.Rhistory

date = as.Date(Sys.time()) # Create Date
date = gsub("-","_",date)
filename = paste("./HerbiTraits_2020_10_01/Changes/3_Output/HerbiTraits_S2_",date,".csv", sep ="") #Create filename
## Save
write.csv(herbiTraits_Master, file = filename)
######################################################################!
#                                                                    #
#      Script 3: CHECK THE MASS METADATA                              #
#                                                                    #
######################################################################!
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# METADATA
# This script checks the references
#
# Output: an updated dataframe with cleaned up references in the form of a csv file. Also an excel file for further processing
# time: less than 1 min
# Status: under construction (23 September 2020)
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––####
##### 1. PREPARING THE DATA #####
#–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––####
# – Clear Memory ####
#–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
rm(list = ls())  # clean memory (= remove)
graphics.off()  # close graphic windows
# – Set working directory ####
#–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
setwd("/Users/au572919/Research/herbiTraits")
getwd()
# – Set up libraries ####
#–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
# – Load Data ####
#–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
#~~ EXPLANATION ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#
#  This script combines the csv files created by S1 and S2. These CSV files have their creation date in their name to keep track of the most recent version.
#  This means there may be many trait files in the output folder. The following lines of code just select the most recent trait dataset, based on the creation date in the filename.
#
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
## Locate all trait datasets that S2 created.
files_in_folder = list.files(path = "./HerbiTraits_2020_10_01/Changes/3_Output") # list all the files occurring is the folder
Trait_Datasets = files_in_folder[which(grepl(pattern = "HerbiTraits_S2_",files_in_folder, fixed = TRUE))] # take all the Bird Trait Files
## Select the most recent version of the datasets
Trait_Datasets = tail(sort(Trait_Datasets), n=1)
## Load HerbiTraits Data
herbiTraits_Master = read.csv(paste("./HerbiTraits_2020_10_01/Changes/3_Output/", Trait_Datasets, sep =""))
herbiTraits_Master[1:10,1:10]
dim(herbiTraits_Master)
## Remove unneccesary column
herbiTraits_Master = herbiTraits_Master[,which(!(colnames(herbiTraits_Master) %in% c("X", "X.1")))]
#–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––####
##### 4. CORRECT REFERENCES #####
#–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––####
## Select variables with references
variables.with.references = which(grepl(pattern = "Reference", colnames(herbiTraits_Master), fixed = TRUE))
colnames(herbiTraits_Master)[variables.with.references]
# – Make a reference list (short notation) ####
#–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
## Select all variables with References
references = herbiTraits_Master[,variables.with.references]
references = as.vector(as.matrix(references))
## Sources
references = unique(unlist(strsplit(references, split = "; "))) # Number of Sources
length(references) # Number of Sources
references = sort(references)
# references[1:50]
# references[51:100]
# references[101:150]
# references[151:200]
# references[201:250]
# references[251:300]
# references[301:350]
# references[351:400]
# references[401:450]
# references[451:500]
# references[501:550]
# references[551:600]
## Correct Typos and mistakes and make citation style consistent
#––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
herbiTraits_Master$Mass.Reference = gsub(pattern = "All About Birds 2020 Cornell Lab of Ornithology ", replacement = "All About Birds 2020 Cornell Lab of Ornithology", x = herbiTraits_Master$Mass.Reference)
herbiTraits_Master$Diet.Reference = gsub(pattern = "All About Birds 2020 Cornell Lab of Ornithology ", replacement = "All About Birds 2020 Cornell Lab of Ornithology", x = herbiTraits_Master$Diet.Reference)
