Code/05-raw-seed-results.R

In davan690/beech-publication-wr: Small mammal dynamics in NZ beech forests

#function for importing information for bsaic manuscript results
#Anthony 
#March2020

#data needed
dat_all_output <- read_csv("./data/plot-all-data1.csv")

#function
raw_estimates_seed_func <- function(dat_all_output = dat_all_output){

    seed_N_144_summary <- dat_all_output %>%
        select(cum.seed, Control, Valley, year, Date, Conditions) %>%
            mutate(year = as.factor(year),
            mean_seed = cum.seed)

return(seed_N_144_summary)

} #function end


#example function 2
#raw_estimates_seed_func(dat_all_output = dat_all_output)


#function
full_grouped_seed_func <- function(dat_all_output = dat_all_output){

# summaries_Control, valley, year
group_seed_N_144_summary <- dat_all_output %>%

    select(cum.seed, Control, Valley, Conditions, year, Date) %>%

      mutate(year = as.factor(year),
             Conditions = as.factor(Conditions)) %>%

        group_by(Control, Valley, Date) %>%
  summarise(N = mean(ifelse(cum.seed > 0, ifelse(cum.seed > 0, log(cum.seed), 0), 0)),
            # Rats = factor("ALL"),
            sd.s = sd(ifelse(cum.seed > 0, log(cum.seed), 0), na.rm = TRUE),
            se.s = sd(ifelse(cum.seed > 0, log(cum.seed), 0)) / sqrt(length(cum.seed)) * 1.96,
            lcl.s = mean(ifelse(cum.seed > 0, log(cum.seed), 0)) - (sd(ifelse(cum.seed > 0, log(cum.seed), 0)) / sqrt(length(cum.seed)) *
                                                                      1.96),
            lcl_seed = exp(lcl.s),
            ucl.s = mean(ifelse(cum.seed > 0, log(cum.seed), 0)) + (sd(ifelse(cum.seed > 0, log(cum.seed), 0)) / sqrt(length(cum.seed)) *
                                                                      1.96),
            ucl_seed = exp(ucl.s), mean_seed = exp(N)) %>%
  ungroup()

return(group_seed_N_144_summary)

} #function end

#example

full_grouped_seed <- full_grouped_seed_func(dat_all_output = dat_all_output)