.Rhistory

write.csv(time_df, path_to_read)
})
}
}
track_time()
track_time()
track_time()
track_time()
track_time <- function(category = "day") {
# Load/Create timesheet
path_to_read <- MyFunctions::my_path("D",name = "project_time_count.csv")
if(category == "day"){
start_time <- Sys.time()
message("Tracking time started.")
on.exit({
end_time <- Sys.time()
time_spent <- end_time - start_time
message("Time spent on the project:", time_spent)
# Create time data frame
df <- data.frame(Start_Time = as.character(start_time), End_Time = as.character(end_time), Time_Spent = as.numeric(time_spent))
if(file.exists(path_to_read)){
time_df <- dplyr::bind_rows(readr::read_csv(path_to_read),
df)
}else{
time_df <- data.frame(Start_Time = start_time, End_Time = end_time, Time_Spent = time_spent)
}
# Save the data frame to a file
write.csv(time_df, path_to_read)
})
}
}
track_time()
track_time <- function(category = "day") {
# Load/Create timesheet
path_to_read <- MyFunctions::my_path("D",name = "project_time_count.csv")
if(category == "day"){
start_time <- Sys.time()
message("Tracking time started.")
on.exit({
end_time <- Sys.time()
time_spent <- end_time - start_time
message("Time spent on the project:", time_spent)
# Create time data frame
df <- data.frame(Start_Time = as.character(start_time), End_Time = as.character(end_time), Time_Spent = as.numeric(time_spent))
if(file.exists(path_to_read)){
time_df <- dplyr::bind_rows(readr::read_csv(path_to_read),
df)
}else{
time_df <- data.frame(Start_Time = start_time, End_Time = end_time, Time_Spent = time_spent)
}
# Save the data frame to a file
write.csv(time_df, path_to_read)
})
}
}
track_time()
track_time()
track_time <- function(category = "day") {
# Load/Create timesheet
path_to_read <- MyFunctions::my_path("D",name = "project_time_count.csv")
if(category == "day"){
start_time <- Sys.time()
message("Tracking time started.")
on.exit({
end_time <- Sys.time()
time_spent <- end_time - start_time
message("Time spent on the project:", time_spent)
# Create time data frame
df <- data.frame(Start_Time = as.character(start_time), End_Time = as.character(end_time), Time_Spent = as.numeric(time_spent))
if(file.exists(path_to_read)){
time_df <- dplyr::bind_rows(read.csv(path_to_read,row.names = F),
df)
}else{
time_df <- data.frame(Start_Time = start_time, End_Time = end_time, Time_Spent = time_spent)
}
# Save the data frame to a file
write.csv(time_df, path_to_read)
})
}
}
track_time()
track_time()
track_time <- function(category = "day") {
# Load/Create timesheet
path_to_read <- MyFunctions::my_path("D",name = "project_time_count.csv")
if(category == "day"){
start_time <- Sys.time()
message("Tracking time started.")
on.exit({
end_time <- Sys.time()
time_spent <- end_time - start_time
message("Time spent on the project:", time_spent)
# Create time data frame
df <- data.frame(Start_Time = as.character(start_time), End_Time = as.character(end_time), Time_Spent = as.numeric(time_spent))
if(file.exists(path_to_read)){
time_df <- dplyr::bind_rows(read.csv(path_to_read,row.names = F),
df)
}else{
time_df <- data.frame(Start_Time = start_time, End_Time = end_time, Time_Spent = time_spent)
}
# Save the data frame to a file
write.csv(time_df, path_to_read)
})
}
}
track_time()
track_time <- function(category = "day") {
# Load/Create timesheet
path_to_read <- MyFunctions::my_path("D",name = "project_time_count.csv")
if(category == "day"){
start_time <- Sys.time()
message("Tracking time started.")