herbiTraits_Master$Fermentation.Type.Reference = gsub(pattern = "All About Birds 2020 Cornell Lab of Ornithology ", replacement = "All About Birds 2020 Cornell Lab of Ornithology", x = herbiTraits_Master$Fermentation.Type.Reference)
herbiTraits_Master$Limb.Morphology.Reference = gsub(pattern = "All About Birds 2020 Cornell Lab of Ornithology ", replacement = "All About Birds 2020 Cornell Lab of Ornithology", x = herbiTraits_Master$Limb.Morphology.Reference)
herbiTraits_Master$Habitat.Reference = gsub(pattern = "All About Birds 2020 Cornell Lab of Ornithology ", replacement = "All About Birds 2020 Cornell Lab of Ornithology", x = herbiTraits_Master$Habitat.Reference)
herbiTraits_Master$Mass.Reference = gsub(pattern = "Czerwonogora et al. 2011 Neues Jahrbuch f¸r Geologie und Pal‰ontologie-Abhandlungen", replacement = "Czerwonogora et al. 2011 Neues Jahrbuch fur Geologie und Paleontologie-Abhandlungen", x = herbiTraits_Master$Mass.Reference)
herbiTraits_Master$Diet.Reference = gsub(pattern = "Czerwonogora et al. 2011 Neues Jahrbuch f¸r Geologie und Pal‰ontologie-Abhandlungen", replacement = "Czerwonogora et al. 2011 Neues Jahrbuch fur Geologie und Paleontologie-Abhandlungen", x = herbiTraits_Master$Diet.Reference)
herbiTraits_Master$Fermentation.Type.Reference = gsub(pattern = "Czerwonogora et al. 2011 Neues Jahrbuch f¸r Geologie und Pal‰ontologie-Abhandlungen", replacement = "Czerwonogora et al. 2011 Neues Jahrbuch fur Geologie und Paleontologie-Abhandlungen", x = herbiTraits_Master$Fermentation.Type.Reference)
herbiTraits_Master$Limb.Morphology.Reference = gsub(pattern = "Czerwonogora et al. 2011 Neues Jahrbuch f¸r Geologie und Pal‰ontologie-Abhandlungen", replacement = "Czerwonogora et al. 2011 Neues Jahrbuch fur Geologie und Paleontologie-Abhandlungen", x = herbiTraits_Master$Limb.Morphology.Reference)
herbiTraits_Master$Habitat.Reference = gsub(pattern = "Czerwonogora et al. 2011 Neues Jahrbuch f¸r Geologie und Pal‰ontologie-Abhandlungen", replacement = "Czerwonogora et al. 2011 Neues Jahrbuch fur Geologie und Paleontologie-Abhandlungen", x = herbiTraits_Master$Habitat.Reference)
herbiTraits_Master$Mass.Reference = gsub(pattern = "Geist 1998 Stackpole books", replacement = "Geist 1998 Deer of the world: their evolution, behaviour, and ecology", x = herbiTraits_Master$Mass.Reference)
herbiTraits_Master$Diet.Reference = gsub(pattern = "Geist 1998 Stackpole books", replacement = "Geist 1998 Deer of the world: their evolution, behaviour, and ecology", x = herbiTraits_Master$Diet.Reference)
herbiTraits_Master$Fermentation.Type.Reference = gsub(pattern = "Geist 1998 Stackpole books", replacement = "Geist 1998 Deer of the world: their evolution, behaviour, and ecology", x = herbiTraits_Master$Fermentation.Type.Reference)
herbiTraits_Master$Limb.Morphology.Reference = gsub(pattern = "Geist 1998 Stackpole books", replacement = "Geist 1998 Deer of the world: their evolution, behaviour, and ecology", x = herbiTraits_Master$Limb.Morphology.Reference)
herbiTraits_Master$Habitat.Reference = gsub(pattern = "Geist 1998 Stackpole books", replacement = "Geist 1998 Deer of the world: their evolution, behaviour, and ecology", x = herbiTraits_Master$Habitat.Reference)
herbiTraits_Master$Mass.Reference = gsub(pattern = "Gillette and Ray 1981 Smithsonian Institution Press", replacement = "Gillette and Ray 1981 Glyptodonts of North America", x = herbiTraits_Master$Mass.Reference)
herbiTraits_Master$Diet.Reference = gsub(pattern = "Gillette and Ray 1981 Smithsonian Institution Press", replacement = "Gillette and Ray 1981 Glyptodonts of North America", x = herbiTraits_Master$Diet.Reference)
herbiTraits_Master$Fermentation.Type.Reference = gsub(pattern = "Gillette and Ray 1981 Smithsonian Institution Press", replacement = "Gillette and Ray 1981 Glyptodonts of North America", x = herbiTraits_Master$Fermentation.Type.Reference)
herbiTraits_Master$Limb.Morphology.Reference = gsub(pattern = "Gillette and Ray 1981 Smithsonian Institution Press", replacement = "Gillette and Ray 1981 Glyptodonts of North America", x = herbiTraits_Master$Limb.Morphology.Reference)
herbiTraits_Master$Habitat.Reference = gsub(pattern = "Gillette and Ray 1981 Smithsonian Institution Press", replacement = "Gillette and Ray 1981 Glyptodonts of North America", x = herbiTraits_Master$Habitat.Reference)
