R/LEEF_1_biomass_bemovi_25_cropped.R

In LEEF-UZH/LEEF.analysis: Access Functions, Tests and Basic Analysis of the RRD Data from the LEEF Project

#' LEEF-1 - Add biomass to traits
#'
#' @param ciliate_traits_25 traits as read from file \code{morph_mvt_TIMESTAMP.rds}
#' @param ciliate_density_25 density as read from file \code{mean_density_per_ml_TIMESTAMP.rds}
#'
#' @return list containing two objects, \code{traits} containing complete traits file
#'   as the argument \code{algai_traits} day includinc biomass column and \code{biomasses}
#'   per timestamp, bottle and species per milliliter.
#' @export
#'
#' @examples
LEEF_1_biomass_bemovi_25_cropped <- function(
    ciliate_traits_25,
    ciliate_density_25
){

  video_biomass_species <- c("Paramecium_bursaria","Paramecium_caudatum","Coleps_irchel", # species for which biomass is calculated
                             "Stylonychia1","Stylonychia2","Colpidium","Euplotes",
                             "Tetrahymena", "Loxocephallus",
                             "Dexiostoma")

  # 25x cropped

  ciliate_traits_25_cropped_normalCases <- ciliate_traits_25 %>%
    dplyr::filter(species %in% video_biomass_species) %>%
    mutate(height = ifelse(
      species %in% c("Euplotes","Stylonychia1","Stylonychia2"),
      mean_minor/3,
      ifelse(
        species %in% c("Paramecium_bursaria"),
        mean_minor/1.5, mean_minor)),
      biomass = (4/3) * pi * (mean_minor/2) * (height/2) * (mean_major/2), # calculate biomass
      biomass = biomass/10^12  # change it from um3 to g, assuming water density
    )
  ciliate_traits_25_cropped_NotBiomass <- ciliate_traits_25 %>%
    dplyr::filter(!(species %in% video_biomass_species)) %>%
    mutate(
      height=as.numeric(NA),
      biomass=as.numeric(NA)
    )



  # join datasets again


  ciliate_traits_25_cropped <- rbind(
    ciliate_traits_25_cropped_normalCases,
    ciliate_traits_25_cropped_NotBiomass
  ) # traits dataset finished here


  # calculate biomass per milliliter

  extrapolation.factor_25 <- 23.367
  cropping.factor  <- 4

  # Make sure, that we have n_frames and not N_frames
  names(ciliate_traits_25_cropped)[names(ciliate_traits_25_cropped) == "N_frames"] <- "n_frames"

  biomasses <- ciliate_traits_25_cropped %>%
    group_by(timestamp, bottle, species) %>%
    summarize(
      biomass = sum(biomass * n_frames, na.rm = TRUE) / (3 * 125) # if not 3 videos corrections is done below with dens_factor
    ) %>%
    mutate(
      biomass = biomass * extrapolation.factor_25 * cropping.factor,
      biomass = ifelse(
        !(species %in% video_biomass_species),
        as.numeric(NA),
        biomass
      )
    ) # add biomass=NA if not a species

  biomasses$timestamp <- as.character(biomasses$timestamp)

  densities <- full_join(
    ciliate_density_25,
    biomasses,
    by = c("timestamp", "bottle", "species")
  )
  densities$biomass[densities$species %in% video_biomass_species & is.na(densities$biomass)] <- 0

  densities <- densities |>
    mutate(
      biomass = biomass * dens_factor
    )

    # mutate(
    #   biomass = case_when(
    #     species %in% flowcam_biomass_species & is.na(biomass) ~ 0,
    #     TRUE ~ biomass)
    # )

  return(
    list(
      traits = ciliate_traits_25,
      density = densities
    )
  )

}