From 705424f03ceca3732d885900cfee7abe6a1710bb Mon Sep 17 00:00:00 2001 From: darkwraith Date: Sun, 4 Jun 2017 11:24:54 -0400 Subject: [PATCH 01/31] added example usage for importing of multiple files. Changed import grep expression to ignore plot tabs from xlsx files for users who genereate plots upon import. --- R/import_functions.R | 63 ++++++++++++++++++++++---------------------- 1 file changed, 32 insertions(+), 31 deletions(-) diff --git a/R/import_functions.R b/R/import_functions.R index ecef310..ff56d3f 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 @@ -18,58 +18,59 @@ #' 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) +#' 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) { - + require(readxl) - + # All the "Channel*" sheets are read in. This function needs the readxl package. - l <- lapply(grep("Channel*", excel_sheets(file), value = TRUE), + 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), @@ -77,18 +78,18 @@ 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$I > 0], 1)) } - + # Raw and statistics data frames are returned as a list. out <- list(raw = x, stats = stats) return(out) @@ -96,7 +97,7 @@ arbin_import <- function(file, step.time = TRUE, energy = TRUE, cycles = 100, ma #' arbin_import_raw -#' +#' #' This function is a simplified version of arbin_import which does not output a separate #' statistics data frame. Consequently the output is a data frame rather than a list. #' @param file The filename, which must end in .xls or .xlsx. @@ -106,48 +107,48 @@ arbin_import <- function(file, step.time = TRUE, energy = TRUE, cycles = 100, ma #' capacities in the raw and statistics data frames will be converted to mAh/g. #' @keywords #' @export -#' @examples +#' @examples #' mydataset <- arbin_import("dataset.xlsx") #' mydataset <- arbin_import("dataset.xlsx", step.time = FALSE) arbin_import_raw <- function(file, step.time = TRUE, energy = TRUE, mass = NULL) { - + require(readxl, quietly = TRUE) - - l <- lapply(grep("Channel*", excel_sheets(file), value = TRUE), + + l <- lapply(grep("Channel_\\d", excel_sheets(file), value = TRUE), read_excel, path = file) - + l <- do.call(rbind, l) - + x <- data.frame(t = l$`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$`Charge_Energy(Wh)` # charge energy (Wh) } - + # Capacities are converted to mAh/g if active mass is specified. if(!is.null(mass) == TRUE) { x$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$En.c * (1E6/mass) } - + return(x) -} \ No newline at end of file +} From e4b27db88b3758a44aa58bf249164c23641dca7d Mon Sep 17 00:00:00 2001 From: darkwraith Date: Sun, 4 Jun 2017 11:59:10 -0400 Subject: [PATCH 02/31] Added arbin_dQdV plotting function. Added example to Qplot. --- R/plotting_functions.R | 132 +++++++++++++++++++++++++++++------------ 1 file changed, 93 insertions(+), 39 deletions(-) diff --git a/R/plotting_functions.R b/R/plotting_functions.R index fb27804..0df55dc 100644 --- a/R/plotting_functions.R +++ b/R/plotting_functions.R @@ -1,10 +1,11 @@ -### Plotting functions. The plotting functions here include arbin_quickplot, +### Plotting functions. The plotting functions here include: arbin_quickplot, ### for quickly plotting any x or y variable; arbin_plotvp, for plotting voltage -### profiles, and arbin_qplot, for plotting capacity vs cycle number with -### multiple datasets. +### profiles; arbin_qplot, for plotting capacity vs cycle number with +### multiple datasets;arbin_dQdV, for plotting differential capacity plot of one +### or multiple cycles of one cell. #' arbin_quickplot -#' +#' #' This function takes a data frame of either raw data or aggregated statistics, #' any argument for x or y-axis plotting, and returns a ggplot with the desired #' formatting and axis labels. Can also do things such as subsetting data with @@ -16,23 +17,23 @@ #' @param size The size of the geom. #' @keywords #' @export -#' @examples +#' @examples #' arbin_quickplot(mydataset$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 <- function(data, x, y, 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)) - + # 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. @@ -52,14 +53,14 @@ arbin_quickplot <- function(data, x, y, geom = geom_point, size = 4) { meanE.d = "mean discharge voltage / V", meanE.c = "mean charge voltage / V" ) - + # Basic plot setup. ================================================ 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]]) - + # 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. @@ -71,22 +72,22 @@ 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 @@ -94,17 +95,17 @@ arbin_quickplot <- function(data, x, y, geom = geom_point, size = 4) { #' @param cycles The cycles to be plotted, expressed as a vector #' @keywords #' @export -#' @examples +#' @examples #' arbin_plotvp(mydataset, 1) #' arbin_plotvp(mydataset, cycles = c(1,5,10)) 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. @@ -116,12 +117,12 @@ 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 @@ -133,7 +134,7 @@ arbin_plotvp <- function(data, cycles) { break } } - + # 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) + @@ -141,7 +142,7 @@ arbin_plotvp <- function(data, cycles) { xlab("Q / mAh g"^-1~"") + ylab("cell voltage / V") + 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. @@ -154,14 +155,14 @@ 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_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 @@ -169,41 +170,42 @@ arbin_plotvp <- function(data, cycles) { #' @param labels A vector of labels corresponding to the datasets in the list, in the correct order. #' @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")) 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]] df$ident <- labels[i] return(df) }) - + # Bind each statistics data frame into one data frame. ======================= stats <- do.call(rbind, stats) - + # Basic plot setup. ========================================================== p <- ggplot(stats) + - geom_point(aes(x = cyc.n, y = Q.d, color = ident), size = 4) + + geom_point(aes(x = cyc.n, y = Q.d, color = ident), size = 4) + xlab("cycle number") + ylab(expression("Q"[discharge] * " / mAh g"^-1~"")) + 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 +218,62 @@ 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$Q.d))) # } - + + return(p) + +} +#' Plot differential capacity plots (dQ/dV) for one cell at one cycle. +#' +#' @param list list of data generated from arbinimport script. +#' @param title input legend for the plot +#' @param cycle number of the cycle of interest, defaults to 1 +#' @param ymin set ploting window range, defaults to 0.1 +#' @param ymax set ploting window range, defaults to 1 +#' @export +#' @examples +#' arbin_dQdV(list,cellfile,1,ymin,ymax) +arbin_dQdV<-function (list,title,cycle=1,ymin=0.1,ymax=1) +{ + require(ggplot2) + require(scales) + require(grid) + require(dplyr) + + #remove the statistics sublist, keep raw data for dQ/dV vs V plot + df <- list[1] + + #Combine discharge and charge capacity into continuous capacity Q. + df$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)+ + xlab(expression("Voltage")) + ylab("dQdV") + + 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========= + p <- p + scale_y_continuous(limits = c(ymin, ymax)) return(p) - -} \ No newline at end of file +} From 394eb684624d9f5448b802836cf7298427c3bec4 Mon Sep 17 00:00:00 2001 From: darkwraith Date: Sun, 4 Jun 2017 12:13:59 -0400 Subject: [PATCH 03/31] Added arbin_dQdV_multi plotting function to allow comparing dQ/dV between different cells. --- R/plotting_functions.R | 65 +++++++++++++++++++++++++++++++++++++++--- 1 file changed, 61 insertions(+), 4 deletions(-) diff --git a/R/plotting_functions.R b/R/plotting_functions.R index 0df55dc..02f3f5c 100644 --- a/R/plotting_functions.R +++ b/R/plotting_functions.R @@ -1,8 +1,9 @@ ### Plotting functions. The plotting functions here include: arbin_quickplot, ### for quickly plotting any x or y variable; arbin_plotvp, for plotting voltage -### profiles; 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. +### 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 #' @@ -262,7 +263,8 @@ arbin_dQdV<-function (list,title,cycle=1,ymin=0.1,ymax=1) # Basic plot