lor_plot: Save and customize lorelogram plot
In FabiolaIannarilli/lorelogram: Correlation in binary data

Description Usage Arguments Details Value Examples

View source: R/lor_plot.R

Estimates of pairwise log-odds ratios and associated 95% confidence intervals for each lag between 1 and max_lag calculated by the lorelogram function are plotted against the temporal or spatial lag (x-axis). The plotted lorelogram provides a graphical description of how correlation between outcomes changes as we increase the distance (in space or time) between sampling occassions. This function provides arguments for the customization of several aspects of the plot.

lor_plot(data, save_LOR_plot = FALSE, outDir = "",
  colour = "#0C71C9", linetype = "solid", title = "",
  x_axis_title = "Lag", y_axis_title = "Log-odds ratio", ylim = NULL,
  x_break = 10, alpha = 1)

`data`	output of `lorelogram` function.
`save_LOR_plot`	logical. Create a .jpg file of the results (default: FALSE)?
`outDir`	character. Conditional on `save_LOR_plot` = TRUE. In which directory should the .jpg file be saved?
`colour`	character. Color to fill the confidence interval band (default: "#0C71C9").
`linetype`	character. Linetype for the average log-odds ratio values (default: "solid"). It accepts all the linetype available for ggplot2::geom_line.
`title`	character. Title of the plot (default: NULL).
`x_axis_title`	character. Title of x-axis of the plot (default: "Lag").
`y_axis_title`	character. Title of y-axis of the plot (default: "Log-odds ratio").
`ylim`	numeric. Vector of two values `c(y_min, y_max)` defining range for the y axis (default: NULL).
`x_break`	numeric. Unit-lag distance between primary breaks in the x_axis (default: 10).
`alpha`	numeric. Set transparency of the band describing the confidence interval. Should be a value between 0 and 1 (default: 1).

data must be a data.frame object containing the numeric output of the lorelogram function. Visual aspects of the lorelogram plot such as color and transparency of the confidence interval band, linetype of the curve representing the average log-odds ratios estimates, title and x- and y-axis labels, can be customized and the resulting plot can be saved in a folder of user choice.

The function returns a plot of the estimates of pairwise log-odds ratios and associated 95% confidence intervals for each lag between 1 and max_lag.

# import data and estimate log-odds ratio
data(GrayFox_Hour)
lor <- lorelogram(GrayFox_Hour, max_lag = 72, plot_LOR = FALSE)

# basic plot
lor_plot(lor)

# customized plot
lor_plot(lor, colour = "red", alpha = 0.7, title = "My lorelogram",
 x_break = 24, x_axis_title = "Time Lag (Hour)")