# SET PROFILE PATH AND ID
# ────────────────────────────────────────────────────
profile_path <- "inst/extdata/first_Visit_1_PB_8.csv"   # <-- Replace with your actual path
profile_id   <- "first_Visit_1_PB_8"                    # <-- Base name, no extension
# ────────────────────────────────────────────────────
# RUN THE PROCESSING FUNCTION
# ────────────────────────────────────────────────────
result_fix <- process_single_profile(profile_id, profile_path, n_rep = 10)
# ────────────────────────────────────────────────────
# SAVE THE RESULT
# ────────────────────────────────────────────────────
out_dir <- "outputs/noisy_dlmo_results"
dir.create(out_dir, showWarnings = FALSE, recursive = TRUE)
saveRDS(result_fix, file.path(out_dir, paste0(profile_id, ".rds")))
iteration_errors_df <- result_fix$errors
readr::write_csv(iteration_errors_df, file.path(out_dir, "noise_simulation_iteration_errors.csv"))
# Save errors (including sim_df!)
readr::write_rds(result_fix$errors, file.path(out_dir, paste0(profile_id, "_iteration_errors.rds")))
# OR save as CSV if you drop sim_df (list-column not supported in CSV)
readr::write_csv(dplyr::select(result_fix$errors, -sim_df), file.path(out_dir, paste0(profile_id, "_iteration_errors.csv")))
# (Optional) view a summary
# print(result)
first_Visit_1_PB_8_iteration_errors <- readRDS("~/Documents/dlmoR/outputs/noisy_dlmo_results/first_Visit_1_PB_8_iteration_errors.rds")
Viow(first_Visit_1_PB_8_iteration_errors)
View(first_Visit_1_PB_8_iteration_errors)
first_Visit_1_PB_8_iteration_errors$sim_df[[1]]
first_Visit_1_PB_8_iteration_errors$sim_df[[2]]
first_Visit_1_PB_8_iteration_errors$sim_df[[3]]
first_Visit_1_PB_8_iteration_errors$sim_df[[4]]
first_Visit_1_PB_8_iteration_errors$sim_df[[5]]
first_Visit_1_PB_8_iteration_errors$sim_df[[6]]
first_Visit_1_PB_8_iteration_errors$sim_df[[7]]
first_Visit_1_PB_8_iteration_errors$sim_df[[8]]
first_Visit_1_PB_8_iteration_errors <- readRDS("~/Documents/dlmoR/outputs/noisy_dlmo_results/first_Visit_1_PB_8_iteration_errors.rds")
first_Visit_1_PB_8 <- readRDS("~/Documents/dlmoR/outputs/noisy_dlmo_results/first_Visit_1_PB_8.rds")
View(first_Visit_1_PB_8)
View(first_Visit_1_PB_8$errors)
first_Visit_1_PB_8$errors$sim_df[[1]]
View(first_Visit_1_PB_8)
View(first_Visit_1_PB_8$results)
all_res <- first_Visit_1_PB_8$results
baseline_df <- all_res %>%
filter(condition == "clean") %>%
select(profile, baseline = dlmo_est)
# 3. Join into full table and compute delta
full_df <- all_res %>%
left_join(baseline_df, by = "profile") %>%
mutate(delta = dlmo_est - baseline)
View(full_df)
# 4. Summary table (includes the clean run as one of the reps)
summary_df <- full_df %>%
group_by(profile, condition) %>%
summarise(
n_reps       = n(),
