R/harmonize_details.R
In shirewoman2/Consultancy: Standardized tools for using R within the Simcyp Consultancy Team
Defines functions
harmonize_details
Documented in
harmonize_details
#' FOR INTERNAL PACKAGE USE. Take as input an existing data.frame or list of
#' experimental details and make it be a list with standard items
#'
#' \code{harmonize_details} takes as input an object created from running
#' extractExpDetails, extractExpDetails_mult, annotateDetails, or
#' deannotateDetails and makes it conform to the data structure the rest of the
#' package needs: a list with the following items, which can be added to in the
#' future: 1) MainDetails, 2) CustomDosing, 3) DissolutionProfiles, 4)
#' ReleaseProfiles, 5) ConcDependent_fup, and 6) ConcDependent_BP.
#'
#' @param existing_exp_details an object created from running extractExpDetails,
#' extractExpDetails_mult, annotateDetails, or deannotateDetails
#'
#' @return Returns a list
#'
#' @examples
#' # none
harmonize_details <- function(existing_exp_details){
# Setting up data structure -----------------------------------------------
# At the end of this function, the output object should be a list with the
# named items saved in the object ExpDetailListItems
if("list" %in% class(existing_exp_details)){
if("MainDetails" %in% names(existing_exp_details)){
# This is when they've run extractExpDetails with versions >= 2.8.0.
# For this scenario, we need to do 2 things: 1. check that they also
# have any other ExpDetailListItems they should have. 2. Make sure that
# the details are not annotated (since that's generally what's required
# for most functions) and then we can return the full list, in order.
if("Detail" %in% names(existing_exp_details$MainDetails)){
# This is when it has already been annotated previously. Need to
# deannotate 1st.
existing_exp_details <- deannotateDetails(existing_exp_details,
apply_class = FALSE)
}
# Checking for whether custom dosing is multiple items b/c I did that
# for a hot minute while I was figuring out how this should work
if(any(c("CustomDosing_sub", "CustomDosing_inhib",
"CustomDosing_inhib2") %in% names(existing_exp_details))){
for(item in c("CustomDosing_sub", "CustomDosing_inhib",
"CustomDosing_inhib2")){
if(nrow(existing_exp_details[[item]]) > 0){
existing_exp_details[[item]] <- existing_exp_details[[item]] %>%
mutate(CompoundID = AllCompounds$CompoundID[
which(AllCompounds$Suffix == sub("CustomDosing", "", item))]) %>%
rename_with(.cols = everything(),
.fn = function(x) sub("_sub|_inhib|_inhib2", "", x))
}
}
CustomDosing <- bind_rows(existing_exp_details[
c("CustomDosing_sub", "CustomDosing_inhib", "CustomDosing_inhib2")])
if(nrow(CustomDosing) > 0){
CustomDosing <- CustomDosing %>%
left_join(Details$MainDetails %>%
select(File, Substrate, Inhibitor1, Inhibitor2) %>%
pivot_longer(cols = -File,
names_to = "DetailNames",
values_to = "Compound") %>%
left_join(AllCompounds %>%
select(DetailNames, CompoundID),
by = "DetailNames"),
by = c("File", "CompoundID")) %>%
select(File, CompoundID, Compound, Time, Time_units, DoseNum,
Dose, Dose_units, DoseRoute)
} else {
CustomDosing <- NULL
}
existing_exp_details$CustomDosing_sub <- NULL
existing_exp_details$CustomDosing_inhib <- NULL
existing_exp_details$CustomDosing_inhib2 <- NULL
existing_exp_details$CustomDosing <- CustomDosing
}
itemstoadd <- setdiff(ExpDetailListItems, names(existing_exp_details))
append_items <- lapply(itemstoadd, function(x) return(NULL))
names(append_items) <- itemstoadd
existing_exp_details <- c(existing_exp_details, append_items)
