R/data wrangling/on hold/battles_2015.r

In chase-lab/BioTIMEx: Aggregating long-term ecological communities data

## battles_2015

dataset_id <- 'battles_2015'

      if(FALSE) {
      load(file='data/raw data/battles_2015/ddata')

      dat <- data.frame(dataset_id = rep(dataset_id, nrow(ddata)))

      dat$year <- ddata$year
      dat$month <- NA
      dat$day <- NA

      dat$site <- 'Hubbard Brook Watershed 5'

      zones <- c('ridge_top_spruce/fir_forest', 'east_side_spruce/fir_forest', 'high_elevation_hardwoods', 'middle_elevation_hardwoods', 'low_elevation_hardwoods')
      dat$block <- zones[match(ddata$Zone, 1:5)]
      dat$plot <- ddata$Plot
      dat$subplot <- NA

      dat$treatment <- 'logging'


      dat$treatment_type <- 'logging'

      dat$design <- 'AI'

      timepoints <- seq_along(unique(ddata$year))
      timepoints <- paste0('T',timepoints[match(ddata$year, unique(ddata$year))])
      dat$timepoint <- timepoints

      dat$time_since_disturbance_days <- ddata$year - 1983


      dat$realm <- 'terrestrial'
      dat$taxon <- 'plants'

      dat$species <- ddata$Species
      dat$metric <- 'density'
      #species_counts <- aggregate(Species ~ Plot, data = ddata, table)
      #reshape2::melt(species_counts, grep(x=colnames(species_counts), 'Species'))

      # Before running, the following changes have to be made
      #  - exclude dead trees
      #  - count individuals only once even if they have several stems



      dat$value <- ddata$n
      dat$unit <- 'ind per m2'

      dat$comment <- 'The blocks represent pre-logging vegetation and are not necessarily meaningful any more. They can be pooled together. Meaning of species codes is found here: https://portal.edirepository.org/nis/metadataviewer?packageid=knb-lter-hbr.39.7'

      dat <- dat[!is.na(dat$value) & dat$value > 0, ]

      # dir.create(paste0('data/wrangled data/', dataset_id), showWarnings = FALSE)
      # write.csv(dat, paste0('data/wrangled data/', dataset_id, "/", dataset_id, '.csv'),
      #           row.names=FALSE)

      }