#Allows plotting functions to perform normalization as needed instead of at import.
+ norm<-list(mass=mass, area=area, vol=vol)
+ # Raw, statistics, and normalization data frames are returned as a list.
+ out <- list(raw = x, stats = stats, norm = norm)
return(out)
}
#' arbin_import_raw
-#'
+#'
#' This function is a simplified version of arbin_import which does not output a separate
#' statistics data frame. Consequently the output is a data frame rather than a list.
#' @param file The filename, which must end in .xls or .xlsx.
@@ -106,48 +103,118 @@ arbin_import <- function(file, step.time = TRUE, energy = TRUE, cycles = 100, ma
#' capacities in the raw and statistics data frames will be converted to mAh/g.
#' @keywords
#' @export
-#' @examples
+#' @examples
#' mydataset <- arbin_import("dataset.xlsx")
#' mydataset <- arbin_import("dataset.xlsx", step.time = FALSE)
-arbin_import_raw <- function(file, step.time = TRUE, energy = TRUE, mass = NULL) {
-
+arbin_import_raw <- function(file, step.time = TRUE, energy = TRUE, mass = NULL, area = NULL , vol = NULL) {
+
require(readxl, quietly = TRUE)
-
- l <- lapply(grep("Channel*", excel_sheets(file), value = TRUE),
+
+ l <- lapply(grep("Channel_\\d", excel_sheets(file), value = TRUE),
read_excel, path = file)
-
+
l <- do.call(rbind, l)
-
+
x <- data.frame(t = l$`Test_Time(s)`, # time (s)
step.n = l$Step_Index, # step number
cyc.n = l$Cycle_Index, # cycle number
I = l$`Current(A)`, # current (A)
E = l$`Voltage(V)`, # voltage (E)
- Q.c = l$`Charge_Capacity(Ah)`, # charge capacity (Ah)
+ Q.c = l$`Charge_Capacity(Ah)`, # charge capacity (Ah)
Q.d = l$`Discharge_Capacity(Ah)` # discharge capacity (Ah)
)
-
+
if(step.time == TRUE) {
x$step.t <- l$`Step_Time(s)` # step time (s)
}
-
+
if(energy == TRUE) {
x$En.d <- l$`Discharge_Energy(Wh)` # discharge energy (Wh)
x$En.c <- l$`Charge_Energy(Wh)` # charge energy (Wh)
}
-
+ # if active mass is specified.=========================================
# Capacities are converted to mAh/g if active mass is specified.
if(!is.null(mass) == TRUE) {
x$Q.c <- x$Q.c * (1E6/mass)
x$Q.d <- x$Q.d * (1E6/mass)
}
-
- # Energies, if present, are converted to Wh/kg if active mass is specified.
+
+ # Energies, if present, are converted to Wh/kg
if(!is.null(mass) == TRUE & energy == TRUE) {
x$En.d <- x$En.d * (1E6/mass)
x$En.c <- x$En.c * (1E6/mass)
}
-
+ # if area is specified.=========================================
+ # Capacities are converted to mAh/cm^2
+ if(!is.null(area) == TRUE) {
+ x$Q.c <- x$Q.c * (1/area)
+ x$Q.d <- x$Q.d * (1/area)
+ }
+ # Energies, if present, are converted to Wh/cm^2
+ if(!is.null(area) == TRUE & energy == TRUE) {
+ x$En.d <- x$En.d * (1/area)
+ x$En.c <- x$En.c * (1/area)
+ }
+ # if volume is specified.=========================================
+ # Capacities are converted to mAh/cm^3
+ if(!is.null(vol) == TRUE) {
+ x$Q.c <- x$Q.c * (1E3/vol)
+ x$Q.d <- x$Q.d * (1E3/vol)
+ }
+ # Energies, if present, are converted to Wh/cm^3
+ if(!is.null(vol) == TRUE & energy == TRUE) {
+ x$En.d <- x$En.d * (1/vol)
+ x$En.c <- x$En.c * (1/vol)
+ }
+
return(x)
-}
\ No newline at end of file
+}
+#' arbin_import_folder
+#'
+#' This function is a simplified version of arbin_import which does not output a separate
+#' statistics data frame. Consequently the output is a data frame rather than a list.
+#' @param path The folder path, which must include .xls or .xlsx files produced by the arbin.
+#' @param mass Defaults to NULL. A vector including the active masses (in MILLIGRAMS, mg) of all cells in the folder being imported.
+#' Use arbin_import_folder_check to ensure correct order.
+#' @param area Defaults to NULL. A vector including the area (in SQUARE CENTIMETERS, cm^2) of all cells in the folder being imported.
+#' Use arbin_import_folder_check to ensure correct order.
+#' @param vol Defaults to Null. A vector including the volume (in cubic CENTIMETERS, cm^3) of all cells in the folder being imported.
+#' Use arbin_import_folder_check to ensure correct order.
+#' @keywords
+#' @export
+#' @examples
+#' mydataset <- arbin_import_folder(path)
+#' mydataset <- arbin_import_folder()
+arbin_import_folder <- function(path=".",mass=NULL, area=NULL, vol=NULL)
+{
+ initfolder<-getwd()
+ setwd(path)
+ #collect the names of all of the xls,xlsx files in a folder
+ f<-list.files(path=path,pattern="(?i).xls")
+ #Import all the files using arbin import
+ l=lapply(1:length(f),function(x) arbin_import(f[x],mass=mass[x],area=area[x],vol=vol[x]))
+ setwd(initfolder)
+ return(l)
+
+}
+
+#' arbin_import_folder_check
+#'
+#' This function is a simplified version of arbin_import which does not output a separate
+#' statistics data frame. Consequently the output is a data frame rather than a list.
+#' @param path The folder path containing only data files from the arbin, which must end in .xls or .xlsx.
+#' @keywords
+#' @export
+#' @examples
+#' mydataset <- arbin_import_folder(path)
+#' mydataset <- arbin_import_folder()
+arbin_import_folder_check <- function(path=".")
+{
+ initfolder<-getwd()
+ setwd(path)
+ #collect the names of all of the xls,xlsx files in a folder
+ f<-list.files(path=path,pattern="(?i).xls")
+ setwd(initfolder)
+ return(f)
+}
diff --git a/R/plotting_functions.R b/R/plotting_functions.R
index fb27804..480c5bb 100644
--- a/R/plotting_functions.R
+++ b/R/plotting_functions.R
@@ -1,65 +1,152 @@
-### Plotting functions. The plotting functions here include arbin_quickplot,
+### Plotting functions. The plotting functions here include: arbin_quickplot,
### for quickly plotting any x or y variable; arbin_plotvp, for plotting voltage
-### profiles, and arbin_qplot, for plotting capacity vs cycle number with
-### multiple datasets.