herbiTraits_Master$Mass.Reference = gsub(pattern = "Kingdon et al. 2013 Mammals of Africa Louys et al. 2011 Journal of Archaeological Science", replacement = "Kingdon et al. 2013 Mammals of Africa; Louys et al. 2011 Journal of Archaeological Science", x = herbiTraits_Master$Mass.Reference)
herbiTraits_Master$Diet.Reference = gsub(pattern = "Kingdon et al. 2013 Mammals of Africa Louys et al. 2011 Journal of Archaeological Science", replacement = "Kingdon et al. 2013 Mammals of Africa; Louys et al. 2011 Journal of Archaeological Science", x = herbiTraits_Master$Diet.Reference)
herbiTraits_Master$Fermentation.Type.Reference = gsub(pattern = "Kingdon et al. 2013 Mammals of Africa Louys et al. 2011 Journal of Archaeological Science", replacement = "Kingdon et al. 2013 Mammals of Africa; Louys et al. 2011 Journal of Archaeological Science", x = herbiTraits_Master$Fermentation.Type.Reference)
herbiTraits_Master$Limb.Morphology.Reference = gsub(pattern = "Kingdon et al. 2013 Mammals of Africa Louys et al. 2011 Journal of Archaeological Science", replacement = "Kingdon et al. 2013 Mammals of Africa; Louys et al. 2011 Journal of Archaeological Science", x = herbiTraits_Master$Limb.Morphology.Reference)
herbiTraits_Master$Habitat.Reference = gsub(pattern = "Kingdon et al. 2013 Mammals of Africa Louys et al. 2011 Journal of Archaeological Science", replacement = "Kingdon et al. 2013 Mammals of Africa; Louys et al. 2011 Journal of Archaeological Science", x = herbiTraits_Master$Habitat.Reference)
herbiTraits_Master$Mass.Reference = gsub(pattern = "Hofreiter et al. 2000 Molecular EcologyGreen 2009 Zoological Journal of the Linnean Society", replacement = "Hofreiter et al. 2000 Molecular Ecology; Green 2009 Zoological Journal of the Linnean Society", x = herbiTraits_Master$Mass.Reference)
herbiTraits_Master$Diet.Reference = gsub(pattern = "Hofreiter et al. 2000 Molecular EcologyGreen 2009 Zoological Journal of the Linnean Society", replacement = "Hofreiter et al. 2000 Molecular Ecology; Green 2009 Zoological Journal of the Linnean Society", x = herbiTraits_Master$Diet.Reference)
herbiTraits_Master$Fermentation.Type.Reference = gsub(pattern = "Hofreiter et al. 2000 Molecular EcologyGreen 2009 Zoological Journal of the Linnean Society", replacement = "Hofreiter et al. 2000 Molecular Ecology; Green 2009 Zoological Journal of the Linnean Society", x = herbiTraits_Master$Fermentation.Type.Reference)
herbiTraits_Master$Limb.Morphology.Reference = gsub(pattern = "Hofreiter et al. 2000 Molecular EcologyGreen 2009 Zoological Journal of the Linnean Society", replacement = "Hofreiter et al. 2000 Molecular Ecology; Green 2009 Zoological Journal of the Linnean Society", x = herbiTraits_Master$Limb.Morphology.Reference)
herbiTraits_Master$Habitat.Reference = gsub(pattern = "Hofreiter et al. 2000 Molecular EcologyGreen 2009 Zoological Journal of the Linnean Society", replacement = "Hofreiter et al. 2000 Molecular Ecology; Green 2009 Zoological Journal of the Linnean Society", x = herbiTraits_Master$Habitat.Reference)
herbiTraits_Master$Mass.Reference = gsub(pattern = "Hollis et al. 1986 Wildlife Research, Osawa 1990 Wildlife Research", replacement = "Hollis et al. 1986 Wildlife Research; Osawa 1990 Wildlife Research", x = herbiTraits_Master$Mass.Reference)
herbiTraits_Master$Diet.Reference = gsub(pattern = "Hollis et al. 1986 Wildlife Research, Osawa 1990 Wildlife Research", replacement = "Hollis et al. 1986 Wildlife Research; Osawa 1990 Wildlife Research", x = herbiTraits_Master$Diet.Reference)
herbiTraits_Master$Fermentation.Type.Reference = gsub(pattern = "Hollis et al. 1986 Wildlife Research, Osawa 1990 Wildlife Research", replacement = "Hollis et al. 1986 Wildlife Research; Osawa 1990 Wildlife Research", x = herbiTraits_Master$Fermentation.Type.Reference)
herbiTraits_Master$Limb.Morphology.Reference = gsub(pattern = "Hollis et al. 1986 Wildlife Research, Osawa 1990 Wildlife Research", replacement = "Hollis et al. 1986 Wildlife Research; Osawa 1990 Wildlife Research", x = herbiTraits_Master$Limb.Morphology.Reference)
herbiTraits_Master$Habitat.Reference = gsub(pattern = "Hollis et al. 1986 Wildlife Research, Osawa 1990 Wildlife Research", replacement = "Hollis et al. 1986 Wildlife Research; Osawa 1990 Wildlife Research", x = herbiTraits_Master$Habitat.Reference)