on.exit({
end_time <- Sys.time()
time_spent <- end_time - start_time
message("Time spent on the project:", time_spent)
# Create time data frame
df <- data.frame(Start_Time = as.character(start_time), End_Time = as.character(end_time), Time_Spent = as.numeric(time_spent))
if(file.exists(path_to_read)){
time_df <- dplyr::bind_rows(read.csv(path_to_read,col.names =  F),
df)
}else{
time_df <- data.frame(Start_Time = start_time, End_Time = end_time, Time_Spent = time_spent)
}
# Save the data frame to a file
write.csv(time_df, path_to_read)
})
}
}
track_time()
track_time <- function(category = "day") {
# Load/Create timesheet
path_to_read <- MyFunctions::my_path("D",name = "project_time_count.csv")
if(category == "day"){
start_time <- Sys.time()
message("Tracking time started.")
on.exit({
end_time <- Sys.time()
time_spent <- end_time - start_time
message("Time spent on the project:", time_spent)
# Create time data frame
df <- data.frame(Start_Time = as.character(start_time), End_Time = as.character(end_time), Time_Spent = as.numeric(time_spent))
if(file.exists(path_to_read)){
time_df <- dplyr::bind_rows(read.csv(path_to_read,col.names =  F),
df)
}else{
time_df <- data.frame(Start_Time = start_time, End_Time = end_time, Time_Spent = time_spent)
}
# Save the data frame to a file
write.csv(time_df, path_to_read)
})
}
}
track_time()
track_time()
track_time <- function(category = "day") {
# Load/Create timesheet
path_to_read <- MyFunctions::my_path("D",name = "project_time_count.csv")
if(category == "day"){
start_time <- Sys.time()
message("Tracking time started.")
on.exit({
end_time <- Sys.time()
time_spent <- end_time - start_time
message("Time spent on the project:", time_spent)
# Create time data frame
df <- data.frame(Start_Time = as.character(start_time), End_Time = as.character(end_time), Time_Spent = as.numeric(time_spent))
if(file.exists(path_to_read)){
time_df <- dplyr::bind_rows(read.csv(path_to_read, row.names =  F,col.names =  F),
df)
}else{
time_df <- data.frame(Start_Time = start_time, End_Time = end_time, Time_Spent = time_spent)
}
# Save the data frame to a file
write.csv(time_df, path_to_read)
})
}
}
track_time()
track_time()
track_time()
track_time <- function(category = "day") {
# Load/Create timesheet
path_to_read <- MyFunctions::my_path("D",name = "project_time_count.csv")
if(category == "day"){
start_time <- Sys.time()
message("Tracking time started.")
on.exit({
end_time <- Sys.time()
time_spent <- end_time - start_time
message("Time spent on the project:", time_spent)
# Create time data frame
df <- data.frame(Start_Time = as.character(start_time), End_Time = as.character(end_time), Time_Spent = as.numeric(time_spent))
if(file.exists(path_to_read)){
time_df <- dplyr::bind_rows(read.csv(path_to_read),
df)
}else{
time_df <- data.frame(Start_Time = start_time, End_Time = end_time, Time_Spent = time_spent)
}
# Save the data frame to a file
write.csv(time_df, path_to_read,col.names =  F)
})
}
}
track_time()
track_time <- function(category = "day") {
# Load/Create timesheet
path_to_read <- MyFunctions::my_path("D",name = "project_time_count.csv")
if(category == "day"){
start_time <- Sys.time()
message("Tracking time started.")
on.exit({
end_time <- Sys.time()
time_spent <- end_time - start_time
message("Time spent on the project:", time_spent)
# Create time data frame
df <- data.frame(Start_Time = as.character(start_time), End_Time = as.character(end_time), Time_Spent = as.numeric(time_spent))
if(file.exists(path_to_read)){
time_df <- dplyr::bind_rows(read.csv(path_to_read),
df)
}else{
time_df <- data.frame(Start_Time = start_time, End_Time = end_time, Time_Spent = time_spent)
}
# Save the data frame to a file
write.csv(time_df, path_to_read, row.names =  F)
})
}
}
track_time()
track_time()
track_time()
track_time()
track_time()
track_time <- function(category = "day") {
# Load/Create timesheet
path_to_read <- MyFunctions::my_path("D",name = "project_time_count.csv")
if(category == "day"){
start_time <- Sys.time()
message("Tracking time started.")