+### vs capacity profiles of one or more cycles of one cell; arbin_qplot, for plotting
+### capacity vs cycle number with multiple datasets;arbin_dQdV, for plotting
+### differential capacity plot of one or multiple cycles of one cell;arbin_dQdV_multi,
+### for plotting differential capacity plot of multiple cells at one cycle number.
#' arbin_quickplot
-#'
+#'
#' This function takes a data frame of either raw data or aggregated statistics,
#' any argument for x or y-axis plotting, and returns a ggplot with the desired
#' formatting and axis labels. Can also do things such as subsetting data with
#' dplyr.
-#' @param data The dataset, which must be a dataframe.
+#' @param data The dataset, which must be a list generated by arbinimport.
#' @param x The variable to be plotted on the x-axis
#' @param y The variable to be plotted on the y-axis
+#' @param norm character string used to select how to normalize your data: "mass", "area", "vol".
+#' @param title Character vector to use for the title of the plot. Defaults to NULL.
#' @param geom The geom to be passed to ggplot; e.g. geom_point or geom_path
-#' @param size The size of the geom.
+#' @param size The size of the geom. Default size =4.
#' @keywords
#' @export
-#' @examples
-#' arbin_quickplot(mydataset$raw, x = t, y = E)
-#' arbin_quickplot(filter(mydataset$raw, cyc.n == 1, x = t, y = E, geom = geom_path, size = 1)
-#' arbin_quickplot(mydataset$stat, x = cyc.n, y = d.Q)
+#' @examples
+#' arbin_quickplot(list, x = "t", y = "E")
+#' arbin_quickplot(list, x = "t", y = "E", norm="mass", geom = geom_path, size = 1)
+#' arbin_quickplot(list, x = "cyc.n", y = "Q.d" , norm="area")
-arbin_quickplot <- function(data, x, y, geom = geom_point, size = 4) {
-
+arbin_quickplot<- function (l, x="cyc.n", y="Q.d", norm=NULL, title=NULL, geom = geom_point, size = 4) {
require(ggplot2)
require(scales)
require(grid)
require(dplyr)
-
- # the x and y arguments are converted to strings so that they can
- # be evaluated correctly by ggplot using aes_string().
- x <- deparse(substitute(x))
- y <- deparse(substitute(y))
-
+
+ #decide whether we need raw or stats to pull from l
+ #If x axis is time, or capacity need to pull raw data
+ if (x=="t" | x=="Q.d" |x=="Q.c"){
+ data<-l$raw
+ }
+ #If x axis is cycle pull stats
+ if (x=="cyc.n"){
+ data<-l$stats
+ }
+
+ #Set units depending on normalization desired============================
# labels is a list of labels with the element names corresponding to
# variable names present in the data files. When plotting, a correctly
# formatted axis label is selected from the list.
- labels <- list(
- t = "time / s",
- step.n = "step number",
- cyc.n = "cycle number",
- I = "I / A",
- E = "cell voltage / V",
- Q.c = "charge capacity / mAh g"^-1~"",
- Q.d = "discharge capacity / mAh g"^-1~"",
- step.t = "step time / s",
- En.d = "discharge energy / Wh kg"^-1~"",
- En.c = "charge energy / Wh kg"^-1~"",
- CE = expression("Q"[d] * " / Q"[c]),
- EE = expression("energy efficiency, E"[d] * " / E"[c]),
- meanE.d = "mean discharge voltage / V",
- meanE.c = "mean charge voltage / V"
- )
-
+
+ #set units for no normalization========================================
+ labels<-NULL
+ if (is.null(norm)){
+ labels <- list(
+ t = "time / s",
+ step.n = "step number",
+ cyc.n = "cycle number",
+ I = "I / A",
+ E = "cell voltage / V",
+ Q.c = "Q charge / mAh",
+ Q.d = "Q discharge / mAh",
+ step.t = "step time / s",
+ En.d = "discharge energy / Wh",
+ En.c = "charge energy / Wh",
+ CE = expression("Q"[d] * " / Q"[c]),
+ EE = expression("energy efficiency, E"[d] * " / E"[c]),
+ meanE.d = "mean discharge voltage / V",
+ meanE.c = "mean charge voltage / V")
+
+ #Do not normalize but convert units from Ah to mAh
+ data$Q.c<-data$Q.c*1e3
+ data$Q.d<-data$Q.d*1e3
+ }
+ #if normalization is used then set the proper labels
+ if (!is.null(norm))
+#set units for mass normalization
+ {if (norm=="mass" & !is.null(l$norm$mass)){
+ labels <- list(
+ t = "time / s",
+ step.n = "step number",
+ cyc.n = "cycle number",
+ I = "I / A",
+ E = "cell voltage / V",
+ Q.c = "Q charge / mAh g"^-1 ~ "",
+ Q.d = "Q discharge / mAh g"^-1 ~ "",
+ step.t = "step time / s",
+ En.d = "discharge energy / Wh kg"^-1 ~ "",
+ En.c = "charge energy / Wh kg"^-1 ~ "",
+ CE = expression("Q"[d] * " / Q"[c]),
+ EE = expression("energy efficiency, E"[d] * " / E"[c]),
+ meanE.d = "mean discharge voltage / V",
+ meanE.c = "mean charge voltage / V")
+
+#normalize by mass and convert units from Ah/mg to mAh/g
+ data$Q.c<-data$Q.c/l$norm$mass*1e6
+ data$Q.d<-data$Q.d/l$norm$mass*1e6
+ }
+ #set units for area normalization
+ if (norm=="area" & !is.null(l$norm$area)){
+ labels <- list(
+ t = "time / s",
+ step.n = "step number",
+ cyc.n = "cycle number",
+ I = "I / A",
+ E = "cell voltage / V",
+ Q.c = "Q charge / mAh cm"^-2 ~ "",
+ Q.d = "Q discharge / mAh cm"^-2 ~ "",
+ step.t = "step time / s",
+ En.d = "discharge energy / mWh cm"^-2 ~ "",
+ En.c = "charge energy / mWh cm"^-2 ~ "",
+ CE = expression("Q"[d] * " / Q"[c]),
+ EE = expression("energy efficiency, E"[d] * " / E"[c]),
+ meanE.d = "mean discharge voltage / V",
+ meanE.c = "mean charge voltage / V")
+
+ #normalize by area and convert units from Ah/cm^2 to mAh/cm^2
+ data$Q.c<-data$Q.c/l$norm$area*1000
+ data$Q.d<-data$Q.d/l$norm$area*1000
+ }
+ #set units for volume normalization
+ if (norm=="vol" & !is.null(l$norm$vol)){
+ labels <- list(t = "time / s",
+ step.n = "step number",
+ cyc.n = "cycle number",
+ I = "I / A",
+ E = "cell voltage / V",
+ Q.c = "Q charge / mAh cm"^-3 ~ "",
+ Q.d = "Q discharge / mAh cm"^-3 ~ "",
+ step.t = "step time / s",
+ En.d = "discharge energy / Wh cm"^-3 ~ "",
+ En.c = "charge energy / Wh cm"^-3 ~ "",
+ CE = expression("Q"[d] * " / Q"[c]),
+ EE = expression("energy efficiency, E"[d] * " / E"[c]),
+ meanE.d = "mean discharge voltage / V",
+ meanE.c = "mean charge voltage / V")
+
+ #normalize by volume and convert units from Ah/cm^3 to mAh/cm^3
+ data$Q.c<-data$Q.c/l$norm$vol*1000
+ data$Q.d<-data$Q.d/l$norm$vol*1000
+ }
+ }
+ #Provide error message if no normalization information is available for the value the user wants.