mean_dlmo    = mean(dlmo_est,   na.rm = TRUE),
sd_dlmo      = sd(dlmo_est,     na.rm = TRUE),
mean_delta   = mean(delta,      na.rm = TRUE),
sd_delta     = sd(delta,        na.rm = TRUE),
mean_mel_sd  = mean(mean_mel_sd, na.rm = TRUE),
min_mel_sd   = min(min_mel_sd,  na.rm = TRUE),
max_mel_sd   = max(max_mel_sd,  na.rm = TRUE),
mean_time_sd = mean(time_sd,     na.rm = TRUE),
.groups      = "drop"
)
print(summary_df)
View(summary_df) #in RStudio for a spreadsheet‐style look
####################
# Raincloud of delta DLMO for each condition
####################
library(dplyr)
library(purrr)
library(ggplot2)
library(gghalves)
# # 1) Read in all of your *_dlmo_time_mel_stats.rds files
# all_res <- list.files(out_dir,
#                       pattern = "_dlmo_time_mel_stats\\.rds$",
#                       full.names = TRUE) %>%
#   map_df(readRDS)
#
# # 2) Pull out the clean (baseline) DLMO per profile
# baseline <- all_res %>%
#   filter(condition == "clean") %>%
#   select(profile, clean_dlmo = dlmo_est)
# 3) Join & compute delta for *every* row (including clean)
# full_df <- all_res %>%
#   left_join(baseline, by = "profile") %>%
#   mutate(
#     delta = dlmo_est - clean_dlmo
#   )
# 4) Select exactly the six conditions you care about
wanted <- c("clean","mel_only","time_5min","time_10min","time_20min","both_axes_10")
labels <- c(
"Clean",
"Melatonin Only",
"Time Only\n(5 min)",
"Time Only\n(10 min)",
"Time Only\n(20 min)",
"Mel + Time\n(10 min)"
)
plot_df <- full_df %>%
filter(condition %in% wanted) %>%
mutate(
condition = factor(condition, levels = wanted, labels = labels)
)
# 5) Split out clean vs noisy
df_clean    <- filter(plot_df, condition == "Clean")
df_no_clean <- filter(plot_df, condition != "Clean")
# 6) Plot—all deltas are pre‑computed, so clean is exactly zero
ggplot() +
# Raincloud for noisy conditions
geom_half_violin(
data = df_no_clean,
aes(x = condition, y = delta, fill = condition),
side  = "l", trim = FALSE, alpha = 0.6, width = 0.6
) +
geom_boxplot(
data = df_no_clean,
aes(x = condition, y = delta),
width = 0.10, outlier.shape = NA,
position = position_nudge(x = 0.1), alpha = 0.8
) +
geom_half_point(
data        = df_no_clean,
aes(x = condition, y = delta),
side        = "r", range_scale = 0.4,
position    = position_nudge(x = 0.1),
alpha       = 0.4, size = 1
) +
# Plot the clean runs as points—delta is already zero
# geom_point(
#   data = df_clean,
#   aes(x = condition, y = delta),
#   color = "black", fill = "black",
#   shape = 21, size = 3
# ) +
labs(
title = "Raincloud Plot of ΔDLMO by Noise Condition",
x     = NULL,
y     = "Δ DLMO (hours)"
) +
theme_minimal() +
theme(
axis.text.x       = element_text(angle = 45, hjust = 1),
legend.position   = "none",
panel.grid.major.x = element_blank()