on.exit({
end_time <- Sys.time()
time_spent <- end_time - start_time
message("Time spent on the project:", time_spent)
# Create time data frame
df <- data.frame(Start_Time = as.character(start_time), End_Time = as.character(end_time), Time_Spent = as.numeric(time_spent))
if(file.exists(path_to_read)){
time_df <- dplyr::bind_rows(read.csv(path_to_read),
df)
}else{
time_df <- data.frame(Start_Time = start_time, End_Time = end_time, Time_Spent = time_spent)
}
# Save the data frame to a file
write.csv(time_df, path_to_read, row.names =  F)
})
}
}
[1] "Perch-likes"            "Other fish & inverts"   "Sharks & rays"          "Tuna & billfishes"      "Other fishes & inverts" "Salmon, smelts, etc"
devtools::document()
devtools::document()
#' Creates a project basic structure
#'
#' This function creates all the directories that I normally
#' use in all my projects. It creats them im bothe the Github
#' R project as rell as the data Repository
#'
#' @param Repo Main data repository. Currently set to HALL2000
#' @return Creates a series of directories that follow the basic structure of all my projects
#' @export
my_project <- function(Repo = "one_drive"){
# Get the projects name
Project <- basename(getwd())
# Create base directories in Github Repo
dir.create("scripts")
dir.create("results")
dir.create("results/figures")
dir.create("results/tables")
dir.create("documents")
# Create data repos in Hall2000
if(Repo == "Enterprise"){
if(dir.exists("/Volumes/Enterprise/") == TRUE){
# Main Data repo for project
dir.create(paste("/Volumes/Enterprise/Data/",Project,sep=""))
# Spatial data repo
dir.create(paste("/Volumes/Enterprise/Data/",Project,"/Spatial",sep=""))
# Species data repo
dir.create(paste("/Volumes/Enterprise/Data/",Project,"/Species",sep=""))
# Raw results
dir.create(paste("/Volumes/Enterprise/Data/",Project,"/Raw",sep=""))
}else{
print("Enterprise is not connected. Do you need to change the Repo?")
}
}
if(Repo == "one_drive"){
if(dir.exists("~/Library/CloudStorage/OneDrive-UBC/Data/") == TRUE){
# Main project repo
dir.create(paste("~/Library/CloudStorage/OneDrive-UBC/",Project,sep=""))
# Main Data repo for project
dir.create(paste("~/Library/CloudStorage/OneDrive-UBC/Data/",Project,sep=""))
# Spatial data repo
dir.create(paste("~/Library/CloudStorage/OneDrive-UBC/Data/",Project,"/data/spatial",sep=""))
# Species data repo
dir.create(paste("~/Library/CloudStorage/OneDrive-UBC/Data/",Project,"/data/species",sep=""))
# Raw results
dir.create(paste("~/Library/CloudStorage/OneDrive-UBC/Data/",Project,"/data/results/",sep=""))
# Scripts repo
dir.create(paste("~/Library/CloudStorage/OneDrive-UBC/Data/",Project,"/scripts/",sep=""))
# Specify the file name and location
file_path <- paste0("~/Library/CloudStorage/OneDrive-UBC/Data/",Project,"/scripts/initial_analysis.Rmd",sep="")
}else{
print("No connection with One Drive UBC Data. Do you need to change the Repo? Try Enterprise")
}
}
}
per_cng_fx <- function(v1,v2,limit=NA){
if(limit == NA){
x = ((v2-v1)/abs(v1))*100
}else{
x <- sign(limit) * 100  # Keep the sign of x and cap it at ±100
}
}
per_cng_fx <- function(v1,v2,limit=NA){
{
{
{
{
{
{
{
#' Estimates percentage change
#'
#' This function loads all necessary packages. If the
#' package is not installed, it will install it first
#' and the it will load the recently installed package
#'
#' @param v1 Type of path needed "D" for Data, "R", for Result and "G" for generic. You need those paths to be load in the global environment
#' @param v2 I normally call my data folder the same as the project so it automatically sets to the project name. Alternatives available.