+if (is.null(labels)){
+ stop("This cell does not have the required normalization information. Please check that it was input correctly during import.")
+}
# Basic plot setup. ================================================
- p <- ggplot(data) +
- geom(aes_string(x = x, y = y), size = size)
-
+ p <- ggplot(data) + geom(aes_string(x = x, y = y), size = size)
+
# Labels looked up from the list of labels. ========================
- p <- p + xlab(labels[[x]]) + ylab(labels[[y]])
-
+ p <- p + xlab(labels[[x]]) + ylab(labels[[y]])+labs(title=title)
+
# If scales and grid are installed, then a custom theme is added.
# This does not seem to work as I thought so it's cut out for now, and scales
# and grid are required packages.
@@ -71,43 +158,46 @@ arbin_quickplot <- function(data, x, y, geom = geom_point, size = 4) {
theme(axis.text.x = element_text(margin = margin(0.5, 0, 0.2, 0, "cm"))) +
theme(axis.text.y = element_text(margin = margin(0, 0.5, 0, 0.2, "cm"))) +
theme(panel.grid.major = element_line(size=0.5))
-
+
# If the y-axis shows capacity, the plot is rescaled from 0 to max capacity.
# Also requires the scales package.
if(y %in% c("Q.c", "Q.d")) {
p <- p + scale_y_continuous(limits=c(0, max(data[y])))
}
-
+
# }
-
+
return(p)
-
+
}
#' arbin_plotvp
-#'
+#'
#' This function takes a data frame of raw data and a specified cycle - or number
#' of cycles, as a vector - and outputs charge and discharge voltage profiles.
-#' @param data The dataset, which can be the list as outputted by arbin_import or the data
-#' frame as arbin_import_raw.
-#' @param cycles The cycles to be plotted, expressed as a vector
+#' @param data The dataset, which is the list as output by arbin_import.
+#' @param cycles The cycles to be plotted, expressed as a vector. Defaults to cycle = 1.
+#' @param norm character string used to select how to normalize your data: "mass", "area", "vol". Deaults to Null which plots absolute capacity.
+#' @param title Character vector to use for the title of the plot. Defaults to NULL.
#' @keywords
#' @export
-#' @examples
-#' arbin_plotvp(mydataset, 1)
-#' arbin_plotvp(mydataset, cycles = c(1,5,10))
+#' @examples
+#' arbin_plotvp(mydataset, cycles=1)
+#' arbin_plotvp(mydataset, cycles = c(1,5,10), norm="mass")
+
+arbin_plotvp <- function(data, cycles=1, norm=NULL, title=NULL) {
-arbin_plotvp <- function(data, cycles) {
-
require(ggplot2)
require(scales)
require(grid)
require(dplyr)
-
+
# Data for the specified cycles is filtered off (uses filter() from
# the dplyr package.) Checks first what format the data is in. If it sees
# a list it assumes it should use the 'raw' data frame.
+
+ #Filter the data to remove I=0 data points and extra cycles.
if (class(data) == "list") {
plotted.data <- filter(data$raw, cyc.n %in% cycles, I != 0)
} else if (class(data) == "data.frame") {
@@ -116,12 +206,12 @@ arbin_plotvp <- function(data, cycles) {
stop("Data doesn't seem to be in a recognisable format! Was it imported with
the arbin_import functions?")
}
-
+
# The function tries to guess whether the discharge or charge
# step is first in the cycle. This affects correct plotting.
for (i in unique(plotted.data$step.n)) {
testI <- mean(plotted.data$I[plotted.data$step.n == i])
-
+
if (testI == 0) {
} else if (testI < 0) {
plotted.data$Q.d[plotted.data$Q.c != 0] <- NA
@@ -133,15 +223,64 @@ arbin_plotvp <- function(data, cycles) {
break
}
}
-
+
+ #Normalize capacity data=========================================
+ #normalize capacity data according to desired norm variable for each cell.
+ if (is.null(norm)){
+ plotted.data$Q.d<-plotted.data$Q.d*1e3
+ plotted.data$Q.c<-plotted.data$Q.c*1e3
+ }
+ if (!is.null(norm))
+ {
+ #Perform mass normalization
+ if (norm=="mass" & !is.null(data$norm$mass)){
+ plotted.data$Q.d<-plotted.data$Q.d/data$norm$mass*1e6
+ plotted.data$Q.c<-plotted.data$Q.c/data$norm$mass*1e6
+ }
+ #Perform area normalization
+ if (norm=="area" & !is.null(data$norm$area)){
+ plotted.data$Q.d<-plotted.data$Q.d/data$norm$area*1e3
+ plotted.data$Q.c<-plotted.data$Q.c/data$norm$area*1e3
+ }
+ #Perform volume normalization
+ if (norm=="vol" & !is.null(data$norm$vol)){
+ plotted.data$Q.d<-plotted.data$Q.d/data$norm$vol*1e3
+ plotted.data$Q.c<-plotted.data$Q.c/data$norm$vol*1e3
+ }
+ }
+
+ #Set axis lables for each normalization case========================
+ normunits<-NULL
+ #set units for no normalization
+ if (is.null(norm)){
+ normunits <- xlab(expression("Capacity" * " / mAh"))
+ }
+ if (!is.null(norm))
+ #set units for mass normalization
+ {if (norm=="mass" & !is.null(data$norm$mass)){
+ normunits <- xlab(expression("Specific Capacity" * " / mAh g"^-1 ~ ""))
+ }
+ #set units for area normalization
+ if (norm=="area" & !is.null(data$norm$area)){
+ normunits <- xlab(expression("Areal Capacity" * " / mAh cm"^-2 ~ ""))
+ }
+ #set units for volume normalization
+ if (norm=="vol" & !is.null(data$norm$vol)){
+ normunits <- xlab(expression("Volumetric Capacity" * " / mAh cm"^-3 ~ ""))
+ }
+ }
+
+ if (is.null(normunits)){
+ stop("This cell does not have the required normalization information. Please check that it was input correctly during import.")