setup. ========================================================== p <- ggplot(df) + geom_point(aes(x = E, y = dQdV,color = factor(cyc.n), group = factor(cyc.n)),size = 1)+ - xlab(expression("Voltage")) + ylab("dQdV") + + # Axis and legend titles set================================================== + xlab(expression("Voltage / V")) + ylab("dQ/dV") + ggtitle(title) #Custom theme is added======================================================== @@ -277,3 +279,58 @@ arbin_dQdV<-function (list,title,cycle=1,ymin=0.1,ymax=1) p <- p + scale_y_continuous(limits = c(ymin, ymax)) return(p) } +#' Compare differential capacity plots from different cells, same cycle. . +#' +#' @param list list of data generated from arbinimport script. +#' @param title 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, default is -1000 +#' @param ymax set ploting window range for the dQ/dV axis, default is 1500 +#' @export +#' @examples +#' arbin_dQdV_multi(l,title=c("Cell1", "Cell2","Cell3"),cycle=1,ymin=-1000,ymax=1500) +arbin_dQdV_multi<-function (list,title,cycle=1,ymin=-1000,ymax=1500) +{ + 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$dQdV<- c(0,x) + #filter out/remove other cycles that you dont want. + df<-filter(df, cyc.n %in% cycle) + #add label to provide coloring for graphing + df$ident <- title[i] + return(df) + }) + stats <- do.call(rbind, stats) + # Basic plot setup. ========================================================== + p <- ggplot(stats) + + geom_point(aes(x = E, y = dQdV, color=ident))+ + + # 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========= + scale_y_continuous(limits = c(ymin, ymax)) + return(p) +} From 450f621695876e6fe094ebb79dd7ee4c35f690db Mon Sep 17 00:00:00 2001 From: darkwraith Date: Sun, 4 Jun 2017 12:21:42 -0400 Subject: [PATCH 04/31] Add plotting function arbin_plotvp_multi for plotting the voltage profiles of multiple cells for rate capability/polarization comparison. --- R/plotting_functions.R | 57 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 57 insertions(+) diff --git a/R/plotting_functions.R b/R/plotting_functions.R index 02f3f5c..55c6707 100644 --- a/R/plotting_functions.R +++ b/R/plotting_functions.R @@ -161,6 +161,57 @@ arbin_plotvp <- function(data, cycles) { } +#' 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. +#' @export +#' @examples +#' arbin_plotvp_multi(l1[1:3],c("test","test2","test3"),cycle=5) +arbin_plotvp_multi<-function (list, labels, cycle=1) +{ + 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.") + } + #need to add some check code to see if there are enough cycles to compare + #remove the statistics sublist, keep raw data for Q vs V plot + stats <- lapply(list, function(x) x[[1]]) + stats <- lapply(seq_along(stats), function(i) { + df <- stats[[i]] + #add column with label names to use for coloring plots. + df$ident <- labels[i] + #remove other cycles that you dont want. + df<-filter(df, cyc.n == cycle) + return(df) + }) + stats <- do.call(rbind, stats) + + # Basic plot setup. ========================================================== + p <- ggplot(stats) + geom_point(aes(x = Q.d, y = E, color = ident), size = 4)+ + geom_point(aes(x = Q.c, y = E, color = ident, group=ident), size = 4)+ + xlab(expression("Q"[discharge] * " / mAh g"^-1 ~ "")) + ylab("Voltage (V)") + + guides(color = guide_legend("Cells")) + + # Plotting theme setup ========================================================== + p <- p + theme_bw() + theme(text = element_text(size = 21)) + theme(legend.position = "bottom")+ + theme(panel.border = element_rect(size = 1, color = "black")) + + theme(axis.ticks.length = unit(-0.25, "cm")) + + theme(axis.text.x = element_text(margin = margin(0.5, 0, 0.2, 0, "cm"))) + + theme(axis.text.y = element_text(margin = margin(0,0.5, 0, 0.2, "cm"))) + + theme(panel.grid.major = element_line(size = 0.5)) + + # Set y axis to continuous and set limits==================================== + p <- p + scale_y_continuous(limits = c(min(stats$E), max(stats$E))) + return(p) +} #' arbin_Qplot #' @@ -226,6 +277,9 @@ arbin_Qplot <- function(list, labels) { return(p) } + +#' arbin_dQdV +#' #' Plot differential capacity plots (dQ/dV) for one cell at one cycle. #' #' @param list list of data generated from arbinimport script. @@ -279,6 +333,9 @@ arbin_dQdV<-function (list,title,cycle=1,ymin=0.1,ymax=1) p <- p + scale_y_continuous(limits = c(ymin, ymax)) return(p) } + +#' arbin_dQdV_multi +#' #' Compare differential capacity plots from different cells, same cycle. . #' #' @param list list of data generated from arbinimport script. From 2c4d57ee1fd9e38309a40086c4d728befab17f90 Mon Sep 17 00:00:00 2001 From: darkwraith Date: Sun, 4 Jun 2017 12:26:58 -0400 Subject: [PATCH 05/31] Ran Roxygen document() to rebuild documentation/manuals. --- .Rbuildignore | 2 ++ DESCRIPTION | 2 +- NAMESPACE | 3 +++ arbintools.Rproj | 5 +++++ man/arbin_Qplot.Rd | 2 +- man/arbin_dQdV.Rd | 25 +++++++++++++++++++++++++ man/arbin_dQdV_multi.Rd | 25 +++++++++++++++++++++++++ man/arbin_import.Rd | 2 +- man/arbin_import_raw.Rd | 1 - man/arbin_plotvp.Rd | 1 - man/arbin_plotvp_multi.Rd | 22 ++++++++++++++++++++++ man/arbin_quickplot.Rd | 1 - 12 files changed, 85 insertions(+), 6 deletions(-) create mode 100644 .Rbuildignore create mode 100644 man/arbin_dQdV.Rd create mode 100644 man/arbin_dQdV_multi.Rd create mode 100644 man/arbin_plotvp_multi.Rd diff --git a/.Rbuildignore b/.Rbuildignore new file mode 100644 index 0000000..91114bf --- /dev/null +++ b/.Rbuildignore @@ -0,0 +1,2 @@ +^.*\.Rproj$ +^\.Rproj\.user$ diff --git a/DESCRIPTION b/DESCRIPTION index 84dd5fe..e7f5c31 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -7,7 +7,7 @@ Depends: R (>= 3.2.0) License: CC0 LazyData: true -RoxygenNote: 5.0.1 +RoxygenNote: 6.0.1 Imports: dplyr, ggplot2, reshape2, diff --git a/NAMESPACE b/NAMESPACE index 8423ad4..a4d94b6 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,7 +1,10 @@ # Generated by roxygen2: do not edit by hand export(arbin_Qplot) +export(arbin_dQdV) +export(arbin_dQdV_multi) export(arbin_import) export(arbin_import_raw) export(arbin_plotvp) +export(arbin_plotvp_multi) export(arbin_quickplot) 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..560ea68 100644 --- a/man/arbin_Qplot.Rd +++ b/man/arbin_Qplot.Rd @@ -18,5 +18,5 @@ 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")) } - diff --git a/man/arbin_dQdV.Rd b/man/arbin_dQdV.Rd new file mode 100644 index 0000000..800c081 --- /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, cycle = 1, ymin = 0.1, ymax = 1) +} +\arguments{ +\item{list}{list of data generated from arbinimport script.} + +\item{title}{input legend for the plot} + +\item{cycle}{number of the cycle of interest, defaults to 1} + +\item{ymin}{set ploting window range, defaults to 0.1} + +\item{ymax}{set ploting window range, defaults to 1} +} +\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..8dc1e36 --- /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, title, cycle = 1, ymin = -1000, ymax = 1500) +} +\arguments{ +\item{list}{list of data generated from arbinimport script.} + +\item{title}{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, default is -1000} + +\item{ymax}{set ploting window range for the dQ/dV axis, default is 1500} +} +\description{ +Compare differential capacity plots from different cells, same cycle. . +} +\examples{ +arbin_dQdV_multi(l,title=c("Cell1", "Cell2","Cell3"),cycle=1,ymin=-1000,ymax=1500) +} diff --git a/man/arbin_import.Rd b/man/arbin_import.Rd index 6cc7700..f7b1e69 100644 --- a/man/arbin_import.Rd +++ b/man/arbin_import.Rd @@ -33,5 +33,5 @@ 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) +l=lapply(1:length(cellfile),function(x) arbinimport(cellfile[x],cycles=100,mass=mass[x])) } - diff --git a/man/arbin_import_raw.Rd b/man/arbin_import_raw.Rd index 290874c..58ca07e 100644 --- a/man/arbin_import_raw.Rd +++ b/man/arbin_import_raw.Rd @@ -24,4 +24,3 @@ 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..be8c850 100644 --- a/man/arbin_plotvp.Rd +++ b/man/arbin_plotvp.Rd @@ -20,4 +20,3 @@ of cycles, as a vector - and outputs charge and discharge voltage profiles. arbin_plotvp(mydataset, 1) arbin_plotvp(mydataset, cycles = c(1,5,10)) } - diff --git a/man/arbin_plotvp_multi.Rd b/man/arbin_plotvp_multi.Rd new file mode 100644 index 0000000..726950c --- /dev/null +++ b/man/arbin_plotvp_multi.Rd @@ -0,0 +1,22 @@ +% 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) +} +\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.