In moggces/Rcurvep: Concentration-Response Data Analysis using Curvep

library(here)
library(tidyverse)

generate zfishdev

zfishdev <- readRDS(here("data-raw", "zfishdev.rds"))

zfishdev <- zfishdev %>%
  filter(stringr::str_detect(well__substance, 'Caffeine|Saccharin|Dieldrin')) %>%
  mutate(directionality = as.integer(directionality), n_in = as.integer(n_in), N = as.integer(N)) %>%
  rename(endpoint = id, chemical = well__substance) %>%
  rename(conc = concs) %>%
  select(-directionality)

usethis::use_data(zfishdev, overwrite =  TRUE)

generate zfishbeh

## the zfish behavior data
zfishbeh <- readRDS(here("data-raw", "zfishbeh.rds"))

zfishbeh <-  zfishbeh %>%
  filter(stringr::str_detect(well__substance, 'Caffeine|Saccharin|Dieldrin')) %>%
  mutate(directionality = as.integer(directionality)) %>%
  rename(endpoint = id, chemical = well__substance) %>%
  rename(conc = concs, resp = resps) %>%
  select(-directionality)


usethis::use_data(zfishbeh, overwrite =  TRUE)

generate zfishdev_all

zfishdev <- readRDS(here("data-raw", "zfishdev.rds"))
zfishdev_all <- zfishdev %>%
  mutate(directionality = as.integer(directionality), n_in = as.integer(n_in), N = as.integer(N)) %>%
  rename(endpoint = id, chemical = well__substance) %>%
  select(-directionality) %>%
  filter(stringr::str_detect(endpoint, "96")) %>%
  rename(conc = concs)
usethis::use_data(zfishdev_all, overwrite =  TRUE)

regenerate simulated data for zfishdev_all

data(zfishdev_all)
set.seed(300)
system.time(zfishdev_act <- combi_run_rcurvep(
  zfishdev_all, n_samples = 100, keep_sets = c("act_set"),TRSH = seq(5, 95, by = 5),
  RNGE = 1000000, CARR = 20
))
usethis::use_data(zfishdev_act, overwrite =  TRUE)
#out_dev_sum <- summarize_rcurvep_output(zfishdev_act, clean_only = TRUE)

test set.seed and will the input be the same

set.seed(300)
data(zfishbeh)
d1 <- create_dataset(zfishbeh, n_samples = 3)

set.seed(300)
data(zfishbeh)
d2 <- create_dataset(zfishbeh, n_samples = 3)

identical(d1, d2)

set.seed(300)
data(zfishdev)
d1 <- create_dataset(zfishdev, n_samples = 3)

set.seed(300)
data(zfishdev)
d2 <- create_dataset(zfishdev, n_samples = 3)

identical(d1, d2)

moggces/Rcurvep documentation built on Feb. 6, 2024, 3:30 a.m.