)
first_Visit_1_PB_8$results[[2]]
first_Visit_1_PB_8$results$sim_df[[2]]
first_Visit_1_PB_8$results$sim_df[[1]]
first_Visit_1_PB_8$results$sim_df[[8]]
first_Visit_1_PB_8$results$sim_df[[10]]
first_Visit_1_PB_8$results$sim_df[[11]]
first_Visit_1_PB_8$results$sim_df[[22]]
first_Visit_1_PB_8$results$sim_df[[23]]
first_Visit_1_PB_8$results$sim_df[[24]]
first_Visit_1_PB_8$results$sim_df[[25]]
first_Visit_1_PB_8$results$sim_df[[26]]
first_Visit_1_PB_8$results
View(first_Visit_1_PB_8$results)
first_Visit_1_PB_8$results$sim_df[[26]]
test_result26 <- calculate_dlmo(first_Visit_1_PB_8$results$sim_df[[26]])
test_result26 <- calculate_dlmo(first_Visit_1_PB_8$results$sim_df[[26]], threshold = 5)
test_result26
# SET PROFILE PATH AND ID
datetime  = decimal_to_posixct(t_pert, df$datetime),
first_Visit_1_PB_2_iteration_errors <- readRDS("~/Documents/Projects/DLMO/clusterRuns/Blume/noisy_dlmo_results/first_Visit_1_PB_2_iteration_errors.rds")
View(first_Visit_1_PB_2_iteration_errors)
first_Visit_1_PB_2_iteration_errors$sim_df[[1]]
test_result1<- calculate_dlmo(first_Visit_1_PB_2_iteration_errors$sim_df[[1]], threshold = 5)
test_result1$dlmoplotfine
first_Visit_1_PB_2_iteration_errors$sim_df[[2]]
test_result2<- calculate_dlmo(first_Visit_1_PB_2_iteration_errors$sim_df[[2]], threshold = 5)
test_result2$dlmoplotfine
test_result3<- calculate_dlmo(first_Visit_1_PB_2_iteration_errors$sim_df[[3]], threshold = 5)
test_result3$dlmoplotfine
first_Visit_1_PB_2 <- readRDS("~/Documents/Projects/DLMO/clusterRuns/Blume/noisy_dlmo_results/first_Visit_1_PB_2.rds")
View(first_Visit_1_PB_2)
test_result31<- calculate_dlmo(first_Visit_1_PB_2_iteration_errors$sim_df[[31]], threshold = 5)
first_Visit_1_PB_2_iteration_errors$sim_df[[31]]
first_Visit_1_PB_2_iteration_errors$sim_df[[34]]
test_result49<- calculate_dlmo(first_Visit_1_PB_2_iteration_errors$sim_df[[49]], threshold = 5)
test_result49$dlmoplotfine
first_Visit_1_PB_6_iteration_errors <- readRDS("~/Documents/Projects/DLMO/clusterRuns/Blume/noisy_dlmo_results/first_Visit_1_PB_6_iteration_errors.rds")
View(first_Visit_1_PB_6_iteration_errors)
test_result6_1<- calculate_dlmo(first_Visit_1_PB_6_iteration_errors$sim_df[[1]], threshold = 5)
first_Visit_1_PB_8_iteration_errors <- readRDS("~/Documents/Projects/DLMO/clusterRuns/Blume/noisy_dlmo_results/first_Visit_1_PB_8_iteration_errors.rds")
test_result6_1$dlmoplotfine
View(first_Visit_1_PB_8_iteration_errors)
test_result8_1<- calculate_dlmo(first_Visit_1_PB_8_iteration_errors$sim_df[[1]], threshold = 5)
test_result8_1$dlmoplotfine
first_Visit_1_PB_8_iteration_errors$sim_df[[40]]
first_Visit_1_PB_16_iteration_errors$sim_df[[16]]
first_Visit_1_PB_8_iteration_errors$sim_df[[16]]
first_Visit_1_PB_8_iteration_errors$sim_df[[32]]