} +} +\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..39fb1b9 100644 --- a/man/arbin_quickplot.Rd +++ b/man/arbin_quickplot.Rd @@ -28,4 +28,3 @@ 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$stat, x = cyc.n, y = d.Q) } - From db79053c3f2f4982abf509242c3e5f11f730d606 Mon Sep 17 00:00:00 2001 From: darkwraith Date: Sun, 4 Jun 2017 13:17:23 -0400 Subject: [PATCH 06/31] Updated arbinimport to allow for non-destructive normalization by storing the normalization value in the generated list (raw, stats, norm). Allows for subsequent plotting functions to specify absolute capacity, specific capacity, areal capacity, or volumetric capacity. --- R/import_functions.R | 54 +++++++++++++++++++++++++++----------------- 1 file changed, 33 insertions(+), 21 deletions(-) diff --git a/R/import_functions.R b/R/import_functions.R index ff56d3f..4fc4122 100644 --- a/R/import_functions.R +++ b/R/import_functions.R @@ -23,11 +23,11 @@ #' mydataset <- arbin_import("dataset.xlsx", step.time = FALSE, cycles = 200, mass = 2.55) #' l=lapply(1:length(cellfile),function(x) arbinimport(cellfile[x],cycles=100,mass=mass[x])) -arbin_import <- function(file, step.time = TRUE, energy = TRUE, cycles = 100, mass = NULL, meanE = FALSE) { - +arbinimport<-function (file, step.time = TRUE, energy = TRUE, cycles = 100, mass = NULL, area = NULL , vol = NULL, meanE = FALSE) + { require(readxl) - # All the "Channel*" sheets are read in. This function needs the readxl package. + # All the "Channel*" sheets are read in, excludes plot sheets. This function needs the readxl package. l <- lapply(grep("Channel_\\d", excel_sheets(file), value = TRUE), read_excel, path = file) @@ -55,18 +55,6 @@ arbin_import <- function(file, step.time = TRUE, energy = TRUE, cycles = 100, ma x$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$cyc.n) - 1) @@ -89,9 +77,11 @@ arbin_import <- function(file, step.time = TRUE, energy = TRUE, cycles = 100, ma stats$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$I > 0], 1)) } - - # Raw and statistics data frames are returned as a list. - out <- list(raw = x, stats = stats) +#Save information for normalization into list. +#Allows plotting functions to perform normalization as needed instead of at import. + norm<-list(mass=mass, area=area, vol=vol) + # Raw, statistics, and normalization data frames are returned as a list. + out <- list(raw = x, stats = stats, norm = norm) return(out) } @@ -111,7 +101,7 @@ arbin_import <- function(file, step.time = TRUE, energy = TRUE, cycles = 100, ma #' mydataset <- arbin_import("dataset.xlsx") #' mydataset <- arbin_import("dataset.xlsx", step.time = FALSE) -arbin_import_raw <- function(file, step.time = TRUE, energy = TRUE, mass = NULL) { +arbin_import_raw <- function(file, step.time = TRUE, energy = TRUE, mass = NULL, area = NULL , vol = NULL) { require(readxl, quietly = TRUE) @@ -137,18 +127,40 @@ arbin_import_raw <- function(file, step.time = TRUE, energy = TRUE, mass = NULL) x$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) } From bc96cb26f12c7f7eca4243d8c47e3c742a79c297 Mon Sep 17 00:00:00 2001 From: darkwraith Date: Sun, 4 Jun 2017 13:21:20 -0400 Subject: [PATCH 07/31] Added manual information for new normalization options. --- R/import_functions.R | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/R/import_functions.R b/R/import_functions.R index 4fc4122..a136e5e 100644 --- a/R/import_functions.R +++ b/R/import_functions.R @@ -12,8 +12,12 @@ #' @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 CENTIMETERS, cm^3 - 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 From c2032d335c1019e4613484c3ca476644257a83df Mon Sep 17 00:00:00 2001 From: darkwraith Date: Sun, 4 Jun 2017 13:45:48 -0400 Subject: [PATCH 08/31] Changed from dataframe to listfor the impored data in order to have the normalization preferences available. Added section to select raw or stats based on which values are being plotted. *Note: this limits the flexibility of the plotting features. Chooses which axis labels depending on the normalization used. Also performs the normalization. --- R/plotting_functions.R | 126 +++++++++++++++++++++++++++++++++-------- 1 file changed, 103 insertions(+), 23 deletions(-) diff --git a/R/plotting_functions.R b/R/plotting_functions.R index 55c6707..b6d3112 100644 --- a/R/plotting_functions.R +++ b/R/plotting_functions.R @@ -11,49 +11,129 @@ #' 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 geom The geom to be passed to ggplot; e.g. geom_point or geom_path #' @param size The size of the geom. #' @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) +#' 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 = d.Q, 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, geom = geom_point, size = 4) { require(ggplot2) require(scales) require(grid) require(dplyr) - + #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 + } # 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)) - + #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======================================== + 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 = "charge capacity / mAh", + Q.d = "discharge capacity / 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") + } + #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 = "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") + +#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 = "charge capacity / mAh cm"^-2 ~ "", + Q.d = "discharge capacity / 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 = "charge capacity / mAh cm"^-3 ~ "", + Q.d = "discharge capacity / 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 + } + } # Basic plot setup. ================================================ p <- ggplot(data) + From 364f49050cfcd132eb397f44f96dd6f9747fadb6 Mon Sep 17 00:00:00 2001 From: darkwraith Date: Sun, 4 Jun 2017 13:58:10 -0400 Subject: [PATCH 09/31] Update arbin_plotvp to normalize data depending on user preference. Plot using correct units. --- R/plotting_functions.R | 54 +++++++++++++++++++++++++++++++++++++----- 1 file changed, 48 insertions(+), 6 deletions(-) diff --git a/R/plotting_functions.R b/R/plotting_functions.R index b6d3112..218ae9c 100644 --- a/R/plotting_functions.R +++ b/R/plotting_functions.R @@ -171,16 +171,16 @@ arbin_quickplot<- function (l, x="cyc.n", y="Q.d", norm=NULL, geom = geom_point, #' #' 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 outputted by arbin_import. +#' @param cycles The cycles to be plotted, expressed as a vector. Defaults to first cycle. +#' @param norm character string used to select how to normalize your data: "mass", "area", "vol". Deaults to Null and plots absolute capacity. #' @keywords #' @export #' @examples #' arbin_plotvp(mydataset, 1) -#' arbin_plotvp(mydataset, cycles = c(1,5,10)) +#' arbin_plotvp(mydataset, cycles = c(1,5,10), norm="mass") -arbin_plotvp <- function(data, cycles) { +arbin_plotvp <- function(data, cycles=1, norm=NULL) { require(ggplot2) require(scales) @@ -190,6 +190,8 @@ arbin_plotvp <- function(data, cycles) { # 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$raw, cyc.n %in% cycles, I != 0) } else if (class(data) == "data.frame") { @@ -216,11 +218,51 @@ arbin_plotvp <- function(data, cycles) { } } + #Normalize capacity data========================================= + #normalize capacity data according to desired norm variable for each cell. + if (!is.null(norm)) + { + #Perform mass normalization + if (norm=="mass" & !is.null(data$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$vol*1e3 + } + } + + #Set axis lables for each normalization case======================== + #set units for no normalization + if (is.null(norm)){ + normunits <- xlab(expression("Q"[discharge] * " / mAh")) + } + if (!is.null(norm)) + #set units for mass normalization + {if (norm=="mass" & !is.null(data$norm$mass)){ + normunits <- xlab(expression("Q"[discharge] * " / mAh g"^-1 ~ "")) + } + #set units for