Modifying the zooplankton files on an ecopart object can be tricky because you need to make the same change to many dataframes (or tibbles) in a list. To accomplish this, there are two functions which work with ecopart_obj and zoo_list to manipulate them: add_zoo() and mod_zoo(). Both these functions are built over lapply() and have a similar syntax: The first argument is an ecopart_obj or zoo_list then the second is a function which will be applied to each zoo_df in the list/object. The functions compatible with add_zoo() and mod_zoo() must take a df as an input. Several EcotaxaTools functions are built intentionally so they work with these approaches. However, it will often be the case you might need to write your own function. For an example of this look at the alternative renaming section. The approach using mod_zoo() and add_zoo() will feel comforable for anyone who regularly uses lapply(). It is worth understanding how these functions both work as they are a key method for organizing ecopart_obj.
To add a new column, or replace an existing column, use add_zoo(). The two required arguments are func and col_name which specify the function to use and what to call the new column respectively. Additional agruments should be specified for the function being used after these are called.
There are several reasons why it might be useful to add or replace a column. For example: #### Adding biovolume for each particle To add a column for each zooplankton’s size you could use add_zoo(). Here, you can also use the biovolume() function from EcotaxaTools. See the details for it here
library(EcotaxaTools)
ecopart_example <- ecopart_example |> add_zoo(func = biovolume,
col_name = 'biovol',
shape = 'ellipsoid',
pixel_mm = unique(ecopart_example$meta$acq_pixel))
ecopart_example |>
get_all('biovol') |>
summary() Min. 1st Qu. Median Mean 3rd Qu. Max.
0.09 0.45 0.62 22.28 1.12 47530.85 To replace taxonomic labels with other ones, you’ll likely want to replace the ‘name’ column. There are several ways to do this which are explained in the renaming page
To selectively remove rows or summarize a zoo_df while still maintaining the ecopart_obj class, use mod_zoo(). Similar to add_zoo(), this function works like lapply() and takes a func argument. However, there is no need to name the new column because the return value should be a zoo_df.
mod_zoo() is particularly useful for removing unwanted taxanomic categories see examples here, or other rows.
For example, you could use mod_zoo() to select a particular depth range of observations:
#First define a function for the observations:
get_mesopelagic_obsv <- function(df) {
row_index <- which(df$depth_including_offset > 200 & df$depth_including_offset < 1200)
if(length(row_index) == 0) {
return(NULL)
}
return(df[row_index, ])
}
# The use the function with mod_zoo()
midwater <- ecopart_example |> mod_zoo(func = get_mesopelagic_obsv)
# observe the data:
midwater |>
get_all('depth_including_offset') |>
range()[1] 200.2 1199.6