herbiTraits_Master$Mass.Reference = gsub(pattern = "Syed and Ilyas 2015 Animal Production Science;Bhattacharya et al. 2012 Proceedings of the Zoological Society", replacement = "Syed and Ilyas 2015 Animal Production Science; Bhattacharya et al. 2012 Proceedings of the Zoological Society", x = herbiTraits_Master$Mass.Reference)
herbiTraits_Master$Diet.Reference = gsub(pattern = "Syed and Ilyas 2015 Animal Production Science;Bhattacharya et al. 2012 Proceedings of the Zoological Society", replacement = "Syed and Ilyas 2015 Animal Production Science; Bhattacharya et al. 2012 Proceedings of the Zoological Society", x = herbiTraits_Master$Diet.Reference)
herbiTraits_Master$Fermentation.Type.Reference = gsub(pattern = "Syed and Ilyas 2015 Animal Production Science;Bhattacharya et al. 2012 Proceedings of the Zoological Society", replacement = "Syed and Ilyas 2015 Animal Production Science; Bhattacharya et al. 2012 Proceedings of the Zoological Society", x = herbiTraits_Master$Fermentation.Type.Reference)
herbiTraits_Master$Limb.Morphology.Reference = gsub(pattern = "Syed and Ilyas 2015 Animal Production Science;Bhattacharya et al. 2012 Proceedings of the Zoological Society", replacement = "Syed and Ilyas 2015 Animal Production Science; Bhattacharya et al. 2012 Proceedings of the Zoological Society", x = herbiTraits_Master$Limb.Morphology.Reference)
herbiTraits_Master$Habitat.Reference = gsub(pattern = "Syed and Ilyas 2015 Animal Production Science;Bhattacharya et al. 2012 Proceedings of the Zoological Society", replacement = "Syed and Ilyas 2015 Animal Production Science; Bhattacharya et al. 2012 Proceedings of the Zoological Society", x = herbiTraits_Master$Habitat.Reference)
herbiTraits_Master$Mass.Reference = gsub(pattern = "Wilman et al. 2014 Ecology;Avaliani et al. 2007", replacement = "Wilman et al. 2014 Ecology; Avaliani et al. 2007", x = herbiTraits_Master$Mass.Reference)
herbiTraits_Master$Diet.Reference = gsub(pattern = "Wilman et al. 2014 Ecology;Avaliani et al. 2007", replacement = "Wilman et al. 2014 Ecology; Avaliani et al. 2007", x = herbiTraits_Master$Diet.Reference)
herbiTraits_Master$Fermentation.Type.Reference = gsub(pattern = "Wilman et al. 2014 Ecology;Avaliani et al. 2007", replacement = "Wilman et al. 2014 Ecology; Avaliani et al. 2007", x = herbiTraits_Master$Fermentation.Type.Reference)
herbiTraits_Master$Limb.Morphology.Reference = gsub(pattern = "Wilman et al. 2014 Ecology;Avaliani et al. 2007", replacement = "Wilman et al. 2014 Ecology; Avaliani et al. 2007", x = herbiTraits_Master$Limb.Morphology.Reference)
herbiTraits_Master$Habitat.Reference = gsub(pattern = "Wilman et al. 2014 Ecology;Avaliani et al. 2007", replacement = "Wilman et al. 2014 Ecology; Avaliani et al. 2007", x = herbiTraits_Master$Habitat.Reference)
herbiTraits_Master$Mass.Reference = gsub(pattern = "Madden 2014 Cambridge University Press", replacement = "Madden 2014 Hypsodonty in Mammals: Evolution, Geomorphology, and the Role of Earth System Processes", x = herbiTraits_Master$Mass.Reference)
herbiTraits_Master$Diet.Reference = gsub(pattern = "Madden 2014 Cambridge University Press", replacement = "Madden 2014 Hypsodonty in Mammals: Evolution, Geomorphology, and the Role of Earth System Processes", x = herbiTraits_Master$Diet.Reference)
herbiTraits_Master$Fermentation.Type.Reference = gsub(pattern = "Madden 2014 Cambridge University Press", replacement = "Madden 2014 Hypsodonty in Mammals: Evolution, Geomorphology, and the Role of Earth System Processes", x = herbiTraits_Master$Fermentation.Type.Reference)
herbiTraits_Master$Limb.Morphology.Reference = gsub(pattern = "Madden 2014 Cambridge University Press", replacement = "Madden 2014 Hypsodonty in Mammals: Evolution, Geomorphology, and the Role of Earth System Processes", x = herbiTraits_Master$Limb.Morphology.Reference)
herbiTraits_Master$Habitat.Reference = gsub(pattern = "Madden 2014 Cambridge University Press", replacement = "Madden 2014 Hypsodonty in Mammals: Evolution, Geomorphology, and the Role of Earth System Processes", x = herbiTraits_Master$Habitat.Reference)