# Check whether MainDetails includes SheetNames b/c need it for other
# functions now.
if(("SheetNames" %in% names(existing_exp_details$MainDetails) &&
any(is.na(existing_exp_details$MainDetails$SheetNames)) |
any(existing_exp_details$MainDetails$SheetNames == "`NA`", na.rm = T)) |
"SheetNames" %in% names(existing_exp_details$MainDetails) == FALSE){
for(i in existing_exp_details$MainDetails$File){
if(file.exists(i) &
!str_detect(i, "\\.db$")){
SheetNames <- tryCatch(readxl::excel_sheets(i),
error = openxlsx::getSheetNames(i))
} else { SheetNames <- NA}
existing_exp_details$MainDetails$SheetNames[
existing_exp_details$MainDetails$File == i] <-
str_c(paste0("`", SheetNames, "`"), collapse = " ")
rm(SheetNames)
}
}
# Adding missing, necessary list items
Missing1 <- setdiff(
paste0(rep(c("DoseInt", "Dose", "DoseRoute", "Regimen", "NumDoses"),
each = 3),
c("_sub", "_inhib", "_inhib2")),
names(existing_exp_details$MainDetails))
if(length(Missing1) > 0){
Missing <- as.data.frame(matrix(data = NA,
ncol = length(Missing1),
nrow = nrow(existing_exp_details$MainDetails),
dimnames = list(NULL, Missing1)))
existing_exp_details$MainDetails <-
cbind(existing_exp_details$MainDetails, Missing)
}
# Making DoseInt_x and Dose_x numeric all the time. We'll get custom dosing
# info from Regimen_x and DoseRexisting_exp_details$MainDetailse_x.
suppressWarnings(
existing_exp_details$MainDetails <- existing_exp_details$MainDetails %>%
mutate(DoseInt_sub = as.numeric(DoseInt_sub),
DoseInt_inhib = as.numeric(DoseInt_inhib),
DoseInt_inhib2 = as.numeric(DoseInt_inhib2),
Dose_sub = as.numeric(Dose_sub),
Dose_inhib = as.numeric(Dose_inhib),
Dose_inhib2 = as.numeric(Dose_inhib2),
# At this point, DoseInt_x and Dose_x will be NA if it's a
# custom dosing regimen. Setting the regimen to
# "multiple". We'll use that downstream for checking for
# appropriate PK parameters, etc.
Regimen_sub =
case_when(is.na(DoseInt_sub) &
(complete.cases(DoseRoute_sub) &
DoseRoute_sub == "custom dosing") ~ "Multiple Dose",
.default = Regimen_sub),
Regimen_inhib =
case_when(is.na(DoseInt_inhib) &
(complete.cases(DoseRoute_inhib) &
DoseRoute_inhib == "custom dosing") ~ "Multiple Dose",
.default = Regimen_inhib),
Regimen_inhib2 =
case_when(is.na(DoseInt_inhib2) &
(complete.cases(DoseRoute_inhib2) &
DoseRoute_inhib2 == "custom dosing") ~ "Multiple Dose",
.default = Regimen_inhib2))
)
# Harmonizing dosing. Note that this must come AFTER making sure that
# the list has items named MainDetails and named CustomDosing!
existing_exp_details <- harmonize_dosing(existing_exp_details)
# Making sure the order is correct
existing_exp_details <- existing_exp_details[ExpDetailListItems]
return(existing_exp_details[ExpDetailListItems])