#' @return A numeric value in percentage change from v2 relative to v1
#' @export
per_cng_fx <- function(v1, v2, limit = NA){
if(is.na(limit){
per_cng_fx <- function(v1, v2, limit = NA){
if(is.na(limit)){
x = ((v2-v1)/abs(v1))*100
}else{
x <- sign(limit) * 100  # Keep the sign of x and cap it at ±100
}
return(x)
}
devtools::document()
devtools::document()
devtools::document()
#' Creates a project basic structure
#'
#' This function creates all the directories that I normally
#' use in all my projects. It creats them im bothe the Github
#' R project as rell as the data Repository
#'
#' @param Repo Main data repository. Currently set to HALL2000
#' @return Creates a series of directories that follow the basic structure of all my projects
#' @export
my_project <- function(Repo = "one_drive"){
# Get the projects name
Project <- basename(getwd())
# Create base directories in Github Repo
dir.create("scripts")
dir.create("results")
dir.create("results/figures")
dir.create("results/tables")
dir.create("documents")
# Create data repos in Hall2000
if(Repo == "Enterprise"){
if(dir.exists("/Volumes/Enterprise/") == TRUE){
# Main Data repo for project
dir.create(paste("/Volumes/Enterprise/Data/",Project,sep=""))
# Spatial data repo
dir.create(paste("/Volumes/Enterprise/Data/",Project,"/Spatial",sep=""))
# Species data repo
dir.create(paste("/Volumes/Enterprise/Data/",Project,"/Species",sep=""))
# Raw results
dir.create(paste("/Volumes/Enterprise/Data/",Project,"/Raw",sep=""))
}else{
print("Enterprise is not connected. Do you need to change the Repo?")
}
}
if(Repo == "one_drive"){
if(dir.exists("~/Library/CloudStorage/OneDrive-UBC/Data/") == TRUE){
# Main project repo
dir.create(paste("~/Library/CloudStorage/OneDrive-UBC/",Project,sep=""))
}
# Main Data repo for project
dir.create(paste("~/Library/CloudStorage/OneDrive-UBC/data/",Project,"/data",sep=""))
# Spatial data repo
dir.create(paste("~/Library/CloudStorage/OneDrive-UBC/data/",Project,"/data/spatial",sep=""))
# Species data repo
dir.create(paste("~/Library/CloudStorage/OneDrive-UBC/data/",Project,"/data/species",sep=""))
# Raw results
dir.create(paste("~/Library/CloudStorage/OneDrive-UBC/data/",Project,"/results/",sep=""))
# Specify the file name and location
file_path <- paste0("~/Library/CloudStorage/OneDrive-UBC/data/",Project,"/scripts/initial_analysis.Rmd",sep="")
}else{
print("No connection with One Drive UBC Data. Do you need to change the Repo? Try Enterprise")
}
}
#'
#' @param path_type Type of path needed "D" for Data, "R", for Result and "G" for generic. You need those paths to be load in the global environment
#' @param project I normally call my data folder the same as the project so it automatically sets to the project name. Alternatives available.