herbiTraits_Master$Mass.Reference = gsub(pattern = "NA Lobo 2015 Thesis", replacement = "Lobo 2015 Thesis", x = herbiTraits_Master$Mass.Reference)
herbiTraits_Master$Diet.Reference = gsub(pattern = "NA Lobo 2015 Thesis", replacement = "Lobo 2015 Thesis", x = herbiTraits_Master$Diet.Reference)
herbiTraits_Master$Fermentation.Type.Reference = gsub(pattern = "NA Lobo 2015 Thesis", replacement = "Lobo 2015 Thesis", x = herbiTraits_Master$Fermentation.Type.Reference)
herbiTraits_Master$Limb.Morphology.Reference = gsub(pattern = "NA Lobo 2015 Thesis", replacement = "Lobo 2015 Thesis", x = herbiTraits_Master$Limb.Morphology.Reference)
herbiTraits_Master$Habitat.Reference = gsub(pattern = "NA Lobo 2015 Thesis", replacement = "Lobo 2015 Thesis", x = herbiTraits_Master$Habitat.Reference)
herbiTraits_Master$Mass.Reference = gsub(pattern = "Prideaux 2009 Proceedings of the National Academy of Sciences of the United States of America", replacement = "Prideaux et al. 2009 Proceedings of the National Academy of Sciences of the United States of America", x = herbiTraits_Master$Mass.Reference)
herbiTraits_Master$Diet.Reference = gsub(pattern = "Prideaux 2009 Proceedings of the National Academy of Sciences of the United States of America", replacement = "Prideaux et al. 2009 Proceedings of the National Academy of Sciences of the United States of America", x = herbiTraits_Master$Diet.Reference)
herbiTraits_Master$Fermentation.Type.Reference = gsub(pattern = "Prideaux 2009 Proceedings of the National Academy of Sciences of the United States of America", replacement = "Prideaux et al. 2009 Proceedings of the National Academy of Sciences of the United States of America", x = herbiTraits_Master$Fermentation.Type.Reference)
herbiTraits_Master$Limb.Morphology.Reference = gsub(pattern = "Prideaux 2009 Proceedings of the National Academy of Sciences of the United States of America", replacement = "Prideaux et al. 2009 Proceedings of the National Academy of Sciences of the United States of America", x = herbiTraits_Master$Limb.Morphology.Reference)
herbiTraits_Master$Habitat.Reference = gsub(pattern = "Prideaux 2009 Proceedings of the National Academy of Sciences of the United States of America", replacement = "Prideaux et al. 2009 Proceedings of the National Academy of Sciences of the United States of America", x = herbiTraits_Master$Habitat.Reference)
herbiTraits_Master$Mass.Reference = gsub(pattern = "Torres et al. 2018 Proc B", replacement = "Torres et al. 2018 Proceedings of the Royal Society B", x = herbiTraits_Master$Mass.Reference)
herbiTraits_Master$Diet.Reference = gsub(pattern = "Torres et al. 2018 Proc B", replacement = "Torres et al. 2018 Proceedings of the Royal Society B", x = herbiTraits_Master$Diet.Reference)
herbiTraits_Master$Fermentation.Type.Reference = gsub(pattern = "Torres et al. 2018 Proc B", replacement = "Torres et al. 2018 Proceedings of the Royal Society B", x = herbiTraits_Master$Fermentation.Type.Reference)
herbiTraits_Master$Limb.Morphology.Reference = gsub(pattern = "Torres et al. 2018 Proc B", replacement = "Torres et al. 2018 Proceedings of the Royal Society B", x = herbiTraits_Master$Limb.Morphology.Reference)
herbiTraits_Master$Habitat.Reference = gsub(pattern = "Torres et al. 2018 Proc B", replacement = "Torres et al. 2018 Proceedings of the Royal Society B", x = herbiTraits_Master$Habitat.Reference)
#–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––####
##### 4. SAVE DATA  #####
#–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––####
## Create filename
date = as.Date(Sys.time()) # Create Date
date = gsub("-","_",date)
filename = paste("./HerbiTraits_2020_10_01/Changes/3_Output/HerbiTraits_S3_",date,".csv", sep ="") #Create filename
## Save
write.csv(herbiTraits_Master, file = filename, row.names = F)
```{r, include = F}
getwd()
```
# Introduction
HerbiTraits is a functional trait dataset that contains functional traits of all large-bodied (≥10 kg), terrestrial, avian and mammalian herbivores that lived during the last 130,000 years (n = 545 species). The mammalian component of the dataset is based on PHYLACINE V1.2 taxonomy and root traits, but we have provided more detailed trait information for the species of interest. The avian component has been added by the authors of HerbiTraits. HerbiTraits includes data on:
