ggplot2 extension for a Chao- and iNEXT-wrapper outputs

BeeBDC::ggRichnessWrapper() takes data output from BeeBDC::iNEXTwrapper() and BeeBDC::ChaoWrapper() to produce plots for multiple groups in one go. The plots can be multiple per page and across multiple pages.

Usage

ggRichnessWrapper(
  iNEXT_in = country_iNEXT,
  iChao_in = NULL,
  filterOut = NULL,
  type = 1,
  se = TRUE,
  facet.var = "None",
  color.var = "Order.q",
  grey = FALSE,
  legendPerPlot = FALSE,
  show_iNEXT = TRUE,
  showPercent = TRUE,
  ChaoColour = "#55AD9B",
  iNEXTcolour = "#FD9B63",
  Chao_estimate = "iChao1 (Chiu et al. 2014)",
  nrow = 3,
  ncol = 4,
  labels = NULL,
  fileName = "richnessPlots",
  outPath = tempdir(),
  base_width = 8.3,
  base_height = 11.7,
  dpi = 300,
  ...
)

Arguments

iNEXT_in: a list of iNEXT objects computed by BeeBDC::iNEXTwrapper().
iChao_in: a list of R data created BeeBDC::ChaoWrapper().
filterOut: Character. A list of sites/countries to exclude from plotting; for example, because sample size was inadequate. Default = NULL.
type: three types of plots: sample-size-based rarefaction/extrapolation curve (type = 1); sample completeness curve (type = 2); coverage-based rarefaction/extrapolation curve (type = 3). From iNEXT::ggiNEXT()
se: a logical variable to display confidence interval around the estimated sampling curve. From iNEXT::ggiNEXT()
facet.var: create a separate plot for each value of a specified variable: no separation
(facet.var="None"); a separate plot for each diversity order (facet.var="Order.q"); a separate plot for each assemblage (facet.var="Assemblage"); a separate plot for each combination of order x assemblage (facet.var="Both"). From iNEXT::ggiNEXT()
color.var: create curves in different colors for values of a specified variable: all curves are in the same color (color.var="None"); use different colors for diversity orders (color.var="Order.q"); use different colors for sites (color.var="Assemblage"); use different colors for combinations of order x assemblage (color.var="Both"). From iNEXT::ggiNEXT()
grey: a logical variable to display grey and white ggplot2 theme. From iNEXT::ggiNEXT()
legendPerPlot: Logical. If TRUE, remove the legend from each plot. Default = FALSE
show_iNEXT: Logical. If TRUE, show the estimate and 95% CIs if specified for iNEXT. Default = TRUE.
showPercent: Logical. If TRUE, show the prrcentage increases. Default = TRUE.
ChaoColour: Character. The to be used to graph Chao estimates (95% confidence intervals are shown with reduced opacity). Default = "#55AD9B".
iNEXTcolour: Character. The to be used to graph iNEXT estimates (95% confidence intervals are shown with reduced opacity). Default = "#FD9B63".
Chao_estimate: Character. The name of the Chao estimate to use from those calculated in SpadeR::ChaoSpecies(). The options are "Homogeneous Model","Homogeneous (MLE)", "Chao1 (Chao, 1984)","Chao1-bc","iChao1 (Chiu et al. 2014)","ACE (Chao & Lee, 1992)", "ACE-1 (Chao & Lee, 1992)","1st order jackknife","2nd order jackknife". Default = "iChao1 (Chiu et al. 2014)".
nrow: Numeric. The number of rows per figure. Figures (that don't fit in the nrow*ncol grid) will be saved into additional files. Default = 3.
ncol: Numeric. The number of columns per figure. Figures (that don't fit in the nrow*ncol grid) will be saved into additional files. Default = 4.
labels: Character. The labels for each sub-plot (a, b, c, ...). The default is NULL, which will provide labels a-z as required.
fileName: Character. Prefix to the output files. Default = "richnessPlots".
outPath: Character. The fodler in which to save the plots. Default = tempdir()
base_width: Numeric. The width, in inches, to save the plot. Default = 8.3.
base_height: Numeric. The height, in inches, to save the plot. Default = 11.7.
dpi: Numeric. Plot resolution. Also accepts a string input: "retina" (320), "print" (300), or "screen" (72). Applies only to raster output types. Default = 300.
...: other arguments passed on to methods. Not currently used. From iNEXT::ggiNEXT()

Value

Saves pdf objects and returns a summary table for all levels

Examples

if (FALSE) { # \dontrun{

data(beesCountrySubset)

   # Transform data for iNEXT
 data_nextWrapper <- beesCountrySubset %>%
   dplyr::group_by(scientificName, country_suggested) %>%
   dplyr::count() 
   
 # Calculate iNEXT with the wrapper function
 output_iNEXTwrapper <- BeeBDC::iNEXTwrapper(data = data_nextWrapper,
                                             variableColumn = "country_suggested",
                                             valueColumn = "n",
                                             mc.cores = 1)

 # Transform data for iChao
data_iChao <- beesCountrySubset %>%
  dplyr::group_by(scientificName, country_suggested) %>%
  dplyr::count() %>%
  dplyr::select(scientificName, country_suggested, n) %>%
  tidyr::pivot_wider(names_from = country_suggested,
                     values_from = n,
                     values_fill = 0) %>%
  ## Create the rownames
  tibble::column_to_rownames("scientificName") %>%
  dplyr::tibble()
  
  # Run the wrapper function
output_iChaowrapper <- BeeBDC::ChaoWrapper(data = data_iChao,
                                             datatype = "abundance",
                                             k = 10,
                                             conf = 0.95,
                                             mc.cores = 1)
                                             
   # Make the plots! 
plot_summary <- BeeBDC::ggRichnessWrapper(
iNEXT_in = output_iNEXTwrapper,
iChao_in = output_iChaowrapper,
nrow = 2,
ncol = 2,
labels = NULL,
fileName = "speciesRichnessPlots",
outPath = tempdir(),
base_width = 8.3,
base_height = 11.7, 
dpi = 300)
      
} # }