test_result8_35<- calculate_dlmo(first_Visit_1_PB_8_iteration_errors$sim_df[[35]], threshold = 5)
test_result8_35$dlmoplotfine
first_Visit_2_PB_2_iteration_errors <- readRDS("~/Documents/Projects/DLMO/clusterRuns/Blume/noisy_dlmo_results/first_Visit_2_PB_2_iteration_errors.rds")
View(first_Visit_2_PB_2_iteration_errors)
first_Visit_2_PB_2_iteration_errors$sim_df[[5]]
first_Visit_2_PB_2_iteration_errors$sim_df[[4]]
first_Visit_2_PB_2_iteration_errors$sim_df[[3]]
first_Visit_2_PB_2_iteration_errors$sim_df[[2]]
test_result2_2<- calculate_dlmo(first_Visit_2_PB_2_iteration_errors$sim_df[[2]], threshold = 5)
test_result2_2$dlmoplotfine
first_Visit_2_PB_2_iteration_errors$sim_df[[1]]
test_result2_1<- calculate_dlmo(first_Visit_2_PB_2_iteration_errors$sim_df[[1]], threshold = 5)
test_result2_1$dlmoplotfine
first_Visit_3_PB_16_iteration_errors <- readRDS("~/Documents/Projects/DLMO/clusterRuns/Blume/noisy_dlmo_results/first_Visit_3_PB_16_iteration_errors.rds")
View(first_Visit_3_PB_16_iteration_errors)
test_result3_16_1<- calculate_dlmo(first_Visit_3_PB_16_iteration_errors$sim_df[[1]], threshold = 5)
test_result3_16_1
first_Visit_3_PB_16 <- readRDS("~/Documents/Projects/DLMO/clusterRuns/Blume/noisy_dlmo_results/first_Visit_3_PB_16.rds")
View(first_Visit_3_PB_16)
first_Visit_3_PB_16$sim_df[[99]]
first_Visit_2_PB_13_iteration_errors <- readRDS("~/Documents/Projects/DLMO/clusterRuns/Blume/noisy_dlmo_results/first_Visit_2_PB_13_iteration_errors.rds")
View(first_Visit_2_PB_13_iteration_errors)
first_Visit_2_PB_13_iteration_errors$sim_df[[2]]
first_Visit_2_PB_13_iteration_errors$sim_df[[1]]
test_result2_13_1<- calculate_dlmo(first_Visit_2_PB_13_iteration_errors$sim_df[[1]], threshold = 5)
test_result2_13_1$dlmoplotfine
first_Visit_3_PB_16$sim_df[[99]]
test_result3_16_99<- calculate_dlmo(first_Visit_3_PB_16_iteration_errors$sim_df[[99]], threshold = 5)
test_result3_16_99<- calculate_dlmo(first_Visit_3_PB_16$sim_df[[99]], threshold = 5)
test_result3_16_99$dlmoplotfine
test_result3_16_99$dlmo
test_result3_16_99$dlmo$fine
test_result3_16_99$dlmo$fine$time
test_result3_16_99$ip$inflection_point_fine$x
first_Visit_3_PB_16$sim_df[[98]]
first_Visit_3_PB_16$sim_df[[95]]
first_Visit_3_PB_16_iteration_errors$sim_df[[1]]
View(first_Visit_3_PB_16_iteration_errors)
first_Visit_3_PB_16_iteration_errors$sim_df[[2]]
second_Visit_3_PB_14_iteration_errors <- readRDS("~/Documents/Projects/DLMO/clusterRuns/Blume/noisy_dlmo_results/second_Visit_3_PB_14_iteration_errors.rds")
View(second_Visit_3_PB_14_iteration_errors)
second_Visit_3_PB_13_iteration_errors <- readRDS("~/Documents/Projects/DLMO/clusterRuns/Blume/noisy_dlmo_results/second_Visit_3_PB_13_iteration_errors.rds")
View(second_Visit_3_PB_13_iteration_errors)