```{r, results = 'hide', include = F}
## Working Directory
getwd()
```
# Introduction
HerbiTraits is a functional trait dataset that contains functional traits of all large-bodied (≥10 kg), terrestrial, avian and mammalian herbivores that lived during the last 130,000 years (n = 545 species). The mammalian component of the dataset is based on PHYLACINE V1.2 taxonomy and root traits, but we have provided more detailed trait information for the species of interest. The avian component has been added by the authors of HerbiTraits. HerbiTraits includes data on:
## Load Data
herbitraits.data = read.csv(xls = "./data/Version_1/HerbiTraits_V1/HerbiTraits_Data_v1.csv")
## Load Data
herbitraits.data = read.csv("./data/Version_1/HerbiTraits_V1/HerbiTraits_Data_v1.csv")
rm(lm())
rm(ls())
rm(list = ls())
## Check Working Directory
getwd()
getwd()
## Check Working Directory
getwd()
## Load Data
herbitraits.data = read.csv("./data/Version_1/HerbiTraits_V1/HerbiTraits_Data_v1.csv")
herbitraits.references = read.csv("./data/Version_1/HerbiTraits_V1/HerbiTraits_References_v1.csv")
View(herbitraits.references)
## Clear Working Memory
rm(list = ls())
## Check Working Directory
getwd()
## Load Data
herbitraits.data = read.csv("./data/Version_1/HerbiTraits_V1/HerbiTraits_Data_v1.csv")
herbitraits.references = read.csv("./data/Version_1/HerbiTraits_V1/HerbiTraits_References_v1.csv")
`r nrow(herbitraits.data)`
## Clear Working Memory
rm(list = ls())
## Check Working Directory
getwd()
## Load Data
herbitraits.data = read.csv("./data/Version_1/HerbiTraits_V1/HerbiTraits_Data_v1.csv")
herbitraits.references = read.csv("./data/Version_1/HerbiTraits_V1/HerbiTraits_References_v1.csv")
## Working Directory
getwd()
path <- "./Version_Dev/HerbiTraits_Dev/"
merge_file_name <- "./Version_Dev/HerbiTraits_Dev//merged_file.xlsx"
list.files(path= path, full.names=TRUE)
## Working Directory
getwd()
path <- "./Data/Version_Dev/HerbiTraits_Dev/"
list.files(path= path, full.names=TRUE)
filenames_list <- list.files(path= path, full.names=TRUE)
merge_file_name <- "./Data/Version_Dev/HerbiTraits_Dev//merged_file.xlsx"
All <- lapply(filenames_list,function(filename){
print(paste("Merging",filename,sep = " "))
read.xlsx(filename)
})
## Load Libraries
library(openxlsx) # Necessary to create Excel file
All <- lapply(filenames_list,function(filename){
print(paste("Merging",filename,sep = " "))
read.xlsx(filename)
})
## Clear Working Memory
rm(list = ls())  # clean memory
graphics.off()  # close graphic windows
## Working Directory
getwd()
## Load Libraries
library(openxlsx) # Necessary to create Excel file
path <- "./Data/Version_Dev/HerbiTraits_Dev/" # File path
merge_file_name <- "./Data/Version_Dev/HerbiTraits_Dev//merged_file.xlsx" #Name of the final excel file
filenames_list <- list.files(path= path, full.names=TRUE) # list files in folder
All <- lapply(filenames_list,function(filename){
print(paste("Merging",filename,sep = " "))
read.xlsx(filename)
})
filename
All <- lapply(filenames_list,function(filename){
print(paste("Merging",filename,sep = " "))
read.xlsx(filename)
})
df <- do.call(rbind.data.frame, All)
library(data.table)  ## for fast fread() function
library(XLConnect)
install.packages("XLConnect")
install.packages("data.table")
# install.packages("XLConnect")
library(XLConnect)
merge_file_name <- "./Data/Version_Dev/HerbiTraits_Dev/merged_file.xlsx" #Name of the final excel file
filenames_list <- list.files(path= path, full.names=TRUE) # list files in folder
All <- lapply(filenames_list,function(filename){
print(paste("Merging",filename,sep = " "))
read.xlsx(filename)
})
folder <- "./Data/Version_Dev/HerbiTraits_Dev/"
f.out <- "./Data/Version_Dev/HerbiTraits_Dev/merged_file.xlsx"
## load in file
wb <- loadWorkbook(f.out, create=TRUE)
wb = createWorkbook()
?createWorkbook
## Clear Working Memory
rm(list = ls())  # clean memory
graphics.off()  # close graphic windows
path <- "sample-data/merge-files/xlsx"
merge_file_name <- "sample-data/merge-files//merged_file.xlsx"
filenames_list <- list.files(path= path, full.names=TRUE)
path <- "./Data/Version_Dev/HerbiTraits_Dev/" # File path
merge_file_name <- "./Data/Version_Dev/HerbiTraits_Dev/merged_file.xlsx" #Name of the final excel file
filenames_list <- list.files(path= path, full.names=TRUE)