} else {
# This is when they may have saved the output from
# extractExpDetails from package versions < 2.8.0, which is when I
# changed the output from extractExpDetails from sometimes being a list
# & sometimes being a data.frame to ALWAYS being a list.
Out <- list(MainDetails = as.data.frame(existing_exp_details[
which(sapply(existing_exp_details, length) == 1)]))
for(i in ExpDetailListItems[2:length(ExpDetailListItems)]){
Out[[i]] <- data.frame()
}
# Check whether MainDetails includes SheetNames b/c need it for other
# functions now.
if(("SheetNames" %in% names(existing_exp_details$MainDetails) &&
any(is.na(existing_exp_details$MainDetails$SheetNames)) |
any(existing_exp_details$MainDetails$SheetNames == "`NA`", na.rm = T)) |
"SheetNames" %in% names(existing_exp_details$MainDetails) == FALSE){
SheetNames <- as.character(c())
for(i in existing_exp_details$MainDetails$File){
if(file.exists(i)){
SheetNames[i] <- tryCatch(readxl::excel_sheets(i),
error = openxlsx::getSheetNames(i))
} else { SheetNames[i] <- NA}
existing_exp_details$MainDetails$SheetNames[
existing_exp_details$MainDetails$File == i] <-
str_c(paste0("`", SheetNames, "`"), collapse = " ")
}
}
# Adding missing, necessary list items
Missing1 <- setdiff(
paste0(rep(c("DoseInt", "Dose", "DoseRoute", "Regimen", "NumDoses"),
each = 3),
c("_sub", "_inhib", "_inhib2")),
names(existing_exp_details$MainDetails))
if(length(Missing1) > 0){
Missing <- as.data.frame(matrix(data = NA,
ncol = length(Missing1),
nrow = nrow(existing_exp_details$MainDetails),
dimnames = list(NULL, Missing1)))
existing_exp_details$MainDetails <-
cbind(existing_exp_details$MainDetails, Missing)
}
# Making DoseInt_x and Dose_x numeric all the time. We'll get custom dosing
# info from Regimen_x and DoseRexisting_exp_details$MainDetailse_x.
suppressWarnings(
existing_exp_details$MainDetails <- existing_exp_details$MainDetails %>%
mutate(DoseInt_sub = as.numeric(DoseInt_sub),
DoseInt_inhib = as.numeric(DoseInt_inhib),
DoseInt_inhib2 = as.numeric(DoseInt_inhib2),
Dose_sub = as.numeric(Dose_sub),
Dose_inhib = as.numeric(Dose_inhib),
Dose_inhib2 = as.numeric(Dose_inhib2),
# At this point, DoseInt_x and Dose_x will be NA if it's a
# custom dosing regimen. Setting the regimen to
# "multiple". We'll use that downstream for checking for
# appropriate PK parameters, etc.
Regimen_sub =
case_when(is.na(DoseInt_sub) &
(complete.cases(DoseRoute_sub) &
DoseRoute_sub == "custom dosing") ~ "Multiple Dose",
.default = Regimen_sub),
Regimen_inhib =
case_when(is.na(DoseInt_inhib) &
(complete.cases(DoseRoute_inhib) &
DoseRoute_inhib == "custom dosing") ~ "Multiple Dose",
.default = Regimen_inhib),
Regimen_inhib2 =
case_when(is.na(DoseInt_inhib2) &
(complete.cases(DoseRoute_inhib2) &
DoseRoute_inhib2 == "custom dosing") ~ "Multiple Dose",
.default = Regimen_inhib2))
)
# Harmonizing dosing. Note that this must come AFTER making sure that
# the list has items named MainDetails and named CustomDosing!
existing_exp_details <- harmonize_dosing(existing_exp_details)
# Making sure the order is correct
existing_exp_details <- existing_exp_details[ExpDetailListItems]
return(Out)