second_Visit_3_PB_7_iteration_errors <- readRDS("~/Documents/Projects/DLMO/clusterRuns/Blume/noisy_dlmo_results/second_Visit_3_PB_7_iteration_errors.rds")
View(second_Visit_3_PB_7_iteration_errors)
second_Visit_3_PB_7_iteration_errors$sim_df[[1]]
second_Visit_3_PB_7_iteration_errors$sim_df[[2]]
second_Visit_3_PB_7 <- readRDS("~/Documents/Projects/DLMO/clusterRuns/Blume/noisy_dlmo_results/second_Visit_3_PB_7.rds")
View(second_Visit_3_PB_7)
second_Visit_3_PB_7$sim_df[[1]]
second_Visit_3_PB_7$sim_df[[2]]
second_Visit_3_PB_7$sim_df[[4]]
second_Visit_3_PB_7$sim_df[[20]]
second_Visit_3_PB_7$sim_df[[79]]
second_Visit_3_PB_7$sim_df[[90]]
second_Visit_3_PB_7$sim_df[[81]]
test_result3_7_1<- calculate_dlmo(first_Visit_3_PB_8_iteration_errors$sim_df[[1]], threshold = 5)
test_result3_7_1<- calculate_dlmo(first_Visit_3_PB_7_iteration_errors$sim_df[[1]], threshold = 5)
test_result3_7_1<- calculate_dlmo(second_Visit_3_PB_7_iteration_errors$sim_df[[1]], threshold = 5)
View(second_Visit_3_PB_7_iteration_errors)
View(second_Visit_3_PB_7_iteration_errors)
second_Visit_3_PB_7$sim_df[[89]]
second_Visit_3_PB_7$sim_df[[88]]
second_Visit_3_PB_7$sim_df[[90]]
second_Visit_3_PB_7$sim_df[[81]]
second_Visit_3_PB_7$sim_df[[79]]
dh<- posixct_to_decimal(second_Visit_3_PB_7$sim_df[[79]]$datetime, second_Visit_3_PB_7$sim_df[[79]]$datetime )
dh
dh<- posixct_to_decimal(second_Visit_3_PB_7$sim_df[[79]]$datetime, second_Visit_3_PB_7$sim_df[[79]]$datetime[3] )
dh
posix<- decimal_to_posixct(dh, second_Visit_3_PB_7$sim_df[[79]]$datetime[3])
posix
posix<- decimal_to_posixct(dh, second_Visit_3_PB_7$sim_df[[79]]$datetime)
posix
second_Visit_3_PB_7$dlmo_full_result[[89]]$ip$inflection_point_fine$x
test_result_3_7_89<- calculate_dlmo(second_Visit_3_PB_7$sim_df[[89]], threshold = 5)
test_result_3_7_89$dlmoplotfine
test_result_3_7_89$ip$inflection_point_fine$x
test_result_3_7_89$prof
second_Visit_3_PB_7$sim_df[[89]]
second_Visit_3_PB_7$dlmo_full_result[[89]]$dlmoplotfine
second_Visit_3_PB_7$dlmo_full_result[[89]]$dlmo$fine$time
View(test_result_3_7_89)
test_result_3_7_89$roi
second_Visit_3_PB_7$dlmo_full_result[[89]]$roi
second_Visit_3_PB_7$dlmo_full_result[[89]]$prof
test_result_3_7_89v2<- dlmoR::calculate_dlmo(second_Visit_3_PB_7$sim_df[[89]], threshold = 5)
second_Visit_3_PB_7$dlmo_full_result[[89]]$ip$inflection_point_fine$x
test_result_3_7_89$roi
second_Visit_3_PB_7$dlmo_full_result[[89]]$roi
roi_dh<-posixct_to_decimal(second_Visit_3_PB_7$dlmo_full_result[[89]]$roi, second_Visit_3_PB_7$dlmo_full_result[[89]]$prof$datetime[3])
roi_dh<-posixct_to_decimal(second_Visit_3_PB_7$dlmo_full_result[[89]]$roi$x_start, second_Visit_3_PB_7$dlmo_full_result[[89]]$prof$datetime[3])
roi_dh
roi_dh<-posixct_to_decimal(second_Visit_3_PB_7$dlmo_full_result[[89]]$roi$x_end, second_Visit_3_PB_7$dlmo_full_result[[89]]$prof$datetime[3])