filenames_list
path <- "./Data/Version_Dev/HerbiTraits_Dev" # File path
merge_file_name <- "./Data/Version_Dev/HerbiTraits_Dev/merged_file.xlsx" #Name of the final excel file
filenames_list <- list.files(path= path, full.names=TRUE)
filenames_list
All <- lapply(filenames_list,function(filename){
print(paste("Merging",filename,sep = " "))
read.csv(filename)
})
df <- do.call(rbind.data.frame, All)
View(All)
lapply(filenames_list,read.csv(filename)
## Clear Working Memory
rm(list = ls())  # clean memory
graphics.off()  # close graphic windows
## Clear Working Memory
rm(list = ls())  # clean memory
graphics.off()  # close graphic windows
path <- "./Data/Version_Dev/HerbiTraits_Dev" # File path
merge_file_name <- "./Data/Version_Dev/HerbiTraits_Dev/merged_file.xlsx" #Name of the final excel file
filenames_list <- list.files(path= path, full.names=TRUE)
All <- lapply(filenames_list,read.csv(filename))
All <- lapply(filenames_list,read.csv(filename){
print(paste("Merging",filename,sep = " "))
read.csv(filename)
})
All <- lapply(filenames_list,read.csv(filename){
print(paste("Merging",filename,sep = " "))
read.csv(filename)
})
path <- "./Data/Version_Dev/HerbiTraits_Dev" # File path
merge_file_name <- "./Data/Version_Dev/HerbiTraits_Dev/merged_file.xlsx" #Name of the final excel file
filenames_list <- list.files(path= path, full.names=TRUE)
All <- lapply(filenames_list,read.csv(filename){
print(paste("Merging",filename,sep = " "))
read.csv(filename)
})
## Clear Working Memory
rm(list = ls())  # clean memory
graphics.off()  # close graphic windows
path <- "./Data/Version_Dev/HerbiTraits_Dev" # File path
merge_file_name <- "./Data/Version_Dev/HerbiTraits_Dev/merged_file.xlsx" #Name of the final excel file
filenames_list <- list.files(path= path, full.names=TRUE)
All <- lapply(filenames_list,read.csv(filename){
print(paste("Merging",filename,sep = " "))
read.csv(filename)
})
All <- lapply(filenames_list,function(filename){
print(paste("Merging",filename,sep = " "))
read.csv(filename)
})
str(All)
df <- do.call(rbind.data.frame, All)
All[1]
filenames_list
grepl("_Data", filenames_list)
which(grepl("_Data", filenames_list))
filenames_list[which(grepl("_Data", filenames_list))]
read.csv(filenames_list[which(grepl("_Data", filenames_list))])
HerbiTraits_Data = read.csv(filenames_list[which(grepl("_Data", filenames_list))])
HerbiTraits_Data = read.csv(filenames_list[which(grepl("_Data", filenames_list))])
HerbiTraits_Metadata = read.csv(filenames_list[which(grepl("_Metadata", filenames_list))])
HerbiTraits_References = read.csv(filenames_list[which(grepl("_References", filenames_list))])
wb = createWorkbook()
sheet = createSheet(wb, "Sheet 1")
sheet = createSheet(wb, "Sheet 1")
library("openxlsx")
sheet = createSheet(wb, "Sheet 1")
wb = createWorkbook()
sheet = createSheet(wb, "Sheet 1")
?createSheet
library("xlsx")
install.packages('xlsx')
library("xlsx")
sheet = createSheet(wb, "Sheet 1")
?write.xlsx
library("openxlsx")
write.xlsx(HerbiTraits_Data, file="HerbiTraits_Dev.xlsx", sheetName="sheet1", row.names=FALSE)
write.xlsx(HerbiTraits_Metadata, file="HerbiTraits_Dev.xlsx", sheetName="sheet2", append=TRUE, row.names=FALSE)
write.xlsx(HerbiTraits_References, file="HerbiTraits_Dev.xlsx", sheetName="sheet2", append=TRUE, row.names=FALSE)
write.xlsx(HerbiTraits_Data, file="HerbiTraits_Dev.xlsx", sheetName="sheet1", row.names=FALSE)
getwd()
write.xlsx(HerbiTraits_Data, file="./Data/Version_Dev/HerbiTraits_Dev/HerbiTraits_Dev.xlsx", sheetName="sheet1", row.names=FALSE)
write.xlsx(HerbiTraits_Metadata, file="./Data/Version_Dev/HerbiTraits_Dev/HerbiTraits_Dev.xlsx", sheetName="sheet2", append=TRUE, row.names=FALSE)
write.xlsx(HerbiTraits_References, file="./Data/Version_Dev/HerbiTraits_Dev/HerbiTraits_Dev.xlsx", sheetName="sheet2", append=TRUE, row.names=FALSE)
## Clear Working Memory
rm(list = ls())  # clean memory
graphics.off()  # close graphic windows
# Create File Paths
path <- "./Data/Version_Dev/HerbiTraits_Dev" # File path
filenames_list <- list.files(path= path, full.names=TRUE) # List of all files in the folder
## Load CSV files
HerbiTraits_Data = read.csv(filenames_list[which(grepl("_Data", filenames_list))])
HerbiTraits_Metadata = read.csv(filenames_list[which(grepl("_Metadata", filenames_list))])
