Description Usage Arguments Examples

View source: R/pirateplot_function.R

The pirateplot function creates an RDI (Raw data, Descriptive and Inferential statistic) plot showing the relationship between 1 to 3 categorical independent variables and 1 continuous dependent variable.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | ```
pirateplot(formula = NULL, data = NULL, plot = TRUE,
avg.line.fun = mean, pal = "basel", mix.col = "white", mix.p = 0,
back.col = NULL, point.cex = NULL, point.pch = NULL, point.lwd = 1,
jitter.val = 0.03, theme = 1, bean.b.o = NULL, bean.f.o = NULL,
point.o = NULL, bar.f.o = NULL, bar.b.o = NULL, inf.f.o = NULL,
inf.b.o = NULL, avg.line.o = NULL, gl.col = NULL, point.col = NULL,
point.bg = NULL, bar.f.col = NULL, bean.b.col = NULL,
bean.f.col = NULL, inf.f.col = NULL, inf.b.col = NULL,
avg.line.col = NULL, bar.b.col = NULL, quant.col = NULL,
avg.line.lwd = 4, bean.lwd = 1, bean.lty = 1, inf.lwd = NULL,
bar.lwd = 1, at = NULL, bw = "nrd0", adjust = 1, add = FALSE,
sortx = "alphabetical", decreasing = FALSE, cex.lab = 1, cex.axis = 1,
cex.names = 1, quant = NULL, quant.length = NULL, quant.lwd = NULL,
quant.boxplot = FALSE, bty = "o", cap.beans = TRUE, family = NULL,
inf.method = "hdi", inf.within = NULL, inf.p = NULL, hdi.iter = 1000,
inf.disp = NULL, cut.min = NULL, cut.max = NULL, width.min = 0.3,
width.max = NA, ylim = NULL, xlim = NULL, xlab = NULL, ylab = NULL,
main = NULL, yaxt = NULL, xaxt = NULL, gl = NULL, gl.lwd = NULL,
gl.lty = NULL, bar.b.lwd = NULL, line.fun = NULL, line.o = NULL,
inf.o = NULL, bean.o = NULL, inf.col = NULL, theme.o = NULL,
bar.o = NULL, inf = NULL, hdi.o = NULL, inf.type = NULL,
inf.band = NULL)
``` |

`formula` |
formula. A formula in the form |

`data` |
Either a dataframe containing the variables specified in formula, a list of numeric vectors, or a numeric dataframe / matrix. |

`plot` |
logical. If |

`avg.line.fun` |
function. A function that determines how average lines and bar heights are determined (default is mean). |

`pal` |
string. The color palette of the plot. Can be a single color, a vector of colors, or the name of a palette in the piratepal() function (e.g.; "basel", "google", "southpark"). To see all the palettes, run |

`mix.col, mix.p` |
Optional color mixing arguments to be passed to |

`back.col` |
string. Color of the plotting background. |

`point.cex, point.pch, point.lwd` |
numeric. The size, pch type, and line width of raw data points. |

`jitter.val` |
numeric. Amount of jitter added to points horizontally. Defaults to 0.05. |

`theme` |
integer. An integer in the set 0, 1, 2 specifying a theme (that is, new default values for opacities and colors). |

`bar.f.o, point.o, inf.f.o, inf.b.o, avg.line.o, bean.b.o, bean.f.o, bar.b.o` |
numeric. A number between 0 and 1 indicating how opaque to make the bars, points, inference band, average line, and beans respectively. These values override whatever is in the specified theme |

`point.col, bar.f.col, bean.b.col, bean.f.col, inf.f.col, inf.b.col, avg.line.col, bar.b.col, quant.col, point.bg` |
string. Vectors of colors specifying the colors of the plotting elements. This will override values in the palette. f stands for filling, b stands for border. |

`bean.lwd, bean.lty, inf.lwd, avg.line.lwd, bar.lwd` |
numeric. Vectors of numbers customizing the look of beans and lines. |

`at` |
integer. Locations of the beans. Especially helpful when adding beans to an existing plot with add = TRUE |

`bw, adjust` |
Arguments passed to density calculations for beans (see ?density) |

`add` |
logical. Should the pirateplot elements be added to an existing plotting space? |

`sortx` |
string. How to sort the x values. Can be "sequential" (as they are found in the original dataframe), "alphabetical", or a string in the set ("mean", "median", "min", "max") indicating a function |