roi_dh
View(second_Visit_3_PB_7_iteration_errors)
View(first_Visit_2_PB_2_iteration_errors)
View(second_Visit_3_PB_7)
View(second_Visit_3_PB_7)
help(package = dlmoR)
help(package = "dlmoR")
View(first_Visit_2_PB_2_iteration_errors)
View(first_Visit_2_PB_2_iteration_errors)
first_Visit_1_PB_2_iteration_errors$sim_df[[3]]
first_Visit_2_PB_2_iteration_errors$sim_df[[3]]
first_Visit_2_PB_2_iteration_errors$sim_df[[4]]
first_Visit_2_PB_2_iteration_errors$sim_df[[5]]
View(second_Visit_3_PB_7_iteration_errors)
View(second_Visit_3_PB_7_iteration_errors)
first_Visit_3_PB_7_iteration_errors$sim_df[[4]]
second_Visit_3_PB_7_iteration_errors$sim_df[[4]]
second_Visit_3_PB_7_iteration_errors$sim_df[[3]]
second_Visit_3_PB_7_iteration_errors$sim_df[[2]]
second_Visit_3_PB_7_iteration_errors$sim_df[[1]]
second_Visit_3_PB_7$sim_df[[5]]
second_Visit_3_PB_7$sim_df[[6]]
second_Visit_3_PB_7$sim_df[[78]]
second_Visit_3_PB_7_iteration_errors$sim_df[[2]]
View(first_Visit_2_PB_2_iteration_errors)
View(first_Visit_2_PB_2_iteration_errors)
first_Visit_2_PB_2_iteration_errors$sim_df[[2]]
first_Visit_2_PB_2_iteration_errors$sim_df[[4]]
first_Visit_2_PB_2_iteration_errors$sim_df[[1]]
test_221<- calculate_dlmo(first_Visit_2_PB_2_iteration_errors$sim_dif[[1]])
test_221<- calculate_dlmo(first_Visit_2_PB_2_iteration_errors$sim_dif[[1]], threshold = 5)
test_221 <- calculate_dlmo(first_Visit_2_PB_2_iteration_errors$sim_dif[[1]], threshold = 5)
test_221 <- calculate_dlmo(first_Visit_2_PB_2_iteration_errors$sim_df[[1]], threshold = 5)
test_221$dlmoplotfine
first_Visit_2_PB_2_iteration_errors$sim_df[[3]]
first_Visit_2_PB_2_iteration_errors$sim_df[[4]]
first_Visit_2_PB_2_iteration_errors$sim_df[[5]]
sd(0)
rnorm(5,0,0)
rnorm(5,0,-1)
View(first_Visit_2_PB_2_iteration_errors)
test_221$dlmoplotfine
devtools::load_all()
test_221v1 <- calculate_dlmo(first_Visit_2_PB_2_iteration_errors$sim_df[[1]], threshold = 5)
test_221v1$dlmoplotfine
test_221v1$dlmoplotfine
first_Visit_3_PB_3 <- readRDS("~/Documents/Projects/DLMO/clusterRuns/Blume/noisy_dlmo_results/first_Visit_3_PB_3.rds")
View(first_Visit_3_PB_3)
pmax(nan,0)
pmax(NaN,0)
source("~/Documents/dlmoR/devcode/noise_trial.R")
library(dplyr)
library(purrr)
library(dlmoR)
library(readr)
library(furrr)
library(future)
library(progressr)
# ────────────────────────────────────────────────────
# SETUP PARALLEL BACKEND
# ────────────────────────────────────────────────────
plan(multisession, workers = 2)
source("~/Documents/dlmoR/devcode/noise_trial.R")
first_Visit_1_PB_1 <- readRDS("~/Documents/dlmoR/outputs/trial_dlmo_results/first_Visit_1_PB_1.rds")
View(first_Visit_1_PB_1)
first_Visit_1_PB_1$sim_df[[8]]
test_1_1 <- calculate_dlmo(first_Visit_1_PB_1$sim_df[[8]], threshold = 5)