area normalization + if (norm=="area" & !is.null(data$norm$area)){ + normunits <- xlab(expression("Q"[discharge] * " / mAh cm"^-2 ~ "")) + } + #set units for volume normalization + if (norm=="vol" & !is.null(data$norm$vol)){ + normunits <- xlab(expression("Q"[discharge] * " / mAh cm"^-3 ~ "")) + } + } # 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~"") + + normunits + ylab("cell voltage / V") + guides(color = guide_legend(title = "cycle")) From 352f6726488f5956c5f2d78c53afee112685a910 Mon Sep 17 00:00:00 2001 From: darkwraith Date: Sun, 4 Jun 2017 14:08:06 -0400 Subject: [PATCH 10/31] Update arbin_plotvp_multi to normalize data, and plot with correct units. Also added data cleaning for I=0, and stagnant C/D capacity during D/C cycle to better match plotvp. --- R/plotting_functions.R | 66 +++++++++++++++++++++++++++++++++++++++--- 1 file changed, 62 insertions(+), 4 deletions(-) diff --git a/R/plotting_functions.R b/R/plotting_functions.R index 218ae9c..90b5f38 100644 --- a/R/plotting_functions.R +++ b/R/plotting_functions.R @@ -291,10 +291,11 @@ arbin_plotvp <- function(data, cycles=1, norm=NULL) { #' @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) +arbin_plotvp_multi<-function (list, labels, cycle=1, norm=NULL) { require(ggplot2) require(scales) @@ -303,23 +304,80 @@ arbin_plotvp_multi<-function (list, labels, cycle=1) if (length(list) != length(labels)) { stop("Problem... it doesn't seem you've specified the same number of datasets as labels.") } - #need to add some check code to see if there are enough cycles to compare + #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$ident <- labels[i] #remove other cycles that you dont want. - df<-filter(df, cyc.n == cycle) + df<-filter(df, cyc.n == cycle, I!=0) + #clean capacity data by setting to NA data that makes plots hard to read. + for (i in unique(df$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)) + {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 + if (is.null(norm)){ + normunits <- xlab(expression("Q"[discharge] * " / mAh")) + } + if (!is.null(norm)) + #set units for mass normalization + {if (norm=="mass" & !is.null(l$norm$mass)){ + normunits <- xlab(expression("Q"[discharge] * " / mAh g"^-1 ~ "")) + } + #set units for area normalization + if (norm=="area" & !is.null(l$norm$area)){ + normunits <- xlab(expression("Q"[discharge] * " / mAh cm"^-2 ~ "")) + } + #set units for volume normalization + if (norm=="vol" & !is.null(l$norm$vol)){ + normunits <- xlab(expression("Q"[discharge] * " / mAh cm"^-3 ~ "")) + } + } # Basic plot setup. ========================================================== p <- ggplot(stats) + geom_point(aes(x = Q.d, y = E, color = ident), size = 4)+ geom_point(aes(x = Q.c, y = E, color = ident, group=ident), size = 4)+ - xlab(expression("Q"[discharge] * " / mAh g"^-1 ~ "")) + ylab("Voltage (V)") + + normunits + ylab("Voltage (V)") + guides(color = guide_legend("Cells")) # Plotting theme setup ========================================================== From ff6c0144c2f940c50e6e3a7a7c4e102038f4912b Mon Sep 17 00:00:00 2001 From: darkwraith Date: Sun, 4 Jun 2017 14:39:18 -0400 Subject: [PATCH 11/31] Update arbin_Qplot to properly handle normalization and plotting normalized units. --- R/plotting_functions.R | 43 ++++++++++++++++++++++++++++++++++++++---- 1 file changed, 39 insertions(+), 4 deletions(-) diff --git a/R/plotting_functions.R b/R/plotting_functions.R index 90b5f38..f8f62d5 100644 --- a/R/plotting_functions.R +++ b/R/plotting_functions.R @@ -400,13 +400,14 @@ arbin_plotvp_multi<-function (list, labels, cycle=1, norm=NULL) #' @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 #' arbin_Qplot(list(mydatasetA, mydatasetB), labels = c("dataset A", "dataset B")) -#' arbin_Qplot(l1[1:3],labels=c("Cell1", "Cell2","Cell3")) +#' arbin_Qplot(l1[1:3],labels=c("Cell1", "Cell2","Cell3"), norm="mass") -arbin_Qplot <- function(list, labels) { +arbin_Qplot <- function(list, labels, norm=NULL) { require(ggplot2) require(scales) @@ -424,18 +425,52 @@ arbin_Qplot <- function(list, labels) { # 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$ident <- labels[i] + if (!is.null(norm)) + {#normalize discharge capacity data according to desired norm variable for each cell. + if (norm=="mass" & !is.null(list[[i]]$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$vol*1e3 + } + } return(df) }) # Bind each statistics data frame into one data frame. ======================= stats <- do.call(rbind, stats) + #create axis label normunits for each normalization condition.================= + #set units for no normalization + if (is.null(norm)){ + normunits <- ylab(expression("Q"[discharge] * " / mAh")) + } + if (!is.null(norm)) + #set units for mass normalization + {if (norm=="mass" & !is.null(l$norm$mass)){ + normunits <- ylab(expression("Q"[discharge] * " / mAh g"^-1 ~ "")) + } + #set units for area normalization + if (norm=="area" & !is.null(l$norm$area)){ + normunits <- ylab(expression("Q"[discharge] * " / mAh cm"^-2 ~ "")) + } + #set units for volume normalization + if (norm=="vol" & !is.null(l$norm$vol)){ + normunits <- ylab(expression("Q"[discharge] * " / mAh cm"^-3 ~ "")) + } + } + # Basic plot setup. ========================================================== 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~"")) + + xlab("cycle number") + normunit + guides(color = guide_legend(title = "")) # If scales and grid are installed, then a custom theme is added. y-axis is From 1c67641dae04e1dae2ef644b0412d27a5fe3afa9 Mon Sep 17 00:00:00 2001 From: darkwraith Date: Sun, 4 Jun 2017 14:43:08 -0400 Subject: [PATCH 12/31] Add multiplot function to group multiple plots into one figure based on an NxN matrix. Code used from cookbook-r. Attribution http://www.cookbook-r.com/Graphs/Multiple_graphs_on_one_page_(ggplot2)/ --- R/plotting_functions.R | 57 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 57 insertions(+) diff --git a/R/plotting_functions.R b/R/plotting_functions.R index f8f62d5..926bc73 100644 --- a/R/plotting_functions.R +++ b/R/plotting_functions.R @@ -606,3 +606,60 @@ arbin_dQdV_multi<-function (list,title,cycle=1,ymin=-1000,ymax=1500) 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)) + } + } +} From 26a310c6e20c49afc3b0450ebf62aa6a28de523b Mon Sep 17 00:00:00 2001 From: darkwraith Date: Sun, 4 Jun 2017 14:47:58 -0400 Subject: [PATCH 13/31] Updated documentation and fixed naming of arbinimpot/arbin_import. --- NAMESPACE | 1 + R/import_functions.R | 2 +- man/arbin_Qplot.Rd | 6 ++++-- man/arbin_import.Rd | 12 +++++++++--- man/arbin_import_raw.Rd | 3 ++- man/arbin_plotvp.Rd | 11 ++++++----- man/arbin_plotvp_multi.Rd | 4 +++- man/arbin_quickplot.Rd | 15 +++++++++------ man/multiplot.Rd | 23 +++++++++++++++++++++++ 9 files changed, 58 insertions(+), 19 deletions(-) create mode 100644 man/multiplot.Rd diff --git a/NAMESPACE b/NAMESPACE index a4d94b6..9430511 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -8,3 +8,4 @@ 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 a136e5e..eaf6939 100644 --- a/R/import_functions.R +++ b/R/import_functions.R @@ -27,7 +27,7 @@ #' mydataset <- arbin_import("dataset.xlsx", step.time = FALSE, cycles = 200, mass = 2.55) #' l=lapply(1:length(cellfile),function(x) arbinimport(cellfile[x],cycles=100,mass=mass[x])) -arbinimport<-function (file, step.time = TRUE, energy = TRUE, cycles = 100, mass = NULL, area = NULL , vol = NULL, meanE = FALSE) +arbin_import<-function (file, step.time = TRUE, energy = TRUE, cycles = 100, mass = NULL, area = NULL , vol = NULL, meanE = FALSE) { require(readxl) diff --git a/man/arbin_Qplot.Rd b/man/arbin_Qplot.Rd index 560ea68..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")) +arbin_Qplot(l1[1:3],labels=c("Cell1", "Cell2","Cell3"), norm="mass") } diff --git a/man/arbin_import.Rd b/man/arbin_import.Rd index f7b1e69..9a029ed 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 CENTIMETERS, cm^3 - 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.} diff --git a/man/arbin_import_raw.Rd b/man/arbin_import_raw.Rd index 58ca07e..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.