}
} else if("data.frame" %in% class(existing_exp_details)){
# This is when they may have saved the output from extractExpDetails_mult
# or annotateDetails or deannotateDetails from package versions < 2.8.0,
# which is when I changed the output from extractExpDetails from sometimes
# being a list & sometimes being a data.frame to ALWAYS being a list.
existing_exp_details <- list(MainDetails = existing_exp_details)
itemstoadd <- setdiff(ExpDetailListItems, names(existing_exp_details))
append_items <- lapply(itemstoadd, function(x) return(NULL))
names(append_items) <- itemstoadd
existing_exp_details <- c(existing_exp_details, append_items)
if(all(c("SimulatorSection", "Sheet") %in% names(existing_exp_details$MainDetails))){
# This is when existing_exp_details has been annotated. Need to
# de-annotate here to make this work well with the rest of the
# function.
existing_exp_details <- deannotateDetails(existing_exp_details)
}
# Check whether MainDetails includes SheetNames b/c need it for other
# functions now.
if(("SheetNames" %in% names(existing_exp_details$MainDetails) &&
any(is.na(existing_exp_details$MainDetails$SheetNames)) |
any(existing_exp_details$MainDetails$SheetNames == "`NA`", na.rm = T)) |
"SheetNames" %in% names(existing_exp_details$MainDetails) == FALSE){
SheetNames <- as.character(c())
for(i in existing_exp_details$MainDetails$File[
str_detect(existing_exp_details$MainDetails$File, "xlsx$")]){
if(file.exists(i)){
SheetNames[i] <-
str_c(paste0("'",
tryCatch(readxl::excel_sheets(i),
error = openxlsx::getSheetNames(i)),
"'"), collapse = " ")
} else { SheetNames[i] <- NA}
existing_exp_details$MainDetails$SheetNames[
existing_exp_details$MainDetails$File == i] <- SheetNames[i]
}
}
# Adding missing, necessary list items
Missing1 <- setdiff(
paste0(rep(c("DoseInt", "Dose", "DoseRoute", "Regimen", "NumDoses"),
each = 3),
c("_sub", "_inhib", "_inhib2")),
names(existing_exp_details$MainDetails))
if(length(Missing1) > 0){
Missing <- as.data.frame(matrix(data = NA,
ncol = length(Missing1),
nrow = nrow(existing_exp_details$MainDetails),
dimnames = list(NULL, Missing1)))
existing_exp_details$MainDetails <-
cbind(existing_exp_details$MainDetails, Missing)
}
# Making DoseInt_x and Dose_x numeric all the time. We'll get custom dosing
# info from Regimen_x and DoseRexisting_exp_details$MainDetailse_x.
suppressWarnings(
existing_exp_details$MainDetails <- existing_exp_details$MainDetails %>%
mutate(DoseInt_sub = as.numeric(DoseInt_sub),
DoseInt_inhib = as.numeric(DoseInt_inhib),
DoseInt_inhib2 = as.numeric(DoseInt_inhib2),
Dose_sub = as.numeric(Dose_sub),
Dose_inhib = as.numeric(Dose_inhib),
Dose_inhib2 = as.numeric(Dose_inhib2),
# At this point, DoseInt_x and Dose_x will be NA if it's a
# custom dosing regimen. Setting the regimen to
# "multiple". We'll use that downstream for checking for
# appropriate PK parameters, etc.
Regimen_sub =
case_when(is.na(DoseInt_sub) &
(complete.cases(DoseRoute_sub) &
DoseRoute_sub == "custom dosing") ~ "Multiple Dose",
.default = Regimen_sub),
Regimen_inhib =
case_when(is.na(DoseInt_inhib) &
(complete.cases(DoseRoute_inhib) &
DoseRoute_inhib == "custom dosing") ~ "Multiple Dose",
.default = Regimen_inhib),
Regimen_inhib2 =
case_when(is.na(DoseInt_inhib2) &
(complete.cases(DoseRoute_inhib2) &
DoseRoute_inhib2 == "custom dosing") ~ "Multiple Dose",
.default = Regimen_inhib2))
)
# Harmonizing dosing. Note that this must come AFTER making sure that
# the list has items named MainDetails and named CustomDosing!
existing_exp_details <- harmonize_dosing(existing_exp_details)
# Making sure the order is correct
existing_exp_details <- existing_exp_details[ExpDetailListItems]
return(existing_exp_details[ExpDetailListItems])
}
}
shirewoman2/Consultancy documentation built on Feb. 18, 2025, 10 p.m.