first_Visit_1_PB_10 <- readRDS("~/Documents/dlmoR/outputs/trial_dlmo_results/first_Visit_1_PB_10.rds")
test_1_1$dlmoplotfine
test_1_1$ip$inflection_point_fine
test_1_1$ip$inflection_point_fine$x
first_Visit_1_PB_1$dlmo_est[[8]]
first_Visit_1_PB_1$dlmo_est[[8]]
first_Visit_1_PB_1$sim_df[8]
test_1_1again <- calculate_dlmo(first_Visit_1_PB_1$sim_df[[8]], threshold = 5)
View(first_Visit_1_PB_10)
View(first_Visit_1_PB_10)
test_1_1again
test_1_1again$dlmo$fine$time
test_1_1again$ip$inflection_point_fine
test_1_1again$prof
first_Visit_1_PB_1$profile
first_Visit_1_PB_1$sim_df[[8]]
first_Visit_1_PB_1$dlmo_est[[8]]
test_1_1again$ip$inflection_point_fine
test_1_1again$ip$inflection_point_fine$x + 24
View(first_Visit_1_PB_1)
first_Visit_1_PB_1$dlmo_est[[9]]
test_1_1_9 <- calculate_dlmo(first_Visit_1_PB_1$sim_df[[9]], threshold = 5)
test_1_1_9$ip$inflection_point_fine
first_Visit_1_PB_1$dlmo_est[[9]]
View(first_Visit_1_PB_1)
View(first_Visit_1_PB_1)
View(first_Visit_1_PB_1[[2]][[9]])
View(first_Visit_1_PB_1[[2]][[9]])
View(first_Visit_1_PB_1[[2]][[9]])
first_Visit_1_PB_1$sim_df[[9]]
test_1_1_9$ip$inflection_point_fine$x
first_Visit_1_PB_1$dlmo_est[[9]]
first_Visit_1_PB_1$dlmo_full_result[[9]]$ip$inflection_point_fine$x
test_1_1_9_v2 <- calculate_dlmo(first_Visit_1_PB_1$sim_df[[9]], threshold = 5)
test_1_1_9_v2$ip$inflection_point_fine$x
first_Visit_1_PB_1$sim_df[[3]]
first_Visit_1_PB_1$sim_df[[6]]
first_Visit_1_PB_1$sim_df[[8]]
View(first_Visit_1_PB_1)
View(first_Visit_1_PB_1)
first_Visit_1_PB_1$sim_df[[10]]
dh1110<-posixct_to_decimal(first_Visit_1_PB_1$sim_df[[10]], first_Visit_1_PB_1$sim_df[[3]])
dh1110<-posixct_to_decimal(first_Visit_1_PB_1$sim_df[[10]]$datetime, first_Visit_1_PB_1$sim_df[[10]]$datetime[3])
dh1110
decimal_to_posixct(dh1110, first_Visit_1_PB_1$sim_df[[10]]$datetime[3])
first_Visit_1_PB_1$sim_df[[10]]$datetime[1]
first_Visit_1_PB_1$sim_df[[10]]$datetime[3]
posixct_to_decimal(first_Visit_1_PB_1$sim_df[[10]]$datetime, first_Visit_1_PB_1$sim_df[[10]]$datetime)
posixct_to_decimal(first_Visit_1_PB_1$sim_df[[10]]$datetime, first_Visit_1_PB_1$sim_df[[10]]$datetime[3])
source("~/Documents/dlmoR/devcode/noise_trial.R")
first_Visit_1_PB_1 <- readRDS("~/Documents/dlmoR/outputs/trial_dlmo_results/first_Visit_1_PB_1.rds")
View(first_Visit_1_PB_1)
devtools::install("dlmoR")
devtools::install()
devtools::install()
source("~/Documents/dlmoR/devcode/noise_trial.R")
devtools::load_all()
git remote -v
devtools::load_all()
?calculate_dlmo
filename <- system.file("extdata/sample_melatonin_profile.csv", package = "dlmoR")
calculate_dlmo(
data = NULL,
file_path = NULL,
threshold = 2.3,
interval_limit = lubridate::hours(2),
fine_flag = TRUE
)
calculate_dlmo(
data = NULL,
file_path = filename,
