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format_raw_data.R
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format_raw_data.R
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library(here)
library(tidyverse)
library(withr)
# Predator prey densities -------------------------------------------------
df <- read_tsv(here::here("data_raw", "predator_prey_density.tsv")) %>%
filter(replicate != 1) %>%
mutate(replicateABC=LETTERS[replicate-1]) %>%
mutate(microcosmID=paste0(treatment, "_", replicateABC),
sample=paste0(treatment, replicate, "-d", day )) %>%
select(sample, microcosmID, treatment, replicate=replicateABC, day, OD, ciliate_per_ml, worm_per_ml)
with_seed(123784,
cil_d <- df %>%
filter(day > 0) %>%
filter(!(treatment %in% c("H", "HN"))) %>%
select(sample, microcosmID, treatment, replicate, day, ciliate_per_ml) %>%
distinct() %>%
mutate(ciliate_per_ml_imp = ifelse(ciliate_per_ml == 0,
rlnorm(100, mean = 5, sd = 0.5),
ciliate_per_ml)) %>%
mutate(ciliate_per_ml_imp = round(ciliate_per_ml_imp))
)
with_seed(123784,
wrm_d <- df %>%
filter(day > 0) %>%
filter(!(treatment %in% c("H", "HPanc", "HPevo"))) %>%
select(sample, microcosmID, treatment, replicate, day, worm_per_ml) %>%
distinct() %>%
mutate(worm_per_ml_imp = ifelse(worm_per_ml == 0,
rlnorm(100, mean = 1, sd = 0.5),
worm_per_ml)) %>%
mutate(worm_per_ml_imp = round(worm_per_ml_imp))
)
od_d <- df %>%
dplyr::select(sample, microcosmID, treatment, replicate, day, OD)
df1 <- left_join(od_d, cil_d) %>%
left_join(., wrm_d) %>%
# for setting NAs to 0
#mutate(across(c(ciliate_count_raw, ciliate_per_ml,
# worm_count_raw, worm_per_ml), ~replace_na(.x, 0))) %>%
mutate(replicate=factor(replicate, levels=c("A", "B", "C", "D"))) %>%
mutate(treatment=factor(treatment, levels=c("H", "HN", "HPanc", "HPevo", "HNPanc", "HNPevo")),
microcosmID=factor(microcosmID))
write_rds(df1, here::here("data", "formatted_predator_prey_density.rds"))