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Defines functions harmonize_details
Documented in harmonize_details
#' FOR INTERNAL PACKAGE USE. Take as input an existing data.frame or list of
#' experimental details and make it be a list with standard items
#'
#' \code{harmonize_details} takes as input an object created from running
#' extractExpDetails, extractExpDetails_mult, annotateDetails, or
#' deannotateDetails and makes it conform to the data structure the rest of the
#' package needs: a list with the following items, which can be added to in the
#' future: 1) MainDetails, 2) CustomDosing, 3) DissolutionProfiles, 4)
#' ReleaseProfiles, 5) ConcDependent_fup, and 6) ConcDependent_BP.
#'
#' @param existing_exp_details an object created from running extractExpDetails,
#' extractExpDetails_mult, annotateDetails, or deannotateDetails
#'
#' @return Returns a list
#'
#' @examples
#' # none
harmonize_details <- function(existing_exp_details){
# Setting up data structure -----------------------------------------------
# At the end of this function, the output object should be a list with the
# named items saved in the object ExpDetailListItems
if("list" %in% class(existing_exp_details)){
if("MainDetails" %in% names(existing_exp_details)){
# This is when they've run extractExpDetails with versions >= 2.8.0.
# For this scenario, we need to do 2 things: 1. check that they also
# have any other ExpDetailListItems they should have. 2. Make sure that
# the details are not annotated (since that's generally what's required
# for most functions) and then we can return the full list, in order.
if("Detail" %in% names(existing_exp_details$MainDetails)){
# This is when it has already been annotated previously. Need to
# deannotate 1st.
existing_exp_details <- deannotateDetails(existing_exp_details,
apply_class = FALSE)
}
# Checking for whether custom dosing is multiple items b/c I did that
# for a hot minute while I was figuring out how this should work
if(any(c("CustomDosing_sub", "CustomDosing_inhib",
"CustomDosing_inhib2") %in% names(existing_exp_details))){
for(item in c("CustomDosing_sub", "CustomDosing_inhib",
"CustomDosing_inhib2")){
if(nrow(existing_exp_details[[item]]) > 0){
existing_exp_details[[item]] <- existing_exp_details[[item]] %>%
mutate(CompoundID = AllCompounds$CompoundID[
which(AllCompounds$Suffix == sub("CustomDosing", "", item))]) %>%
rename_with(.cols = everything(),
.fn = function(x) sub("_sub|_inhib|_inhib2", "", x))
}
}
CustomDosing <- bind_rows(existing_exp_details[
c("CustomDosing_sub", "CustomDosing_inhib", "CustomDosing_inhib2")])
if(nrow(CustomDosing) > 0){
CustomDosing <- CustomDosing %>%
left_join(Details$MainDetails %>%
select(File, Substrate, Inhibitor1, Inhibitor2) %>%
pivot_longer(cols = -File,
names_to = "DetailNames",
values_to = "Compound") %>%
left_join(AllCompounds %>%
select(DetailNames, CompoundID),
by = "DetailNames"),
by = c("File", "CompoundID")) %>%
select(File, CompoundID, Compound, Time, Time_units, DoseNum,
Dose, Dose_units, DoseRoute)
} else {
CustomDosing <- NULL
}
existing_exp_details$CustomDosing_sub <- NULL
existing_exp_details$CustomDosing_inhib <- NULL
existing_exp_details$CustomDosing_inhib2 <- NULL
existing_exp_details$CustomDosing <- CustomDosing
}
itemstoadd <- setdiff(ExpDetailListItems, names(existing_exp_details))
append_items <- lapply(itemstoadd, function(x) return(NULL))
names(append_items) <- itemstoadd
existing_exp_details <- c(existing_exp_details, append_items)