+ }
+
# Basic plot setup. =============================================
p <- ggplot(plotted.data) +
geom_path(aes(x = Q.d, y = E, color = factor(cyc.n), group = factor(cyc.n)), size = 1) +
geom_path(aes(x = Q.c, y = E, color = factor(cyc.n), group = factor(cyc.n)), size = 1) +
- xlab("Q / mAh g"^-1~"") +
- ylab("cell voltage / V") +
+ normunits + ylab("Cell Voltage / V") + labs(title=title)+
guides(color = guide_legend(title = "cycle"))
-
+
# If scales and grid are installed, then a custom theme is added.
# This does not seem to work as I thought so it's cut out for now, and scales
# and grid are required packages.
@@ -154,56 +293,216 @@ arbin_plotvp <- function(data, cycles) {
theme(axis.text.y = element_text(margin = margin(0, 0.5, 0, 0.2, "cm"))) +
theme(panel.grid.major = element_line(size=0.5))
# }
-
+
return(p)
-
+
}
+#' arbin_plotvp_multi
+#'
+#' Plot voltage vs capacity for multiple cells at one cycle. Used for rate capability
+#' comparison and polarization comparison of multiple cells.
+#'
+#' @param list list containing list of data from multiple cells generated by arbinimport.
+#' @param labels character vector containing the text to use for the plot legend. Must be as long as the number of cells being plotted
+#' @param cycle The number of the cycle that is desired to be plotted. Default is cycle =1.
+#' @param norm character string used to select how to normalize your data: "mass", "area", "vol". Defaults to Null.
+#' @export
+#' @examples
+#' arbin_plotvp_multi(l1[1:3],c("test","test2","test3"),cycle=5)
+arbin_plotvp_multi<-function (list, labels, cycle=1, norm=NULL)
+{
+ require(ggplot2)
+ require(scales)
+ require(grid)
+ require(dplyr)
+ if (length(list) != length(labels)) {
+ stop("Problem... it doesn't seem you've specified the same number of datasets as labels.")
+ }
+
+ #remove the statistics sublist, keep raw data for Q vs V plot
+ stats <- lapply(list, function(x) x[[1]])
+
+ #Step through each cell. Clean data for better plotting. Normalize data.
+ stats <- lapply(seq_along(stats), function(i) {
+ #give a warning message if not enough cycles in one cell.
+ if (cycle>max(stats[[i]]$cyc.n)){
+ warning("One cell doesn't have enough cycles to be included in this comparison. It will not be shown in the plot.")
+ }
+ df <- stats[[i]]
+ #add column with label names to use for coloring plots.
+ df$ident <- labels[i]
+ #remove other cycles that you dont want.
+ df<-filter(df, cyc.n == cycle, I!=0)
+ #clean capacity data by setting to NA data that makes plots hard to read.
+ for (i in unique(df$step.n)) {
+ testI <- mean(df$I[df$step.n == i])
+ if (testI == 0) {
+ }
+ else if (testI < 0) {
+ df$Q.d[df$Q.c != 0] <- NA
+ df$Q.c[df$Q.d != 0] <- NA
+ break
+ }
+ else if (testI > 0) {
+ df$Q.c[df$Q.d != 0] <- NA
+ df$Q.d[df$Q.c != 0] <- NA
+ break
+ }
+ }
+ #normalize discharge capacity data according to desired norm variable for each cell.
+ if (is.null(norm)){
+ df$Q.d<-df$Q.d*1e3
+ df$Q.c<-df$Q.c*1e3
+ }
+ if (!is.null(norm))
+ {if (norm=="mass" & !is.null(list[[i]]$norm$mass)){
+ df$Q.d<-df$Q.d/list[[i]]$norm$mass*1e6
+ df$Q.c<-df$Q.c/list[[i]]$norm$mass*1e6
+ }
+ #set units for area normalization
+ if (norm=="area" & !is.null(list[[i]]$norm$area)){
+ df$Q.d<-df$Q.d/list[[i]]$norm$area*1e3
+ df$Q.c<-df$Q.c/list[[i]]$norm$area*1e3
+ }
+ #set units for volume normalization
+ if (norm=="vol" & !is.null(list[[i]]$norm$vol)){
+ df$Q.d<-df$Q.d/list[[i]]$norm$vol*1e3
+ df$Q.c<-df$Q.c/list[[i]]$norm$vol*1e3
+ }
+ }
+ return(df)
+ })
+ stats <- do.call(rbind, stats)
+
+ #set units for no normalization
+ normunits<-NULL
+ if (is.null(norm)){
+ normunits <- xlab(expression("Q"[discharge] * " / mAh"))
+ }
+ if (!is.null(norm))
+ #set units for mass normalization
+ {if (norm=="mass" & !is.null(list[[1]]$norm$mass)){
+ normunits <- xlab(expression("Q"[discharge] * " / mAh g"^-1 ~ ""))
+ }
+ #set units for area normalization
+ if (norm=="area" & !is.null(list[[1]]$norm$area)){
+ normunits <- xlab(expression("Q"[discharge] * " / mAh cm"^-2 ~ ""))
+ }
+ #set units for volume normalization
+ if (norm=="vol" & !is.null(list[[1]]$norm$vol)){
+ normunits <- xlab(expression("Q"[discharge] * " / mAh cm"^-3 ~ ""))
+ }
+ }
+ if (is.null(normunits)){
+ stop("This cell does not have the required normalization information. Please check that it was input correctly during import.")
+ }
+ # Basic plot setup. ==========================================================
+ p <- ggplot(stats) + geom_path(aes(x = Q.d, y = E, color = ident), size = 1)+
+ geom_path(aes(x = Q.c, y = E, color = ident, group=ident), size = 1)+
+ normunits + ylab("Voltage (V)") +
+ guides(color = guide_legend("Cells"))
+
+ # Plotting theme setup ==========================================================
+ p <- p + theme_bw() + theme(text = element_text(size = 21)) + theme(legend.position = "bottom")+
+ theme(panel.border = element_rect(size = 1, color = "black")) +
+ theme(axis.ticks.length = unit(-0.25, "cm")) +
+ theme(axis.text.x = element_text(margin = margin(0.5, 0, 0.2, 0, "cm"))) +
+ theme(axis.text.y = element_text(margin = margin(0,0.5, 0, 0.2, "cm"))) +
+ theme(panel.grid.major = element_line(size = 0.5))
+
+ # Set y axis to continuous and set limits====================================
+ p <- p + scale_y_continuous(limits = c(min(stats$E), max(stats$E)))
+ return(p)
+}
#' arbin_Qplot
-#'
+#'
#' This function takes a list of datasets, a vector of labels for those datasets and
#' returns a formatted capacity vs cycle number plot.
#' @param list A list of datasets, as exported from the arbin_import function - so each
#' list element is also a list
#' @param labels A vector of labels corresponding to the datasets in the list, in the correct order.
+#' @param norm character string used to select how to normalize your data: "mass", "area", "vol". Defaults to Null.