#' @param extra_path Any sub-path to add WITHIN the folders. Note, if it is before, include it on the "Folder" parameter -e.g. project/SubFolder -
#' @param name Dataset name in case you want the option to load data
#' @param repo Normally set to jepa88 but if connection to Drobo is available use repo = "FALSE"
#' @param read Default read = FALSE. read = FALSE will only return a path wile read = TURE will read a dataset
#' @param system If you want to override the automatic system identification
#' @return Paths to save and load data within a project
#' @export
my_path <- function(path_type, extra_path= "", name = "", list_files ="NA", repo = TRUE, read=FALSE, header=TRUE, project = TRUE, system = NA){
# Overrride automati path
if(is.na(system)){
user <-  Sys.info()[7]
}else{
user <- system
}
# Main path where I store my data
if(user== "juliano"){
Main_Path <- "/Volumes/Enterprise/Data" # jepa88 (pre-selected)
}
if(user == "jepa88"){
Main_Path <- "~/Library/CloudStorage/OneDrive-UBC/Data/"
}
if(user == "drobo"){
Main_Path <- "/Volumes/DATA/JULIANO_NEYMAR" #If Drobo is needed
}
# Automatically sets the project name
if(project == TRUE){
# Get projecet name (only working for carmelia right now)
Project_root <- rprojroot::find_rstudio_root_file()
Project <- sub("^.*([^/]*/[^/]*)", "\\1", Project_root)
}
# Set project Data, Generic Data, Results and Figures paths
if(path_type %in% c("R","r","Result","result")){
Path <- paste(Main_Path,Project,"/Results",sep="")
}
if(path_type %in% c("D","Data","d","data")){
Path <- paste(Main_Path,Project,"/Data",sep="")
}
if(path_type%in% c("G","Generic","g","generic")){
Path <- Main_Path
}
if(path_type%in% c("Spa","Spatial","spa","spatial")){
Path <- paste(Main_Path,"/Spatial",sep="")
}
if(path_type%in% c("Spp","Species","spp","species")){
Path <- paste(Main_Path,"/Species",sep="")
}
if(path_type%in% c("F","f","Figures","Figure","figure","figures")){
Path <- "./Figures"
}
# Error messages for misspelled variables
Options = c("R","Results","D","Data","G","Generic","F","Figures","Spa","Spatial","Spp","Species")
if(!path_type %in% Options){
print("Data type value not accepted. Current acceptable options:")
print(Options)
stop()
}
# If the reading option is TRUE
if(read == TRUE){
My_Path <- paste(Path,extra_path,name,sep="/")
# Fix any double // in the path
My_Path <- gsub("//","/",My_Path)
if(stringr::str_detect(name,".xlsx") == TRUE){
My_Path <- readxl::read_excel(My_Path) %>% janitor::clean_names()
}
if(stringr::str_detect(name,".csv") == TRUE){
My_Path <- data.table::fread(My_Path, header=header) %>% janitor::clean_names()
}
if(stringr::str_detect(name,"txt") == TRUE){
My_Path <- data.table::fread(My_Path, header=header) %>% janitor::clean_names()
}
if(stringr::str_detect(name,".RData") == TRUE){
load(My_Path)
}
# Already load the coords with names
if(name == "DBEM_coords"){
name == "Lon_Lat_DBEM.txt"
colnames(My_Path) <- c("index","lon","lat")
}
}else{
if(list_files == "names"){
My_Path <- paste(Path,extra_path,name,sep="/")
# Fix any double // in the path
My_Path <- gsub("//","/",My_Path)
My_Path <- list.files(My_Path,full.names = F)
}else{
My_Path <- paste(Path,extra_path,name,sep="/")
# Fix any double // in the path
My_Path<- gsub("//","/",My_Path)
}
if(list_files == "paths"){
My_Path <- paste(Path,extra_path,name,sep="/")
# Fix any double // in the path
My_Path <- gsub("//","/",My_Path)
My_Path <- list.files(My_Path,full.names = T)
}else{
My_Path <- paste(Path,extra_path,name,sep="/")
# Fix any double // in the path
My_Path<- gsub("//","/",My_Path)
}
}
# Function returns the selected path
return(My_Path)
}
devtools::document()
devtools::document()
devtools::install_github("jepa/MyFunctions", force = T)