# Check whether MainDetails includes SheetNames b/c need it for other
# functions now.
if(("SheetNames" %in% names(existing_exp_details$MainDetails) &&
any(is.na(existing_exp_details$MainDetails$SheetNames)) |
any(existing_exp_details$MainDetails$SheetNames == "`NA`", na.rm = T)) |
"SheetNames" %in% names(existing_exp_details$MainDetails) == FALSE){
for(i in existing_exp_details$MainDetails$File){
if(file.exists(i) &
!str_detect(i, "\\.db$")){
SheetNames <- tryCatch(readxl::excel_sheets(i),
error = openxlsx::getSheetNames(i))
} else { SheetNames <- NA}
existing_exp_details$MainDetails$SheetNames[
existing_exp_details$MainDetails$File == i] <-
str_c(paste0("`", SheetNames, "`"), collapse = " ")
rm(SheetNames)
}
}
# Adding missing, necessary list items
Missing1 <- setdiff(
paste0(rep(c("DoseInt", "Dose", "DoseRoute", "Regimen", "NumDoses"),
each = 3),
c("_sub", "_inhib", "_inhib2")),
names(existing_exp_details$MainDetails))
if(length(Missing1) > 0){
Missing <- as.data.frame(matrix(data = NA,
ncol = length(Missing1),
nrow = nrow(existing_exp_details$MainDetails),
dimnames = list(NULL, Missing1)))
existing_exp_details$MainDetails <-
cbind(existing_exp_details$MainDetails, Missing)
}
# Making DoseInt_x and Dose_x numeric all the time. We'll get custom dosing
# info from Regimen_x and DoseRexisting_exp_details$MainDetailse_x.
suppressWarnings(
existing_exp_details$MainDetails <- existing_exp_details$MainDetails %>%
mutate(DoseInt_sub = as.numeric(DoseInt_sub),
DoseInt_inhib = as.numeric(DoseInt_inhib),
DoseInt_inhib2 = as.numeric(DoseInt_inhib2),
Dose_sub = as.numeric(Dose_sub),
Dose_inhib = as.numeric(Dose_inhib),
Dose_inhib2 = as.numeric(Dose_inhib2),
# At this point, DoseInt_x and Dose_x will be NA if it's a
# custom dosing regimen. Setting the regimen to
# "multiple". We'll use that downstream for checking for
# appropriate PK parameters, etc.
Regimen_sub =
case_when(is.na(DoseInt_sub) &
(complete.cases(DoseRoute_sub) &
DoseRoute_sub == "custom dosing") ~ "Multiple Dose",
.default = Regimen_sub),
Regimen_inhib =
case_when(is.na(DoseInt_inhib) &
(complete.cases(DoseRoute_inhib) &
DoseRoute_inhib == "custom dosing") ~ "Multiple Dose",
.default = Regimen_inhib),
Regimen_inhib2 =
case_when(is.na(DoseInt_inhib2) &
(complete.cases(DoseRoute_inhib2) &
DoseRoute_inhib2 == "custom dosing") ~ "Multiple Dose",
.default = Regimen_inhib2))
)
# Harmonizing dosing. Note that this must come AFTER making sure that
# the list has items named MainDetails and named CustomDosing!
existing_exp_details <- harmonize_dosing(existing_exp_details)
# Making sure the order is correct
existing_exp_details <- existing_exp_details[ExpDetailListItems]
return(existing_exp_details[ExpDetailListItems])
