Code/raw-results-datasets-func.R

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

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

#import ploting data
# source("./R/Davidson_2019_Data_wrangling2.R")
dat_all_output <- read_csv("./data/plot-all-data1.csv")
# names(dat_all_output)

###summaries for inline chuncks below:
mouse_N_144_summary <- dat_all_output %>%
  select(N,se.N, lcl.N, ucl.N, Valley, Control, Conditions, var, year, Date, trip) %>%
  mutate(grid = factor(paste(Control, Valley)),
         Conditions = factor(Conditions, labels = c("Rats unmodified", "Rats removed")))
# names(dat_all_output)

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