#' @keywords
#' @export
-#' @examples
+#' @examples
#' arbin_Qplot(list(mydatasetA, mydatasetB), labels = c("dataset A", "dataset B"))
+#' arbin_Qplot(l1[1:3],labels=c("Cell1", "Cell2","Cell3"), norm="mass")
+
+arbin_Qplot <- function(list, labels, norm=NULL) {
-arbin_Qplot <- function(list, labels) {
-
require(ggplot2)
require(scales)
require(grid)
require(dplyr)
-
+
# Check that there are the same number of datasets as labels, and stop if not.
if (length(list) != length(labels)) {
stop("Problem... it doesn't seem you've specified the same number of datasets as labels.")
}
-
+
# Pull out the statistics from the datasets. =================================
stats <- lapply(list, function(x) x[[2]])
-
+
# Attach the label to the statistics. ========================================
stats <- lapply(seq_along(stats), function(i) {
df <- stats[[i]]
+ #set ident for use in color coding the plot.
df$ident <- labels[i]
+ if (is.null(norm)){
+ #Change from Ah to mAh if no normalization required
+ df$Q.d<-df$Q.d*1e3}
+ if (!is.null(norm))
+ {#normalize discharge capacity data according to desired norm variable for each cell.
+ if (norm=="mass" & !is.null(list[[i]]$norm$mass)){
+ df$Q.d<-df$Q.d/list[[i]]$norm$mass*1e6
+ }
+ #set units for area normalization
+ if (norm=="area" & !is.null(list[[i]]$norm$area)){
+ df$Q.d<-df$Q.d/list[[i]]$norm$area*1e3
+ }
+ #set units for volume normalization
+ if (norm=="vol" & !is.null(list[[i]]$norm$vol)){
+ df$Q.d<-df$Q.d/list[[i]]$norm$vol*1e3
+ }
+ }
return(df)
})
-
+
# Bind each statistics data frame into one data frame. =======================
stats <- do.call(rbind, stats)
-
+
+ #create axis label normunits for each normalization condition.=================
+ #set units for no normalization
+ normunits<-NULL
+ if (is.null(norm)){
+ normunits <- ylab(expression("Q"[discharge] * " / mAh"))
+ }
+ if (!is.null(norm))
+ #set units for mass normalization
+ {if (norm=="mass" & !is.null(list[[1]]$norm$mass)){
+ normunits <- ylab(expression("Q"[discharge] * " / mAh g"^-1 ~ ""))
+ }
+ #set units for area normalization
+ if (norm=="area" & !is.null(list[[1]]$norm$area)){
+ normunits <- ylab(expression("Q"[discharge] * " / mAh cm"^-2 ~ ""))
+ }
+ #set units for volume normalization
+ if (norm=="vol" & !is.null(list[[1]]$norm$vol)){
+ normunits <- ylab(expression("Q"[discharge] * " / mAh cm"^-3 ~ ""))
+ }
+ }
+
# Basic plot setup. ==========================================================
+ if (is.null(normunits)){
+ stop("Data for this normalization was missing upon import.")
+ }
p <- ggplot(stats) +
- geom_point(aes(x = cyc.n, y = Q.d, color = ident), size = 4) +
- xlab("cycle number") +
- ylab(expression("Q"[discharge] * " / mAh g"^-1~"")) +
+ geom_point(aes(x = cyc.n, y = Q.d, color = ident), size = 4) +
+ xlab("cycle number") + normunits +
guides(color = guide_legend(title = ""))
-
+
# If scales and grid are installed, then a custom theme is added. y-axis is
# also rescaled.
# This does not seem to work as I thought so it's cut out for now, and scales
@@ -216,10 +515,194 @@ arbin_Qplot <- function(list, labels) {
theme(axis.text.x = element_text(margin = margin(0.5, 0, 0.2, 0, "cm"))) +
theme(axis.text.y = element_text(margin = margin(0, 0.5, 0, 0.2, "cm"))) +
theme(panel.grid.major = element_line(size=0.5))
-
+
p <- p + scale_y_continuous(limits=c(0, max(stats$Q.d)))
# }
-
+
return(p)
-
-}
\ No newline at end of file
+
+}
+
+#' arbin_dQdV
+#'
+#' Plot differential capacity plots (dQ/dV) for one cell at one cycle.
+#'
+#' @param list list of data generated from arbinimport script.
+#' @param title Character vector to use for the title of the plot. Defaults to NULL.
+#' @param cycle number of the cycle of interest, defaults to 1
+#' @param ymin set ploting window range, defaults to NULL which uses the minimum value. May need to be adjusted manually to avoid outliers.
+#' @param ymax set ploting window range, defaults to NULL which uses the maximum value. May need to be adjusted manually to avoid outliers.
+#' @export
+#' @examples
+#' arbin_dQdV(list,cellfile,1,ymin,ymax)
+arbin_dQdV<-function (list,title=NULL,cycle=1,ymin=NULL,ymax=NULL)
+{
+ require(ggplot2)
+ require(scales)
+ require(grid)
+ require(dplyr)
+
+ #remove the statistics sublist, keep raw data for dQ/dV vs V plot
+ df <- list[1]
+
+ #Combine discharge and charge capacity into continuous capacity Q.
+ df$raw$Q<-df$raw$Q.c+df$raw$Q.d
+ #Calculate dQ/dV
+ x <- diff(df$raw$Q)/diff(df$raw$E)
+
+ #Set non finite values to zero
+ x[!is.finite(x)] <- 0
+
+ #add zero to the beginning of the dQdV to recover the length of the vector after diff
+ df$raw$dQdV<- c(0,x)
+ df <- do.call(rbind, df)
+
+ #remove other cycles than ones of interest.
+ df<-filter(df, cyc.n == cycle)
+
+ # Basic plot setup. ==========================================================
+ p <- ggplot(df) + geom_point(aes(x = E, y = dQdV,color = factor(cyc.n), group = factor(cyc.n)),size = 1)+
+ # Axis and legend titles set==================================================
+ xlab(expression("Voltage / V")) + ylab("dQ/dV") +
+ ggtitle(title)
+
+ #Custom theme is added========================================================
+ p <- p + theme_bw() + theme(text = element_text(size = 21)) + theme(legend.position = "bottom")+
+ theme(panel.border = element_rect(size = 1, color = "black")) +
+ theme(axis.ticks.length = unit(-0.25, "cm")) +
+ theme(axis.text.x = element_text(margin = margin(0.5, 0, 0.2, 0, "cm"))) +
+ theme(axis.text.y = element_text(margin = margin(0,0.5, 0, 0.2, "cm"))) +
+ theme(panel.grid.major = element_line(size = 0.5))
+ #Y axis is made to be continuous with limits set using ymin and ymax=========
+ #if no set values, use autoscale to min and mix values
+ if (is.null(ymin)|is.null(ymax)){
+ p <- p + scale_y_continuous(limits = c(min(df$dQdV), max(df$dQdV)))
+ }
+
+ if (!is.null(ymin)&!is.null(ymax)){
+ p <- p + scale_y_continuous(limits = c(ymin, ymax))
+ }
+ return(p)
+}
+
+#' arbin_dQdV_multi
+#'
+#' Compare differential capacity plots from different cells, same cycle. .