} diff --git a/man/arbin_plotvp.Rd b/man/arbin_plotvp.Rd index be8c850..f75794e 100644 --- a/man/arbin_plotvp.Rd +++ b/man/arbin_plotvp.Rd @@ -4,13 +4,14 @@ \alias{arbin_plotvp} \title{arbin_plotvp} \usage{ -arbin_plotvp(data, cycles) +arbin_plotvp(data, cycles = 1, norm = 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 outputted 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 first cycle.} + +\item{norm}{character string used to select how to normalize your data: "mass", "area", "vol". Deaults to Null and plots absolute capacity.} } \description{ This function takes a data frame of raw data and a specified cycle - or number @@ -18,5 +19,5 @@ 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 = c(1,5,10), norm="mass") } diff --git a/man/arbin_plotvp_multi.Rd b/man/arbin_plotvp_multi.Rd index 726950c..7ae966a 100644 --- a/man/arbin_plotvp_multi.Rd +++ b/man/arbin_plotvp_multi.Rd @@ -4,7 +4,7 @@ \alias{arbin_plotvp_multi} \title{arbin_plotvp_multi} \usage{ -arbin_plotvp_multi(list, labels, cycle = 1) +arbin_plotvp_multi(list, labels, cycle = 1, norm = NULL) } \arguments{ \item{list}{list containing list of data from multiple cells generated by arbinimport.} @@ -12,6 +12,8 @@ arbin_plotvp_multi(list, labels, cycle = 1) \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 diff --git a/man/arbin_quickplot.Rd b/man/arbin_quickplot.Rd index 39fb1b9..f0cb1bf 100644 --- a/man/arbin_quickplot.Rd +++ b/man/arbin_quickplot.Rd @@ -4,18 +4,21 @@ \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, + 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{geom}{The geom to be passed to ggplot; e.g. geom_point or geom_path} \item{size}{The size of the geom.} + +\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, @@ -24,7 +27,7 @@ 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 = d.Q, 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) +} From cf41cc8a4ab96954b53b1741460b5cfe95554039 Mon Sep 17 00:00:00 2001 From: darkwraith Date: Sun, 4 Jun 2017 15:12:19 -0400 Subject: [PATCH 14/31] Fixed logic expression for setting norm units. Added a error expression for when user calls a normalization method that the data is not available. Fixed typo in normunits call upon plotting. --- R/plotting_functions.R | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/R/plotting_functions.R b/R/plotting_functions.R index 926bc73..677dff0 100644 --- a/R/plotting_functions.R +++ b/R/plotting_functions.R @@ -449,28 +449,32 @@ arbin_Qplot <- function(list, labels, norm=NULL) { #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(l$norm$mass)){ + {if (norm=="mass" & !is.null(l[[1]]$norm$mass)){ normunits <- ylab(expression("Q"[discharge] * " / mAh g"^-1 ~ "")) } #set units for area normalization - if (norm=="area" & !is.null(l$norm$area)){ + if (norm=="area" & !is.null(l[[1]]$norm$area)){ normunits <- ylab(expression("Q"[discharge] * " / mAh cm"^-2 ~ "")) } #set units for volume normalization - if (norm=="vol" & !is.null(l$norm$vol)){ + if (norm=="vol" & !is.null(l[[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") + normunit + + xlab("cycle number") + normunits + guides(color = guide_legend(title = "")) # If scales and grid are installed, then a custom theme is added. y-axis is From ce9a75a4758b563336ad2d06b09290509bd2b78d Mon Sep 17 00:00:00 2001 From: darkwraith Date: Sun, 4 Jun 2017 15:54:37 -0400 Subject: [PATCH 15/31] Change axis labels to shorten to Q dis/charge. Inputs need to be character strings. substitute/deparse not working correctly. --- R/plotting_functions.R | 32 ++++++++++++++++---------------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/R/plotting_functions.R b/R/plotting_functions.R index 677dff0..43e36ab 100644 --- a/R/plotting_functions.R +++ b/R/plotting_functions.R @@ -25,11 +25,11 @@ #' arbin_quickplot(list, x = cyc.n, y = d.Q, norm="area") arbin_quickplot<- function (l, x="cyc.n", y="Q.d", norm=NULL, geom = geom_point, size = 4) { - require(ggplot2) require(scales) require(grid) require(dplyr) + #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"){ @@ -39,16 +39,14 @@ arbin_quickplot<- function (l, x="cyc.n", y="Q.d", norm=NULL, geom = geom_point, if (x=="cyc.n"){ data<-l$stats } - # 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)) + #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. #set units for no normalization======================================== + labels<-NULL if (is.null(norm)){ labels <- list( t = "time / s", @@ -56,8 +54,8 @@ arbin_quickplot<- function (l, x="cyc.n", y="Q.d", norm=NULL, geom = geom_point, cyc.n = "cycle number", I = "I / A", E = "cell voltage / V", - Q.c = "charge capacity / mAh", - Q.d = "discharge capacity / mAh", + 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", @@ -76,8 +74,8 @@ arbin_quickplot<- function (l, x="cyc.n", y="Q.d", norm=NULL, geom = geom_point, 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 ~ "", + 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 ~ "", @@ -98,8 +96,8 @@ arbin_quickplot<- function (l, x="cyc.n", y="Q.d", norm=NULL, geom = geom_point, cyc.n = "cycle number", I = "I / A", E = "cell voltage / V", - Q.c = "charge capacity / mAh cm"^-2 ~ "", - Q.d = "discharge capacity / mAh cm"^-2 ~ "", + 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 ~ "", @@ -119,8 +117,8 @@ arbin_quickplot<- function (l, x="cyc.n", y="Q.d", norm=NULL, geom = geom_point, cyc.n = "cycle number", I = "I / A", E = "cell voltage / V", - Q.c = "charge capacity / mAh cm"^-3 ~ "", - Q.d = "discharge capacity / mAh cm"^-3 ~ "", + 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 ~ "", @@ -134,10 +132,12 @@ arbin_quickplot<- function (l, x="cyc.n", y="Q.d", norm=NULL, geom = geom_point, 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]]) From e785879ed5e549440d8489987e87c010529da55d Mon Sep 17 00:00:00 2001 From: darkwraith Date: Sun, 4 Jun 2017 16:01:07 -0400 Subject: [PATCH 16/31] Provide error messages if user wants to normalize by variable that doesn't exist. --- R/plotting_functions.R | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/R/plotting_functions.R b/R/plotting_functions.R index 43e36ab..42ae3fe 100644 --- a/R/plotting_functions.R +++ b/R/plotting_functions.R @@ -240,6 +240,7 @@ arbin_plotvp <- function(data, cycles=1, norm=NULL) { } #Set axis lables for each normalization case======================== + normunits<-NULL #set units for no normalization if (is.null(norm)){ normunits <- xlab(expression("Q"[discharge] * " / mAh")) @@ -258,6 +259,11 @@ arbin_plotvp <- function(data, cycles=1, norm=NULL) { 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(plotted.data) + geom_path(aes(x = Q.d, y = E, color = factor(cyc.n), group = factor(cyc.n)), size = 1) + @@ -357,6 +363,7 @@ arbin_plotvp_multi<-function (list, labels, cycle=1, norm=NULL) stats <- do.call(rbind, stats) #set units for no normalization + normunits<-NULL if (is.null(norm)){ normunits <- xlab(expression("Q"[discharge] * " / mAh")) } @@ -374,6 +381,9 @@ arbin_plotvp_multi<-function (list, labels, cycle=1, norm=NULL) 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_point(aes(x = Q.d, y = E, color = ident), size = 4)+ geom_point(aes(x = Q.c, y = E, color = ident, group=ident), size = 4)+ From 759e76b312a1ff5c38b32fa18a4677b51ff455ab Mon Sep 17 00:00:00 2001 From: darkwraith Date: Sun, 4 Jun 2017 16:41:54 -0400 Subject: [PATCH 17/31] fixed logic for formation of normunits in arbin_plotvp_multi. Set plot type from point to line for arbin_plotvp_multi to make consistent with arbin_plotvp. Made title optional for arbin_dQdV. sets to Null by default. Clarified the label variable in arbin_dQdV_multi to avoid confusion with the title. --- R/plotting_functions.R | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/R/plotting_functions.R b/R/plotting_functions.R index 42ae3fe..6b03b29 100644 --- a/R/plotting_functions.R +++ b/R/plotting_functions.R @@ -369,15 +369,15 @@ arbin_plotvp_multi<-function (list, labels, cycle=1, norm=NULL) } if (!is.null(norm)) #set units for mass normalization - {if (norm=="mass" & !is.null(l$norm$mass)){ + {if (norm=="mass" & !is.null(l[[1]]$norm$mass)){ normunits <- xlab(expression("Q"[discharge] * " / mAh g"^-1 ~ "")) } #set units for area normalization - if (norm=="area" & !is.null(l$norm$area)){ + if (norm=="area" & !is.null(l[[1]]$norm$area)){ normunits <- xlab(expression("Q"[discharge] * " / mAh cm"^-2 ~ "")) } #set units for volume normalization - if (norm=="vol" & !is.null(l$norm$vol)){ + if (norm=="vol" & !is.null(l[[1]]$norm$vol)){ normunits <- xlab(expression("Q"[discharge] * " / mAh cm"^-3 ~ "")) } } @@ -385,8 +385,8 @@ arbin_plotvp_multi<-function (list, labels, cycle=1, norm=NULL) 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_point(aes(x = Q.d, y = E, color = ident), size = 4)+ - geom_point(aes(x = Q.c, y = E, color = ident, group=ident), size = 4)+ + 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")) @@ -519,7 +519,7 @@ arbin_Qplot <- function(list, labels, norm=NULL) { #' @export #' @examples #' arbin_dQdV(list,cellfile,1,ymin,ymax) -arbin_dQdV<-function (list,title,cycle=1,ymin=0.1,ymax=1) +arbin_dQdV<-function (list,title=NULL,cycle=1,ymin=-0.1,ymax=1) { require(ggplot2) require(scales) @@ -568,14 +568,14 @@ arbin_dQdV<-function (list,title,cycle=1,ymin=0.1,ymax=1) #' Compare differential capacity plots from different cells, same cycle. . #' #' @param list list of data generated from arbinimport script. -#' @param title character vector containing the legend for each Cell for the legend +#' @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, default is -1000 #' @param ymax set ploting window range for the dQ/dV axis, default is 1500 #' @export #' @examples #' arbin_dQdV_multi(l,title=c("Cell1", "Cell2","Cell3"),cycle=1,ymin=-1000,ymax=1500) -arbin_dQdV_multi<-function (list,title,cycle=1,ymin=-1000,ymax=1500) +arbin_dQdV_multi<-function (list,label,cycle=1,ymin=-1,ymax=1) { require(ggplot2) require(scales) @@ -593,13 +593,13 @@ arbin_dQdV_multi<-function (list,title,cycle=1,ymin=-1000,ymax=1500) #filter out/remove other cycles that you dont want. df<-filter(df, cyc.n %in% cycle) #add label to provide coloring for graphing - df$ident <- title[i] + df$label <- label[i] return(df) }) stats <- do.call(rbind, stats) # Basic plot setup. ========================================================== p <- ggplot(stats) + - geom_point(aes(x = E, y = dQdV, color=ident))+ + geom_path(aes(x = E, y = dQdV, color=label), size=1)+ # Axis and legend titles/colors set================================================ xlab("Voltage (V)") + ylab("dQdV") + From 1a598ce670ee859fbb8f290eca9648bdd8b5cc3c Mon Sep 17 00:00:00 2001 From: darkwraith Date: Sun, 4 Jun 2017 16:52:26 -0400 Subject: [PATCH 18/31] Generated manual files from Roxygen document(). --- man/arbin_dQdV.Rd | 2 +- man/arbin_dQdV_multi.Rd | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/man/arbin_dQdV.Rd b/man/arbin_dQdV.Rd index 800c081..a0b5714 100644 --- a/man/arbin_dQdV.Rd +++ b/man/arbin_dQdV.Rd @@ -4,7 +4,7 @@ \alias{arbin_dQdV} \title{arbin_dQdV} \usage{ -arbin_dQdV(list, title, cycle = 1, ymin = 0.1, ymax = 1) +arbin_dQdV(list, title = NULL, cycle = 1, ymin = -0.1, ymax = 1) } \arguments{ \item{list}{list of data generated from arbinimport script.} diff --git a/man/arbin_dQdV_multi.Rd b/man/arbin_dQdV_multi.Rd index 8dc1e36..6682c44 100644 --- a/man/arbin_dQdV_multi.Rd +++ b/man/arbin_dQdV_multi.Rd @@ -4,12 +4,12 @@ \alias{arbin_dQdV_multi} \title{arbin_dQdV_multi} \usage{ -arbin_dQdV_multi(list, title, cycle = 1, ymin = -1000, ymax = 1500) +arbin_dQdV_multi(list, label, cycle = 1, ymin = -1, ymax = 1) } \arguments{ \item{list}{list of data generated from arbinimport script.} -\item{title}{character vector containing the legend for each Cell for the legend} +\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} From 06e614a676778fac6cbd17eb53154b7b56d4bfe2 Mon Sep 17 00:00:00 2001 From: darkwraith Date: Tue, 6 Jun 2017 10:54:30 -0400 Subject: [PATCH 19/31] add entire folder import tools and folder check functions to enable easier mass data analysis. --- R/import_functions.R | 51 +++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 50 insertions(+), 1 deletion(-) diff --git a/R/import_functions.R b/R/import_functions.R index eaf6939..dc92ceb 100644 --- a/R/import_functions.R +++ b/R/import_functions.R @@ -27,7 +27,8 @@ #' mydataset <- arbin_import("dataset.xlsx", step.time = FALSE, cycles = 200, mass = 2.55) #' 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, area = NULL , vol = NULL, meanE = FALSE) +arbin_import<-function (file, step.time = TRUE, energy = TRUE, cycles = 100, mass = NULL, area = NULL , + vol = NULL, meanE = FALSE) { require(readxl) @@ -168,3 +169,51 @@ arbin_import_raw <- function(file, step.time = TRUE, energy = TRUE, mass = NULL, return(x) } +#' 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=".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=".xls") + setwd(initfolder) + return(f) +} From 2c6bc92028921039311577b946e575485e734dfa Mon Sep 17 00:00:00 2001 From: darkwraith Date: Tue, 6 Jun 2017 10:56:07 -0400 Subject: [PATCH 20/31] Re-generated documentations. --- NAMESPACE | 2 ++ man/arbin_import_folder.Rd | 28 ++++++++++++++++++++++++++++ man/arbin_import_folder_check.Rd | 19 +++++++++++++++++++ 3 files changed, 49 insertions(+) create mode 100644 man/arbin_import_folder.Rd create mode 100644 man/arbin_import_folder_check.Rd diff --git a/NAMESPACE b/NAMESPACE index 9430511..a6808c5 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -4,6 +4,8 @@ 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) 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() +} From 2047df7cfcf680b14f50c2f32a5018c2f8bf615d Mon Sep 17 00:00:00 2001 From: darkwraith Date: Tue, 6 Jun 2017 11:04:49 -0400 Subject: [PATCH 21/31] Make file extension matching case insensitive with (?i).xls --- R/import_functions.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/import_functions.R b/R/import_functions.R index dc92ceb..bb3b4fa 100644 --- a/R/import_functions.R +++ b/R/import_functions.R @@ -190,7 +190,7 @@ 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=".xls") + 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) @@ -213,7 +213,7 @@ 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=".xls") + f<-list.files(path=path,pattern="(?i).xls") setwd(initfolder) return(f) } From 60063e45c07ae4650247356cd16b8feca61a775c Mon Sep 17 00:00:00 2001 From: darkwraith Date: Mon, 12 Jun 2017 13:00:10 -0400 Subject: [PATCH 22/31] During plotting convert to mAh as units suggest. --- R/plotting_functions.R | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/R/plotting_functions.R b/R/plotting_functions.R index 6b03b29..9113e7c 100644 --- a/R/plotting_functions.R +++ b/R/plotting_functions.R @@ -63,6 +63,10 @@ arbin_quickplot<- function (l, x="cyc.n", y="Q.d", norm=NULL, geom = geom_point, 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$Q.d*1e3 } #if normalization is used then set the proper labels if (!is.null(norm)) @@ -220,6 +224,10 @@ arbin_plotvp <- function(data, cycles=1, norm=NULL) { #Normalize capacity data========================================= #normalize capacity data according to desired norm variable for each cell. + if (is.null(norm)){ + plotted.data$Q.d<-plotted.data$Q.d*1e3 + plotted.data$Q.c<-plotted.data$Q.c*1e3 + } if (!is.null(norm)) { #Perform mass normalization @@ -342,6 +350,10 @@ arbin_plotvp_multi<-function (list, labels, cycle=1, norm=NULL) } } #normalize discharge capacity data according to desired norm variable for each cell. + if (is.null(norm)){ + df$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$mass*1e6 @@ -437,6 +449,9 @@ arbin_Qplot <- function(list, labels, norm=NULL) { df <- stats[[i]] #set ident for use in color coding the plot. df$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)){ From 65ffbd33447b14400a702141b5c2976f7bc32bfd Mon Sep 17 00:00:00 2001 From: darkwraith Date: Tue, 20 Jun 2017 13:57:33 -0400 Subject: [PATCH 23/31] Fix variable from test variable to function variable. --- R/plotting_functions.R | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/R/plotting_functions.R b/R/plotting_functions.R index 6b03b29..fd49e2f 100644 --- a/R/plotting_functions.R +++ b/R/plotting_functions.R @@ -465,15 +465,15 @@ arbin_Qplot <- function(list, labels, norm=NULL) { } if (!is.null(norm)) #set units for mass normalization - {if (norm=="mass" & !is.null(l[[1]]$norm$mass)){ + {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(l[[1]]$norm$area)){ + 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(l[[1]]$norm$vol)){ + if (norm=="vol" & !is.null(list[[1]]$norm$vol)){ normunits <- ylab(expression("Q"[discharge] * " / mAh cm"^-3 ~ "")) } } From c0b52d3f7f40e801b2cc0c8047db967780a905a8 Mon Sep 17 00:00:00 2001 From: darkwraith Date: Tue, 20 Jun 2017 14:31:44 -0400 Subject: [PATCH 24/31] Fix list name for arbin_plotvp_multi for logic to set correct normalizations. --- R/plotting_functions.R | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/R/plotting_functions.R b/R/plotting_functions.R index f643dfc..4a6c146 100644 --- a/R/plotting_functions.R +++ b/R/plotting_functions.R @@ -381,15 +381,15 @@ arbin_plotvp_multi<-function (list, labels, cycle=1, norm=NULL) } if (!is.null(norm)) #set units for mass normalization - {if (norm=="mass" & !is.null(l[[1]]$norm$mass)){ + {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(l[[1]]$norm$area)){ + 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(l[[1]]$norm$vol)){ + if (norm=="vol" & !is.null(list[[1]]$norm$vol)){ normunits <- xlab(expression("Q"[discharge] * " / mAh cm"^-3 ~ "")) } } From 3f999b9648bd53ea3656e446b2cbb89c162faad1 Mon Sep 17 00:00:00 2001 From: darkwraith Date: Thu, 22 Jun 2017 12:50:51 -0400 Subject: [PATCH 25/31] Fix errors in the quickplot documentation and rebuild the documentation files. Include correct quotation usage ie: "t" and added the default info for size. --- R/plotting_functions.R | 8 ++++---- man/arbin_quickplot.Rd | 8 ++++---- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/R/plotting_functions.R b/R/plotting_functions.R index 4a6c146..0365e94 100644 --- a/R/plotting_functions.R +++ b/R/plotting_functions.R @@ -16,13 +16,13 @@ #' @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 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(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 = d.Q, norm="area") +#' 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 (l, x="cyc.n", y="Q.d", norm=NULL, geom = geom_point, size = 4) { require(ggplot2) diff --git a/man/arbin_quickplot.Rd b/man/arbin_quickplot.Rd index f0cb1bf..95b4834 100644 --- a/man/arbin_quickplot.Rd +++ b/man/arbin_quickplot.Rd @@ -16,7 +16,7 @@ arbin_quickplot(l, x = "cyc.n", y = "Q.d", norm = 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.} } @@ -27,7 +27,7 @@ formatting and axis labels. Can also do things such as subsetting data with dplyr. } \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 = d.Q, norm="area") +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") } From 680c5d411aac35f8c6a9af9c7b2f783c8bc37718 Mon Sep 17 00:00:00 2001 From: darkwraith Date: Thu, 22 Jun 2017 12:56:49 -0400 Subject: [PATCH 26/31] Fix arbinimport help documentation, units for area normalization. Provided more details for example usage for lapply example. Generate documentation. --- R/import_functions.R | 5 +++-- man/arbin_import.Rd | 5 +++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/R/import_functions.R b/R/import_functions.R index bb3b4fa..b8772f3 100644 --- a/R/import_functions.R +++ b/R/import_functions.R @@ -14,7 +14,7 @@ #' aggregating the statistics dataset. #' @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 CENTIMETERS, cm^3 - it is stored +#' @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. @@ -24,7 +24,8 @@ #' @export #' @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, area = NULL , diff --git a/man/arbin_import.Rd b/man/arbin_import.Rd index 9a029ed..9380c8b 100644 --- a/man/arbin_import.Rd +++ b/man/arbin_import.Rd @@ -20,7 +20,7 @@ aggregating the statistics dataset.} \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 CENTIMETERS, cm^3 - it is stored +\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 @@ -38,6 +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])) } From e68d971641b4bfc86ff80a1b488abea9577810f6 Mon Sep 17 00:00:00 2001 From: darkwraith Date: Thu, 22 Jun 2017 13:07:05 -0400 Subject: [PATCH 27/31] Fix x axis labels for plotvp to Capacity/Specific Capacity/Areal Capacity/Volumetric Capacity to avoid confusion with charge/discharge capacity. Updated documentation. --- R/plotting_functions.R | 18 +++++++++--------- man/arbin_plotvp.Rd | 8 ++++---- 2 files changed, 13 insertions(+), 13 deletions(-) diff --git a/R/plotting_functions.R b/R/plotting_functions.R index 0365e94..b95b0f5 100644 --- a/R/plotting_functions.R +++ b/R/plotting_functions.R @@ -175,13 +175,13 @@ if (is.null(labels)){ #' #' 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 is the list as outputted by arbin_import. -#' @param cycles The cycles to be plotted, expressed as a vector. Defaults to first cycle. -#' @param norm character string used to select how to normalize your data: "mass", "area", "vol". Deaults to Null and plots absolute capacity. +#' @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. #' @keywords #' @export #' @examples -#' arbin_plotvp(mydataset, 1) +#' arbin_plotvp(mydataset, cycles=1) #' arbin_plotvp(mydataset, cycles = c(1,5,10), norm="mass") arbin_plotvp <- function(data, cycles=1, norm=NULL) { @@ -251,20 +251,20 @@ arbin_plotvp <- function(data, cycles=1, norm=NULL) { normunits<-NULL #set units for no normalization if (is.null(norm)){ - normunits <- xlab(expression("Q"[discharge] * " / mAh")) + 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("Q"[discharge] * " / mAh g"^-1 ~ "")) + normunits <- xlab(expression("Specific Capacity" * " / mAh g"^-1 ~ "")) } #set units for area normalization if (norm=="area" & !is.null(data$norm$area)){ - normunits <- xlab(expression("Q"[discharge] * " / mAh cm"^-2 ~ "")) + normunits <- xlab(expression("Areal Capacity" * " / mAh cm"^-2 ~ "")) } #set units for volume normalization if (norm=="vol" & !is.null(data$norm$vol)){ - normunits <- xlab(expression("Q"[discharge] * " / mAh cm"^-3 ~ "")) + normunits <- xlab(expression("Volumetric Capacity" * " / mAh cm"^-3 ~ "")) } } @@ -277,7 +277,7 @@ arbin_plotvp <- function(data, cycles=1, norm=NULL) { 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) + normunits + - ylab("cell voltage / V") + + ylab("Cell Voltage / V") + guides(color = guide_legend(title = "cycle")) # If scales and grid are installed, then a custom theme is added. diff --git a/man/arbin_plotvp.Rd b/man/arbin_plotvp.Rd index f75794e..b516130 100644 --- a/man/arbin_plotvp.Rd +++ b/man/arbin_plotvp.Rd @@ -7,17 +7,17 @@ arbin_plotvp(data, cycles = 1, norm = NULL) } \arguments{ -\item{data}{The dataset, which is the list as outputted by arbin_import.} +\item{data}{The dataset, which is the list as output by arbin_import.} -\item{cycles}{The cycles to be plotted, expressed as a vector. Defaults to first cycle.} +\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 and plots absolute capacity.} +\item{norm}{character string used to select how to normalize your data: "mass", "area", "vol". Deaults to Null which plots absolute capacity.} } \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=1) arbin_plotvp(mydataset, cycles = c(1,5,10), norm="mass") } From 9c563e1b60503dea1a7721b0d085516c2a5c8c0b Mon Sep 17 00:00:00 2001 From: darkwraith Date: Thu, 22 Jun 2017 13:32:41 -0400 Subject: [PATCH 28/31] Added ability to include title to all plots that only use one cell of data. Multi cell data don't need titles because the cell labels are in the legend. Updated documentation to match. Fix #6 --- R/plotting_functions.R | 15 ++++++++------- man/arbin_dQdV.Rd | 4 ++-- man/arbin_plotvp.Rd | 4 +++- man/arbin_quickplot.Rd | 4 +++- 4 files changed, 16 insertions(+), 11 deletions(-) diff --git a/R/plotting_functions.R b/R/plotting_functions.R index b95b0f5..cab6083 100644 --- a/R/plotting_functions.R +++ b/R/plotting_functions.R @@ -15,6 +15,7 @@ #' @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. Default size =4. #' @keywords @@ -24,7 +25,7 @@ #' 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 (l, x="cyc.n", y="Q.d", norm=NULL, 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) @@ -144,7 +145,7 @@ if (is.null(labels)){ 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 @@ -178,13 +179,14 @@ if (is.null(labels)){ #' @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, cycles=1) #' arbin_plotvp(mydataset, cycles = c(1,5,10), norm="mass") -arbin_plotvp <- function(data, cycles=1, norm=NULL) { +arbin_plotvp <- function(data, cycles=1, norm=NULL, title=NULL) { require(ggplot2) require(scales) @@ -276,8 +278,7 @@ arbin_plotvp <- function(data, cycles=1, norm=NULL) { 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) + - normunits + - 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. @@ -527,14 +528,14 @@ arbin_Qplot <- function(list, labels, norm=NULL) { #' Plot differential capacity plots (dQ/dV) for one cell at one cycle. #' #' @param list list of data generated from arbinimport script. -#' @param title input legend for the plot +#' @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 0.1 #' @param ymax set ploting window range, defaults to 1 #' @export #' @examples #' arbin_dQdV(list,cellfile,1,ymin,ymax) -arbin_dQdV<-function (list,title=NULL,cycle=1,ymin=-0.1,ymax=1) +arbin_dQdV<-function (list,title=NULL,cycle=1,ymin=-0.1,ymax=0.1) { require(ggplot2) require(scales) diff --git a/man/arbin_dQdV.Rd b/man/arbin_dQdV.Rd index a0b5714..6b55e22 100644 --- a/man/arbin_dQdV.Rd +++ b/man/arbin_dQdV.Rd @@ -4,12 +4,12 @@ \alias{arbin_dQdV} \title{arbin_dQdV} \usage{ -arbin_dQdV(list, title = NULL, cycle = 1, ymin = -0.1, ymax = 1) +arbin_dQdV(list, title = NULL, cycle = 1, ymin = -0.1, ymax = 0.1) } \arguments{ \item{list}{list of data generated from arbinimport script.} -\item{title}{input legend for the plot} +\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} diff --git a/man/arbin_plotvp.Rd b/man/arbin_plotvp.Rd index b516130..2b5aadd 100644 --- a/man/arbin_plotvp.Rd +++ b/man/arbin_plotvp.Rd @@ -4,7 +4,7 @@ \alias{arbin_plotvp} \title{arbin_plotvp} \usage{ -arbin_plotvp(data, cycles = 1, norm = NULL) +arbin_plotvp(data, cycles = 1, norm = NULL, title = NULL) } \arguments{ \item{data}{The dataset, which is the list as output by arbin_import.} @@ -12,6 +12,8 @@ arbin_plotvp(data, cycles = 1, norm = NULL) \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 diff --git a/man/arbin_quickplot.Rd b/man/arbin_quickplot.Rd index 95b4834..14ca723 100644 --- a/man/arbin_quickplot.Rd +++ b/man/arbin_quickplot.Rd @@ -4,7 +4,7 @@ \alias{arbin_quickplot} \title{arbin_quickplot} \usage{ -arbin_quickplot(l, x = "cyc.n", y = "Q.d", norm = NULL, +arbin_quickplot(l, x = "cyc.n", y = "Q.d", norm = NULL, title = NULL, geom = geom_point, size = 4) } \arguments{ @@ -14,6 +14,8 @@ arbin_quickplot(l, x = "cyc.n", y = "Q.d", norm = NULL, \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. Default size =4.} From ddcfe8729920fcb556eae1cb5faaf82c4430c6b4 Mon Sep 17 00:00:00 2001 From: darkwraith Date: Thu, 22 Jun 2017 14:41:22 -0400 Subject: [PATCH 29/31] Makes dQdV and dQdV_multi y scaling more robust. Defaults to set the yscale to the max and min value of the cell or all of the cells, but still allows for manual y range setting if extreme points are observed. Updated documentation to reflect changes. Fixes #4 --- R/plotting_functions.R | 37 +++++++++++++++++++++++++------------ man/arbin_dQdV.Rd | 6 +++--- man/arbin_dQdV_multi.Rd | 8 ++++---- 3 files changed, 32 insertions(+), 19 deletions(-) diff --git a/R/plotting_functions.R b/R/plotting_functions.R index cab6083..480c5bb 100644 --- a/R/plotting_functions.R +++ b/R/plotting_functions.R @@ -530,12 +530,12 @@ arbin_Qplot <- function(list, labels, norm=NULL) { #' @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 0.1 -#' @param ymax set ploting window range, 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=-0.1,ymax=0.1) +arbin_dQdV<-function (list,title=NULL,cycle=1,ymin=NULL,ymax=NULL) { require(ggplot2) require(scales) @@ -573,9 +573,15 @@ arbin_dQdV<-function (list,title=NULL,cycle=1,ymin=-0.1,ymax=0.1) 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========= - p <- p + scale_y_continuous(limits = c(ymin, 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) } @@ -586,12 +592,12 @@ arbin_dQdV<-function (list,title=NULL,cycle=1,ymin=-0.1,ymax=0.1) #' @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, default is -1000 -#' @param ymax set ploting window range for the dQ/dV axis, default is 1500 +#' @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=-1000,ymax=1500) -arbin_dQdV_multi<-function (list,label,cycle=1,ymin=-1,ymax=1) +#' 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) @@ -630,10 +636,17 @@ arbin_dQdV_multi<-function (list,label,cycle=1,ymin=-1,ymax=1) 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))+ - + theme(panel.grid.major = element_line(size = 0.5)) #Y axis is made to be continuous with limits set using ymin and ymax========= - scale_y_continuous(limits = c(ymin, 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) } diff --git a/man/arbin_dQdV.Rd b/man/arbin_dQdV.Rd index 6b55e22..772706e 100644 --- a/man/arbin_dQdV.Rd +++ b/man/arbin_dQdV.Rd @@ -4,7 +4,7 @@ \alias{arbin_dQdV} \title{arbin_dQdV} \usage{ -arbin_dQdV(list, title = NULL, cycle = 1, ymin = -0.1, ymax = 0.1) +arbin_dQdV(list, title = NULL, cycle = 1, ymin = NULL, ymax = NULL) } \arguments{ \item{list}{list of data generated from arbinimport script.} @@ -13,9 +13,9 @@ arbin_dQdV(list, title = NULL, cycle = 1, ymin = -0.1, ymax = 0.1) \item{cycle}{number of the cycle of interest, defaults to 1} -\item{ymin}{set ploting window range, defaults to 0.1} +\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 1} +\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. diff --git a/man/arbin_dQdV_multi.Rd b/man/arbin_dQdV_multi.Rd index 6682c44..f46ebd3 100644 --- a/man/arbin_dQdV_multi.Rd +++ b/man/arbin_dQdV_multi.Rd @@ -4,7 +4,7 @@ \alias{arbin_dQdV_multi} \title{arbin_dQdV_multi} \usage{ -arbin_dQdV_multi(list, label, cycle = 1, ymin = -1, ymax = 1) +arbin_dQdV_multi(list, label, cycle = 1, ymin = NULL, ymax = NULL) } \arguments{ \item{list}{list of data generated from arbinimport script.} @@ -13,13 +13,13 @@ arbin_dQdV_multi(list, label, cycle = 1, ymin = -1, ymax = 1) \item{cycle}{Number of the cycle of interest, default is cycle=1} -\item{ymin}{set ploting window range for the dQ/dV axis, default is -1000} +\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, default is 1500} +\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=-1000,ymax=1500) +arbin_dQdV_multi(l,title=c("Cell1", "Cell2","Cell3"),cycle=1,ymin=-0.01,ymax=0.01) } From e9d0e77eb8f296dc66902374bdcceb909fcc637d Mon Sep 17 00:00:00 2001 From: darkwraith Date: Thu, 22 Jun 2017 20:54:59 -0400 Subject: [PATCH 30/31] Update description file. Bump version and add Jim as author. --- DESCRIPTION | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index e7f5c31..0a8f29d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,15 @@ 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) From 43c2cf796b302355cf19856f7e96d9ff80e82ba6 Mon Sep 17 00:00:00 2001 From: darkwraith Date: Thu, 22 Jun 2017 20:58:23 -0400 Subject: [PATCH 31/31] Create LICENSE --- LICENSE | 674 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 674 insertions(+) create mode 100644 LICENSE 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 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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If the +Program specifies that a certain numbered version of the GNU General +Public License "or any later version" applies to it, you have the +option of following the terms and conditions either of that numbered +version or of any later version published by the Free Software +Foundation. If the Program does not specify a version number of the +GNU General Public License, you may choose any version ever published +by the Free Software Foundation. + + If the Program specifies that a proxy can decide which future +versions of the GNU General Public License can be used, that proxy's +public statement of acceptance of a version permanently authorizes you +to choose that version for the Program. + + Later license versions may give you additional or different +permissions. However, no additional obligations are imposed on any +author or copyright holder as a result of your choosing to follow a +later version. + + 15. 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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 +.