} else {
# This is when they may have saved the output from
# extractExpDetails from package versions < 2.8.0, which is when I
# changed the output from extractExpDetails from sometimes being a list
# & sometimes being a data.frame to ALWAYS being a list.
Out <- list(MainDetails = as.data.frame(existing_exp_details[
which(sapply(existing_exp_details, length) == 1)]))
for(i in ExpDetailListItems[2:length(ExpDetailListItems)]){
Out[[i]] <- data.frame()
}
# Check whether MainDetails includes SheetNames b/c need it for other
# functions now.
if(("SheetNames" %in% names(existing_exp_details$MainDetails) &&
any(is.na(existing_exp_details$MainDetails$SheetNames)) |
any(existing_exp_details$MainDetails$SheetNames == "`NA`", na.rm = T)) |
"SheetNames" %in% names(existing_exp_details$MainDetails) == FALSE){
SheetNames <- as.character(c())
for(i in existing_exp_details$MainDetails$File){
if(file.exists(i)){
SheetNames[i] <- tryCatch(readxl::excel_sheets(i),
error = openxlsx::getSheetNames(i))
} else { SheetNames[i] <- NA}
existing_exp_details$MainDetails$SheetNames[
existing_exp_details$MainDetails$File == i] <-
str_c(paste0("`", SheetNames, "`"), collapse = " ")
}
}
# Adding missing, necessary list items
Missing1 <- setdiff(
paste0(rep(c("DoseInt", "Dose", "DoseRoute", "Regimen", "NumDoses"),
each = 3),
c("_sub", "_inhib", "_inhib2")),
names(existing_exp_details$MainDetails))
if(length(Missing1) > 0){
Missing <- as.data.frame(matrix(data = NA,
ncol = length(Missing1),
nrow = nrow(existing_exp_details$MainDetails),
dimnames = list(NULL, Missing1)))
existing_exp_details$MainDetails <-
cbind(existing_exp_details$MainDetails, Missing)
}
# Making DoseInt_x and Dose_x numeric all the time. We'll get custom dosing
# info from Regimen_x and DoseRexisting_exp_details$MainDetailse_x.
suppressWarnings(
existing_exp_details$MainDetails <- existing_exp_details$MainDetails %>%
mutate(DoseInt_sub = as.numeric(DoseInt_sub),
DoseInt_inhib = as.numeric(DoseInt_inhib),
DoseInt_inhib2 = as.numeric(DoseInt_inhib2),
Dose_sub = as.numeric(Dose_sub),
Dose_inhib = as.numeric(Dose_inhib),
Dose_inhib2 = as.numeric(Dose_inhib2),
# At this point, DoseInt_x and Dose_x will be NA if it's a
# custom dosing regimen. Setting the regimen to
# "multiple". We'll use that downstream for checking for
# appropriate PK parameters, etc.
Regimen_sub =
case_when(is.na(DoseInt_sub) &
(complete.cases(DoseRoute_sub) &
DoseRoute_sub == "custom dosing") ~ "Multiple Dose",
.default = Regimen_sub),
Regimen_inhib =
case_when(is.na(DoseInt_inhib) &
(complete.cases(DoseRoute_inhib) &
DoseRoute_inhib == "custom dosing") ~ "Multiple Dose",
.default = Regimen_inhib),
Regimen_inhib2 =
case_when(is.na(DoseInt_inhib2) &
(complete.cases(DoseRoute_inhib2) &
DoseRoute_inhib2 == "custom dosing") ~ "Multiple Dose",
.default = Regimen_inhib2))
)
# Harmonizing dosing. Note that this must come AFTER making sure that
# the list has items named MainDetails and named CustomDosing!
existing_exp_details <- harmonize_dosing(existing_exp_details)
# Making sure the order is correct
existing_exp_details <- existing_exp_details[ExpDetailListItems]
return(Out)