+#'
+#' @param list list of data generated from arbinimport script.
+#' @param label character vector containing the legend for each Cell for the legend
+#' @param cycle Number of the cycle of interest, default is cycle=1
+#' @param ymin set ploting window range for the dQ/dV axis, defaults to NULL which uses the minimum value. May need to be adjusted manually to avoid outliers.
+#' @param ymax set ploting window range for the dQ/dV axis, defaults to NULL which uses the maximum value. May need to be adjusted manually to avoid outliers.
+#' @export
+#' @examples
+#' arbin_dQdV_multi(l,title=c("Cell1", "Cell2","Cell3"),cycle=1,ymin=-0.01,ymax=0.01)
+arbin_dQdV_multi<-function (list,label,cycle=1,ymin=NULL,ymax=NULL)
+{
+ require(ggplot2)
+ require(scales)
+ require(grid)
+ require(dplyr)
+
+ #remove the statistics sublist, keep raw data for dQ/dV vs V plot
+ stats <- lapply(list, function(x) x[[1]])
+ stats <- lapply(seq_along(stats), function(i) {
+ df<-stats[[i]]
+ df$Q<-df$Q.c+df$Q.d
+ x <- diff(df$Q)/diff(df$E)
+ x[!is.finite(x)] <- 0
+ df$dQdV<- c(0,x)
+ #filter out/remove other cycles that you dont want.
+ df<-filter(df, cyc.n %in% cycle)
+ #add label to provide coloring for graphing
+ df$label <- label[i]
+ return(df)
+ })
+ stats <- do.call(rbind, stats)
+ # Basic plot setup. ==========================================================
+ p <- ggplot(stats) +
+ geom_path(aes(x = E, y = dQdV, color=label), size=1)+
+
+ # Axis and legend titles/colors set================================================
+ xlab("Voltage (V)") + ylab("dQdV") +
+ ggtitle(paste("Cycle",cycle))+
+ labs(color="Sample")+
+
+ #Custom theme is added========================================================
+ theme_bw() +
+ theme(text = element_text(size = 21)) +
+ theme(legend.position = "right")+
+ theme(panel.border = element_rect(size = 1, color = "black")) +
+ theme(axis.ticks.length = unit(-0.25, "cm")) +
+ theme(axis.text.x = element_text(margin = margin(0.5, 0, 0.2, 0, "cm"))) +
+ theme(axis.text.y = element_text(margin = margin(0,0.5, 0, 0.2, "cm"))) +
+ theme(panel.grid.major = element_line(size = 0.5))
+ #Y axis is made to be continuous with limits set using ymin and ymax=========
+ #if no set values, use autoscale to min and mix values
+ if (is.null(ymin)|is.null(ymax)){
+ p <- p + scale_y_continuous(limits = c(min(stats$dQdV), max(stats$dQdV)))
+ }
+
+ if (!is.null(ymin)&!is.null(ymax)){
+ p <- p + scale_y_continuous(limits = c(ymin, ymax))
+ }
+
+ return(p)
+}
+
+# Multiple plot function, coppied from http://www.cookbook-r.com/Graphs/Multiple_graphs_on_one_page_(ggplot2)/
+#
+# ggplot objects can be passed in ..., or to plotlist (as a list of ggplot objects)
+# - cols: Number of columns in layout
+# - layout: A matrix specifying the layout. If present, 'cols' is ignored.
+#
+# If the layout is something like matrix(c(1,2,3,3), nrow=2, byrow=TRUE),
+# then plot 1 will go in the upper left, 2 will go in the upper right, and
+# 3 will go all the way across the bottom.
+#
+#' Combine plots from many arbin plots into one for ease of report creation
+#'
+#' @param ... list of plot variables saved from an arbin plot function
+#' @param labels character vector with the legends to use in the plots
+#' @export
+#' @examples
+#' p1<-arbin_Qplot(l1[1:3],c("Cell1", "Cell2","Cell3"))
+#' p2<-arbin_Qplot(l1[4:6],c("Cell4", "Cell5","Cell6"))
+#' p3<-arbin_quickplot(l1[[1]],x="Q.d",y="E",norm="mass"))
+#' multiplot(p1,p2,p3,cols=1)
+#' multiplot(p1,p2,p3,cols=2)
+multiplot <- function(..., plotlist=NULL, file, cols=1, layout=NULL) {
+ library(grid)
+
+ # Make a list from the ... arguments and plotlist
+ plots <- c(list(...), plotlist)
+
+ numPlots = length(plots)
+
+ # If layout is NULL, then use 'cols' to determine layout
+ if (is.null(layout)) {
+ # Make the panel
+ # ncol: Number of columns of plots
+ # nrow: Number of rows needed, calculated from # of cols
+ layout <- matrix(seq(1, cols * ceiling(numPlots/cols)),
+ ncol = cols, nrow = ceiling(numPlots/cols))
+ }
+
+ if (numPlots==1) {
+ print(plots[[1]])
+
+ } else {
+ # Set up the page
+ grid.newpage()
+ pushViewport(viewport(layout = grid.layout(nrow(layout), ncol(layout))))
+
+ # Make each plot, in the correct location
+ for (i in 1:numPlots) {
+ # Get the i,j matrix positions of the regions that contain this subplot
+ matchidx <- as.data.frame(which(layout == i, arr.ind = TRUE))
+
+ print(plots[[i]], vp = viewport(layout.pos.row = matchidx$row,
+ layout.pos.col = matchidx$col))
+ }
+ }
+}
diff --git a/arbintools.Rproj b/arbintools.Rproj
index d848a9f..cba1b6b 100644
--- a/arbintools.Rproj
+++ b/arbintools.Rproj
@@ -5,8 +5,13 @@ SaveWorkspace: No
AlwaysSaveHistory: Default
EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
Encoding: UTF-8
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
AutoAppendNewline: Yes
StripTrailingWhitespace: Yes
diff --git a/man/arbin_Qplot.Rd b/man/arbin_Qplot.Rd
index 0a9cdf4..b4a38cf 100644
--- a/man/arbin_Qplot.Rd
+++ b/man/arbin_Qplot.Rd
@@ -4,13 +4,15 @@
\alias{arbin_Qplot}
\title{arbin_Qplot}
\usage{
-arbin_Qplot(list, labels)
+arbin_Qplot(list, labels, norm = NULL)
}
\arguments{
\item{list}{A list of datasets, as exported from the arbin_import function - so each
list element is also a list}
\item{labels}{A vector of labels corresponding to the datasets in the list, in the correct order.}
+
+\item{norm}{character string used to select how to normalize your data: "mass", "area", "vol". Defaults to Null.}
}
\description{
This function takes a list of datasets, a vector of labels for those datasets and
@@ -18,5 +20,5 @@ returns a formatted capacity vs cycle number plot.