`decreasing` |
logical. If sortx is a named function, should values be sorted in decreasing order? |

`cex.lab, cex.axis, cex.names` |
Size of the labels, axes, and bean names. |

`quant` |
numeric. Adds horizontal lines representing custom quantiles. |

`quant.length, quant.lwd` |
numeric. Specifies line lengths/widths of |

`quant.boxplot` |
logical. Should standard values be included? |

`bty, xlim, ylim, xlab, ylab, main, yaxt, xaxt` |
General plotting arguments |

`cap.beans` |
logical. Should maximum and minimum values of the bean densities be capped at the limits found in the data? Default is FALSE. |

`family` |
a font family (Not currently in use) |

`inf.method` |
string. A string indicating what types of inference bands to calculate. "ci" means frequentist confidence intervals, "hdi" means Bayesian Highest Density Intervals (HDI), "iqr" means interquartile range, "sd" means standard deviation, "se" means standard error, "withinci" means frequentist confidence intervals in a within design (Morey, 2008). |

`inf.within` |
string. The variable which serves as an ID variable in a within design. |

`inf.p` |
numeric. A number adjusting how inference ranges are calculated. for |

`hdi.iter` |
integer. Number of iterations to run when calculating the HDI. Larger values lead to better estimates, but can be more time consuming. |

`inf.disp` |
string. How should inference ranges be displayed? |

`cut.min, cut.max` |
numeric. Optional minimum and maximum values of the beans. |

`width.min, width.max` |
numeric. The minimum/maximum width of the beans. |

`gl` |
numeric. Locations of the horizontal grid lines |

`gl.lwd, gl.lty, gl.col` |
Customization for grid lines. Can be entered as vectors for alternating gridline types |

`bar.b.lwd, line.fun, inf.o, bean.o, inf.col, theme.o, inf, inf.type, inf.band, bar.o, line.o, hdi.o` |
depricated arguments |

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 | ```
# Default pirateplot of weight by Time
pirateplot(formula = weight ~ Time,
data = ChickWeight)
# Same but in grayscale
pirateplot(formula = weight ~ Time,
data = ChickWeight,
pal = "gray")
# Now using theme 2
pirateplot(formula = weight ~ Time,
data = ChickWeight,
main = "Chicken weight by time",
theme = 2) # theme 2
# theme 3
pirateplot(formula = weight ~ Time,
data = ChickWeight,
main = "Chicken weight by time",
theme = 3) # theme 3
# theme 4
pirateplot(formula = weight ~ Time,
data = ChickWeight,
main = "Chicken weight by time",
theme = 4) # theme 4
# Start with theme 2, but then customise!
pirateplot(formula = weight ~ Time,
data = ChickWeight,
theme = 2, # theme 2
pal = "xmen", # xmen palette
main = "Chicken weights by Time",
point.o = .4, # Add points
point.col = "black",
point.bg = "white",
point.pch = 21,
bean.f.o = .2, # Turn down bean filling
inf.f.o = .8, # Turn up inf filling
gl.col = "gray", # gridlines
gl.lwd = c(.5, 0)) # turn off minor grid lines
# 2 IVs
pirateplot(formula = len ~ dose + supp,
data = ToothGrowth,
main = "Guinea pig tooth length by supplement",
point.pch = 16, # Point specifications...
point.col = "black",
point.o = .7,
inf.f.o = .9, # inference band opacity
gl.col = "gray")
# Build everything from scratch with theme 0
# And use 3 IVs
pirateplot(formula = height ~ headband + eyepatch + sex,
data = pirates,
pal = gray(.1), # Dark gray palette
theme = 0, # Start from scratch
inf.f.o = .7, # Band opacity
inf.f.col = piratepal("basel"), # Add color to bands
point.o = .1, # Point opacity
avg.line.o = .8, # Average line opacity
gl.col = gray(.6), # Gridline specifications
gl.lty = 1,
gl.lwd = c(.5, 0))
# See the vignette for more details
vignette("pirateplot", package = "yarrr")
``` |

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