}
} else if("data.frame" %in% class(existing_exp_details)){
# This is when they may have saved the output from extractExpDetails_mult
# or annotateDetails or deannotateDetails from package versions < 2.8.0,
# which is when I changed the output from extractExpDetails from sometimes
# being a list & sometimes being a data.frame to ALWAYS being a list.
existing_exp_details <- list(MainDetails = existing_exp_details)
itemstoadd <- setdiff(ExpDetailListItems, names(existing_exp_details))
append_items <- lapply(itemstoadd, function(x) return(NULL))
names(append_items) <- itemstoadd
existing_exp_details <- c(existing_exp_details, append_items)
if(all(c("SimulatorSection", "Sheet") %in% names(existing_exp_details$MainDetails))){
# This is when existing_exp_details has been annotated. Need to
# de-annotate here to make this work well with the rest of the
# function.
existing_exp_details <- deannotateDetails(existing_exp_details)
}
# Check whether MainDetails includes SheetNames b/c need it for other
# functions now.
if(("SheetNames" %in% names(existing_exp_details$MainDetails) &&
any(is.na(existing_exp_details$MainDetails$SheetNames)) |
any(existing_exp_details$MainDetails$SheetNames == "`NA`", na.rm = T)) |
"SheetNames" %in% names(existing_exp_details$MainDetails) == FALSE){
SheetNames <- as.character(c())
for(i in existing_exp_details$MainDetails$File[
str_detect(existing_exp_details$MainDetails$File, "xlsx$")]){
if(file.exists(i)){
SheetNames[i] <-
str_c(paste0("'",
tryCatch(readxl::excel_sheets(i),
error = openxlsx::getSheetNames(i)),
"'"), collapse = " ")
} else { SheetNames[i] <- NA}
existing_exp_details$MainDetails$SheetNames[
existing_exp_details$MainDetails$File == i] <- SheetNames[i]
}
}
# Adding missing, necessary list items
Missing1 <- setdiff(
paste0(rep(c("DoseInt", "Dose", "DoseRoute", "Regimen", "NumDoses"),
each = 3),
c("_sub", "_inhib", "_inhib2")),
names(existing_exp_details$MainDetails))
if(length(Missing1) > 0){
Missing <- as.data.frame(matrix(data = NA,
ncol = length(Missing1),
nrow = nrow(existing_exp_details$MainDetails),
dimnames = list(NULL, Missing1)))
existing_exp_details$MainDetails <-
cbind(existing_exp_details$MainDetails, Missing)
}
# Making DoseInt_x and Dose_x numeric all the time. We'll get custom dosing
# info from Regimen_x and DoseRexisting_exp_details$MainDetailse_x.
suppressWarnings(
existing_exp_details$MainDetails <- existing_exp_details$MainDetails %>%
mutate(DoseInt_sub = as.numeric(DoseInt_sub),
DoseInt_inhib = as.numeric(DoseInt_inhib),
DoseInt_inhib2 = as.numeric(DoseInt_inhib2),
Dose_sub = as.numeric(Dose_sub),
Dose_inhib = as.numeric(Dose_inhib),
Dose_inhib2 = as.numeric(Dose_inhib2),
# At this point, DoseInt_x and Dose_x will be NA if it's a
# custom dosing regimen. Setting the regimen to
# "multiple". We'll use that downstream for checking for
# appropriate PK parameters, etc.
Regimen_sub =
case_when(is.na(DoseInt_sub) &
(complete.cases(DoseRoute_sub) &
DoseRoute_sub == "custom dosing") ~ "Multiple Dose",
.default = Regimen_sub),
Regimen_inhib =
case_when(is.na(DoseInt_inhib) &
(complete.cases(DoseRoute_inhib) &
DoseRoute_inhib == "custom dosing") ~ "Multiple Dose",
.default = Regimen_inhib),
Regimen_inhib2 =
case_when(is.na(DoseInt_inhib2) &
(complete.cases(DoseRoute_inhib2) &
DoseRoute_inhib2 == "custom dosing") ~ "Multiple Dose",
.default = Regimen_inhib2))
)
# Harmonizing dosing. Note that this must come AFTER making sure that
# the list has items named MainDetails and named CustomDosing!
existing_exp_details <- harmonize_dosing(existing_exp_details)
# Making sure the order is correct
existing_exp_details <- existing_exp_details[ExpDetailListItems]
return(existing_exp_details[ExpDetailListItems])
}
}
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