threshold = 2.3,
interval_limit = lubridate::hours(2),
fine_flag = TRUE
)
sample_dlmo <- calculate_dlmo(file_path = filename, threshold = 5)
library(dlmoR)
sample_dlmo <- calculate_dlmo(file_path = filename, threshold = 5)
devtools::load_all()
?calculate_dlmo
filename <- system.file("extdata/sample_melatonin_profile.csv", package = "dlmoR")
filename <- system.file("extdata/sample_melatonin_profile.csv", package = "dlmoR")
sample_dlmo <- calculate_dlmo(file_path = filename, threshold = 5)
devtools::document()
devtools::load_all()
sample_dlmo <- calculate_dlmo(file_path = filename, threshold = 5)
sample_dlmo$dlmoplotcoarse
sample_dlmo$dlmoplotfine
sample_dlmo$dlmoplotcoarse
sample_dlmo$dlmoplotfiine
sample_dlmo$dlmoplotfine
sample_dlmo$dlmo$coarse
sample_dlmo$dlmo$coarse$time
sample_dlmo$dlmo$coarse$fit_lines
sample_dlmo$dlmo$coarse$fit_lines
devtools::document()
devtools::load_all()
sample_dlmo <- calculate_dlmo(file_path = filename, threshold = 5)
devtools::document()
devtools::load_all()
sample_dlmo <- calculate_dlmo(file_path = filename, threshold = 5)
sample_dlmo$dlmoplotcoarse
str(sample_dlmo$dlmo$coarse$fit_lines$ascending)
devtools::document()
devtools::load_all()
sample_dlmo <- calculate_dlmo(file_path = filename, threshold = 5)
sample_dlmo$dlmoplotcoarse
sample_dlmo$dlmo$coarse$fit_lines
devtools::document()
devtools::load_all()
sample_dlmo <- calculate_dlmo(file_path = filename, threshold = 5)
sample_dlmo$dlmoplotcoarse
sample_dlmo$dlmoplotfine
sample_dlmo$dlmo$coarse$fit_lines
sample_dlmo$dlmo$fine$fit_lines
sample_dlmo$prof
devtools::document()
devtools::load_all()
sample_dlmo <- calculate_dlmo(file_path = filename, threshold = 5)
sample_dlmo$dlmo$fine$fit_lines
sample_dlmo$dlmo$coarse$fit_lines
sample_dlmo$dlmoplotfine
sample_dlmo$dlmoplotcoarse
sample_dlmo$dlmo$coarse$fit_lines
sample_dlmo$dlmo$fine$fit_lines
devtools::document()
devtools::load_all()
sample_dlmo <- calculate_dlmo(file_path = filename, threshold = 5)
sample_dlmo$dlmo$fine$fit_lines
sample_dlmo$dlmo$coarse$fit_lines
sample_dlmo$dlmoplotcoarse
sample_dlmo$dlmoplotfine
devtools::document()
devtools::load_all()
sample_dlmo <- calculate_dlmo(file_path = filename, threshold = 5)
sample_dlmo$dlmoplotfine
sample_dlmo$dlmoplotcoarse
devtools::document()
devtools::load_all()
devtools::document()
devtools::load_all()
sample_dlmo <- calculate_dlmo(file_path = filename, threshold = 5)
sample_dlmo$dlmoplotcoarse
sample_dlmo$dlmoplotfine
sample_dlmo$dlmoplotcoarse
sample_dlmo$dlmoplotfine
devtools::document()
devtools::load_all()
sample_dlmo <- calculate_dlmo(file_path = filename, threshold = 5)
devtools::check()
devtools::document()
devtools::check()
1-NULL
devtools::document()
devtools::check()
devtools::document()
devtools::load_all()
