This folder contains a selection of functions and code snippets which are useful to process synthesis datasets.
Next action/ vision: this folder will be converted to an R package containing useful functions for synthesis.
add_back_missing_plots_species_combinationsBEplotZerosBEplotNonZerosBEaddRegionBEaddHabitathead2D
R function to use together with the synthesis diversity dataset. Some plots x species combinations with 0 species were removed from Bacteria and soilfungi in order to save memory. Adding back the missing combinations sometimes requires adding a plot which is completely missing from the dataset, which is exactly what this function does. Find further information about the "missing zeros" in the synthesis dataset manual.
Example:
bacteria.RNA <- add_back_missing_plots_species_combinations(bacteria.RNA, all_plots)
See the documentation of the function in the script itself.
The function requires the package data.table.
R function that adds the sortable plot names to an existing dataset. Based on a column with Bexis plot names (e.g. AEG1), the function creates a column with sortable plot names (e.g. AEG01). Note: This function does the opposite of the BEplotNonZeros.R function (below).
Example:
#create a dataset with a plot name column
dat <- data.frame(Plot_name = c("AEG1", "AEG2", "HEW4", "SEG8", "SEW10"), Values=1:5)
dat <- BEplotZeros(dat, "Plot_name", plotnam = "Sorted_plot_name")
R function that adds the original Bexis plot names (non sortable) to an existing dataset. Based on a column with sortable plot names (e.g. AEG01), the function creates a column with Bexis plot names (e.g. AEG1). Note: this function does the opposite of the BEplotZeros function (above).
Example:
#create a dataset with a Bexis plot name column
dat <- data.frame(Bexis_plot_name = c("AEG01", "AEG02", "HEW04", "SEG08", "SEW10"), Values=1:5)
dat <- BEplotNonZeros(dat, "Bexis_plot_name", plotnam = "New_plot_name")
R function that adds the Biodiversity Exploratories region code (ALB, SCH, HAI) to a dataset that contains a column with the Exploratories plot names.Note that the function currently only works with sortable plot names (e.g. "AEG01"), but not yet with Bexis plot names (e.g. "AEG1"). I will update it soon! In the meantime, please use the function BEplotZeros to add a column with sortable plot names.
Example:
#create a dataset with a plot name column
#' dat <- data.frame(Plot_name = c("AEG01", "AEG02", "HEW04", "SEG08", "SEW10"), Values=1:5)
#' dat <- BEaddRegion(dat, "Plot_name", regionam = "Explo")
This function adds the Biodiversity Exploratories habitat type (forest/grassland) to a dataset that contains a column with the Exploratories plot names.
Example:
#create a dataset with a plot name column (with or without zeros)
dat <- data.frame(Plot_name = c("AEG01", "AEG02", "HEW04", "SEG8", "SEW10"), Values=1:5)
dat <- BEaddHabitat(dat, "Plot_name", habitatname = "Habitat")
This function prints the first 10 lines and 10 columns of a data.frame into the console. It is an expanded version of the head() function. The head() function prints out the first 10 lines of a data.frame, but is not handy for data.frames with many columns, as the output gets messy.
Example :
# create a data.frame with many rows and many columns
dat <- cbind(data.frame(Plot_name = paste(c("AEG", "HEG", "SEG"), seq(1, 50), sep= "")),
data.frame(matrix(0, nrow = 150, ncol = 50, dimnames = list(NULL, paste("Species", seq(1, 50), sep = "_")))))
head(dat) # messy output with head
head2D(dat) # clear output, only first 10 rows and columns