}
\examples{
arbin_Qplot(list(mydatasetA, mydatasetB), labels = c("dataset A", "dataset B"))
+arbin_Qplot(l1[1:3],labels=c("Cell1", "Cell2","Cell3"), norm="mass")
}
-
diff --git a/man/arbin_dQdV.Rd b/man/arbin_dQdV.Rd
new file mode 100644
index 0000000..772706e
--- /dev/null
+++ b/man/arbin_dQdV.Rd
@@ -0,0 +1,25 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plotting_functions.R
+\name{arbin_dQdV}
+\alias{arbin_dQdV}
+\title{arbin_dQdV}
+\usage{
+arbin_dQdV(list, title = NULL, cycle = 1, ymin = NULL, ymax = NULL)
+}
+\arguments{
+\item{list}{list of data generated from arbinimport script.}
+
+\item{title}{Character vector to use for the title of the plot. Defaults to NULL.}
+
+\item{cycle}{number of the cycle of interest, defaults to 1}
+
+\item{ymin}{set ploting window range, defaults to NULL which uses the minimum value. May need to be adjusted manually to avoid outliers.}
+
+\item{ymax}{set ploting window range, defaults to NULL which uses the maximum value. May need to be adjusted manually to avoid outliers.}
+}
+\description{
+Plot differential capacity plots (dQ/dV) for one cell at one cycle.
+}
+\examples{
+arbin_dQdV(list,cellfile,1,ymin,ymax)
+}
diff --git a/man/arbin_dQdV_multi.Rd b/man/arbin_dQdV_multi.Rd
new file mode 100644
index 0000000..f46ebd3
--- /dev/null
+++ b/man/arbin_dQdV_multi.Rd
@@ -0,0 +1,25 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plotting_functions.R
+\name{arbin_dQdV_multi}
+\alias{arbin_dQdV_multi}
+\title{arbin_dQdV_multi}
+\usage{
+arbin_dQdV_multi(list, label, cycle = 1, ymin = NULL, ymax = NULL)
+}
+\arguments{
+\item{list}{list of data generated from arbinimport script.}
+
+\item{label}{character vector containing the legend for each Cell for the legend}
+
+\item{cycle}{Number of the cycle of interest, default is cycle=1}
+
+\item{ymin}{set ploting window range for the dQ/dV axis, defaults to NULL which uses the minimum value. May need to be adjusted manually to avoid outliers.}
+
+\item{ymax}{set ploting window range for the dQ/dV axis, defaults to NULL which uses the maximum value. May need to be adjusted manually to avoid outliers.}
+}
+\description{
+Compare differential capacity plots from different cells, same cycle. .
+}
+\examples{
+arbin_dQdV_multi(l,title=c("Cell1", "Cell2","Cell3"),cycle=1,ymin=-0.01,ymax=0.01)
+}
diff --git a/man/arbin_import.Rd b/man/arbin_import.Rd
index 6cc7700..9380c8b 100644
--- a/man/arbin_import.Rd
+++ b/man/arbin_import.Rd
@@ -5,7 +5,7 @@
\title{arbin_import}
\usage{
arbin_import(file, step.time = TRUE, energy = TRUE, cycles = 100,
- mass = NULL, meanE = FALSE)
+ mass = NULL, area = NULL, vol = NULL, meanE = FALSE)
}
\arguments{
\item{file}{The filename, which must end in .xls or .xlsx.}
@@ -17,8 +17,14 @@ arbin_import(file, step.time = TRUE, energy = TRUE, cycles = 100,
\item{cycles}{Defaults to 100. Determines the maximum number of cycles to be considered when
aggregating the statistics dataset.}
-\item{mass}{Defaults to NULL. If an active material mass is specified - in MILLIGRAMS - the
-capacities in the raw and statistics data frames will be converted to mAh/g.}
+\item{mass}{Defaults to NULL. If an active material mass is specified - in MILLIGRAMS, mg - it is stored
+in the norm parameter for normalization options during plotting.}
+
+\item{area}{Defaults to NULL. If an electrode area is specified - in SQUARE CENTIMETERS, cm^2 - it is stored
+in the norm parameter for normalization options during plotting.}
+
+\item{vol}{Defaults to NULL. If an active material volume is specified - in CUBIC CENTIMETERS, cm^3 - it is stored
+in the norm parameter for normalization options during plotting.}
\item{meanE}{Defaults to FALSE. Will calculate a statistic for average charge and discharge voltage
if set to TRUE.}
@@ -32,6 +38,7 @@ sheet as outputted to the Excel file is not read.
}
\examples{
mydataset <- arbin_import("dataset.xlsx")
-mydataset <- arbin_import("dataset.xlsx", step.time = FALSE, cycles = 200, mass = 2.55)
+mydataset <- arbin_import("dataset.xlsx", step.time = FALSE, cycles = 200, mass = 2.55, area=1.267)
+Batch import of multiple cells from list, useful for Qplot, plotvp_multi, dQdV_multi, etc.
+l=lapply(1:length(cellfile),function(x) arbinimport(cellfile[x],cycles=100,mass=mass[x]))
}
-
diff --git a/man/arbin_import_folder.Rd b/man/arbin_import_folder.Rd
new file mode 100644
index 0000000..fbe1936
--- /dev/null
+++ b/man/arbin_import_folder.Rd
@@ -0,0 +1,28 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/import_functions.R
+\name{arbin_import_folder}
+\alias{arbin_import_folder}
+\title{arbin_import_folder}
+\usage{
+arbin_import_folder(path = ".", mass = NULL, area = NULL, vol = NULL)
+}
+\arguments{
+\item{path}{The folder path, which must include .xls or .xlsx files produced by the arbin.}
+
+\item{mass}{Defaults to NULL. A vector including the active masses (in MILLIGRAMS, mg) of all cells in the folder being imported.
+Use arbin_import_folder_check to ensure correct order.}
+
+\item{area}{Defaults to NULL. A vector including the area (in SQUARE CENTIMETERS, cm^2) of all cells in the folder being imported.
+Use arbin_import_folder_check to ensure correct order.}
+
+\item{vol}{Defaults to Null. A vector including the volume (in cubic CENTIMETERS, cm^3) of all cells in the folder being imported.
+Use arbin_import_folder_check to ensure correct order.}
+}
+\description{
+This function is a simplified version of arbin_import which does not output a separate
+statistics data frame. Consequently the output is a data frame rather than a list.
+}
+\examples{
+mydataset <- arbin_import_folder(path)
+mydataset <- arbin_import_folder()
+}
diff --git a/man/arbin_import_folder_check.Rd b/man/arbin_import_folder_check.Rd
new file mode 100644
index 0000000..a31489e
--- /dev/null
+++ b/man/arbin_import_folder_check.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/import_functions.R
+\name{arbin_import_folder_check}
+\alias{arbin_import_folder_check}
+\title{arbin_import_folder_check}
+\usage{
+arbin_import_folder_check(path = ".")
+}
+\arguments{
+\item{path}{The folder path containing only data files from the arbin, which must end in .xls or .xlsx.}
+}
+\description{
+This function is a simplified version of arbin_import which does not output a separate
+statistics data frame. Consequently the output is a data frame rather than a list.
+}
+\examples{
+mydataset <- arbin_import_folder(path)
+mydataset <- arbin_import_folder()
+}
diff --git a/man/arbin_import_raw.Rd b/man/arbin_import_raw.Rd
index 290874c..4a720b9 100644
--- a/man/arbin_import_raw.Rd
+++ b/man/arbin_import_raw.Rd
@@ -4,7 +4,8 @@
\alias{arbin_import_raw}
\title{arbin_import_raw}
\usage{
-arbin_import_raw(file, step.time = TRUE, energy = TRUE, mass = NULL)
+arbin_import_raw(file, step.time = TRUE, energy = TRUE, mass = NULL,
+ area = NULL, vol = NULL)
}
\arguments{
\item{file}{The filename, which must end in .xls or .xlsx.}
@@ -24,4 +25,3 @@ statistics data frame. Consequently the output is a data frame rather than a lis
mydataset <- arbin_import("dataset.xlsx")
mydataset <- arbin_import("dataset.xlsx", step.time = FALSE)
}
-
diff --git a/man/arbin_plotvp.Rd b/man/arbin_plotvp.Rd
index 65c4746..2b5aadd 100644
--- a/man/arbin_plotvp.Rd
+++ b/man/arbin_plotvp.Rd
@@ -4,20 +4,22 @@
\alias{arbin_plotvp}
\title{arbin_plotvp}
\usage{
-arbin_plotvp(data, cycles)
+arbin_plotvp(data, cycles = 1, norm = NULL, title = NULL)
}
\arguments{
-\item{data}{The dataset, which can be the list as outputted by arbin_import or the data
-frame as arbin_import_raw.}
+\item{data}{The dataset, which is the list as output by arbin_import.}
-\item{cycles}{The cycles to be plotted, expressed as a vector}
+\item{cycles}{The cycles to be plotted, expressed as a vector. Defaults to cycle = 1.}
+
+\item{norm}{character string used to select how to normalize your data: "mass", "area", "vol". Deaults to Null which plots absolute capacity.}
+
+\item{title}{Character vector to use for the title of the plot. Defaults to NULL.}
}
\description{
This function takes a data frame of raw data and a specified cycle - or number
of cycles, as a vector - and outputs charge and discharge voltage profiles.
}
\examples{
-arbin_plotvp(mydataset, 1)
-arbin_plotvp(mydataset, cycles = c(1,5,10))
+arbin_plotvp(mydataset, cycles=1)
+arbin_plotvp(mydataset, cycles = c(1,5,10), norm="mass")
}
-
diff --git a/man/arbin_plotvp_multi.Rd b/man/arbin_plotvp_multi.Rd
new file mode 100644
index 0000000..7ae966a
--- /dev/null
+++ b/man/arbin_plotvp_multi.Rd
@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plotting_functions.R
+\name{arbin_plotvp_multi}
+\alias{arbin_plotvp_multi}
+\title{arbin_plotvp_multi}
+\usage{
+arbin_plotvp_multi(list, labels, cycle = 1, norm = NULL)
+}
+\arguments{
+\item{list}{list containing list of data from multiple cells generated by arbinimport.}
+
+\item{labels}{character vector containing the text to use for the plot legend. Must be as long as the number of cells being plotted}
+
+\item{cycle}{The number of the cycle that is desired to be plotted. Default is cycle =1.}
+
+\item{norm}{character string used to select how to normalize your data: "mass", "area", "vol". Defaults to Null.}
+}
+\description{
+Plot voltage vs capacity for multiple cells at one cycle. Used for rate capability
+comparison and polarization comparison of multiple cells.
+}
+\examples{
+arbin_plotvp_multi(l1[1:3],c("test","test2","test3"),cycle=5)
+}
diff --git a/man/arbin_quickplot.Rd b/man/arbin_quickplot.Rd
index 4db98f9..14ca723 100644
--- a/man/arbin_quickplot.Rd
+++ b/man/arbin_quickplot.Rd
@@ -4,18 +4,23 @@
\alias{arbin_quickplot}
\title{arbin_quickplot}
\usage{
-arbin_quickplot(data, x, y, geom = geom_point, size = 4)
+arbin_quickplot(l, x = "cyc.n", y = "Q.d", norm = NULL, title = NULL,
+ geom = geom_point, size = 4)
}
\arguments{
-\item{data}{The dataset, which must be a dataframe.}
-
\item{x}{The variable to be plotted on the x-axis}
\item{y}{The variable to be plotted on the y-axis}
+\item{norm}{character string used to select how to normalize your data: "mass", "area", "vol".}
+
+\item{title}{Character vector to use for the title of the plot. Defaults to NULL.}
+
\item{geom}{The geom to be passed to ggplot; e.g. geom_point or geom_path}
-\item{size}{The size of the geom.}
+\item{size}{The size of the geom. Default size =4.}
+
+\item{data}{The dataset, which must be a list generated by arbinimport.}
}
\description{
This function takes a data frame of either raw data or aggregated statistics,
@@ -24,8 +29,7 @@ formatting and axis labels. Can also do things such as subsetting data with
dplyr.
}
\examples{
-arbin_quickplot(mydataset$raw, x = t, y = E)
-arbin_quickplot(filter(mydataset$raw, cyc.n == 1, x = t, y = E, geom = geom_path, size = 1)
-arbin_quickplot(mydataset$stat, x = cyc.n, y = d.Q)
+arbin_quickplot(list, x = "t", y = "E")
+arbin_quickplot(list, x = "t", y = "E", norm="mass", geom = geom_path, size = 1)
+arbin_quickplot(list, x = "cyc.n", y = "Q.d" , norm="area")
}
-
diff --git a/man/multiplot.Rd b/man/multiplot.Rd
new file mode 100644
index 0000000..8c0b0bc
--- /dev/null
+++ b/man/multiplot.Rd
@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plotting_functions.R
+\name{multiplot}
+\alias{multiplot}
+\title{Combine plots from many arbin plots into one for ease of report creation}
+\usage{
+multiplot(..., plotlist = NULL, file, cols = 1, layout = NULL)
+}
+\arguments{
+\item{...}{list of plot variables saved from an arbin plot function}
+
+\item{labels}{character vector with the legends to use in the plots}
+}
+\description{
+Combine plots from many arbin plots into one for ease of report creation
+}
+\examples{
+p1<-arbin_Qplot(l1[1:3],c("Cell1", "Cell2","Cell3"))
+p2<-arbin_Qplot(l1[4:6],c("Cell4", "Cell5","Cell6"))
+p3<-arbin_quickplot(l1[[1]],x="Q.d",y="E",norm="mass"))
+multiplot(p1,p2,p3,cols=1)
+multiplot(p1,p2,p3,cols=2)
+}