HerbiTraits_References = read.csv(filenames_list[which(grepl("_References", filenames_list))])
write.xlsx(HerbiTraits_Metadata, file="./Data/Version_Dev/HerbiTraits_Dev/HerbiTraits_Dev.xlsx", sheetName="sheet1",  row.names=FALSE)
write.xlsx(HerbiTraits_Data, file="./Data/Version_Dev/HerbiTraits_Dev/HerbiTraits_Dev.xlsx", sheetName="sheet2",append=TRUE, row.names=FALSE)
write.xlsx(HerbiTraits_References, file="./Data/Version_Dev/HerbiTraits_Dev/HerbiTraits_Dev.xlsx", sheetName="sheet3", append=TRUE, row.names=FALSE)
write.xlsx(HerbiTraits_Metadata, file="./Data/Version_Dev/HerbiTraits_Dev/HerbiTraits_Dev.xlsx", sheetName="sheet1",  row.names=FALSE)
write.xlsx(HerbiTraits_Metadata, file="./Data/Version_Dev/HerbiTraits_Dev/HerbiTraits_Dev.xlsx", sheetName="sheet1",  row.names=FALSE)
write.xlsx(HerbiTraits_Data, file="./Data/Version_Dev/HerbiTraits_Dev/HerbiTraits_Dev.xlsx", sheetName="sheet2",append=TRUE, row.names=FALSE)
?write.xlsx
write.xlsx(HerbiTraits_Metadata, file="./Data/Version_Dev/HerbiTraits_Dev/HerbiTraits_Dev.xlsx", sheetName="Metadata",  row.names=FALSE)
library("openxlsx")
# Create a blank workbook
OUT <- createWorkbook()
# Add some sheets to the workbook
addWorksheet(OUT, "Sheet 1 Name")
addWorksheet(OUT, "Sheet 2 Name")
# Write the data to the sheets
writeData(OUT, sheet = "Sheet 1 Name", x = HerbiTraits_Metadata)
writeData(OUT, sheet = "Sheet 2 Name", x = HerbiTraits_Data)
# Export the file
saveWorkbook(OUT, "My output file.xlsx")
# install.packages("data.table")
#install.packages('openxlsx')
library("openxlsx")
# Create File Paths
path <- "./Data/Version_Dev/HerbiTraits_Dev" # File path
filenames_list <- list.files(path= path, full.names=TRUE) # List of all files in the folder
## Load CSV files
HerbiTraits_Data = read.csv(filenames_list[which(grepl("_Data", filenames_list))])
HerbiTraits_Metadata = read.csv(filenames_list[which(grepl("_Metadata", filenames_list))])
HerbiTraits_References = read.csv(filenames_list[which(grepl("_References", filenames_list))])
## Add sheets to the workbook
addWorksheet(OUT, "MetaData")
addWorksheet(OUT, "Data")
######################################################################!
#                                                                    #
#     S999: Create Excel File                                        #
#                                                                    #
######################################################################!
# Explanation: This files takes the three CSV files (HerbiTraits_Metadata, HerbiTraits_Data, HerbiTraits_References) and combines them into an excel file.
# Output: An Excel file named "HerbiTraits_vX"
# Duration:
# Status: finished (2020/11/25)
#–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––
## Clear Working Memory
rm(list = ls())  # clean memory
graphics.off()  # close graphic windows
## Working Directory
getwd()
## Load Libraries
#install.packages('openxlsx')
library("openxlsx")
# Create File Paths
path <- "./Data/Version_Dev/HerbiTraits_Dev" # File path
filenames_list <- list.files(path= path, full.names=TRUE) # List of all files in the folder
## Load CSV files
HerbiTraits_Data = read.csv(filenames_list[which(grepl("_Data", filenames_list))])
HerbiTraits_Metadata = read.csv(filenames_list[which(grepl("_Metadata", filenames_list))])
HerbiTraits_References = read.csv(filenames_list[which(grepl("_References", filenames_list))])
## Create a blank workbook
OUT <- createWorkbook()
## Add sheets to the workbook
addWorksheet(OUT, "MetaData")
addWorksheet(OUT, "Data")
addWorksheet(OUT, "References")
## Write the data to the sheets
writeData(OUT, sheet = "MetaData", x = HerbiTraits_Metadata)
writeData(OUT, sheet = "Data", x = HerbiTraits_Data)
writeData(OUT, sheet = "References", x = HerbiTraits_References)
## Export the file
saveWorkbook(OUT, "/Data/Version_Dev/HerbiTraits_Dev/HerbiTraits_Dev.xlsx")
## Clear Working Memory
rm(list = ls())  # clean memory
graphics.off()  # close graphic windows
## Working Directory
getwd()
## Load Libraries
#install.packages('openxlsx')
library("openxlsx")
# Create File Paths
path <- "./Data/Version_Dev/HerbiTraits_Dev" # File path
filenames_list <- list.files(path= path, full.names=TRUE) # List of all files in the folder
## Load CSV files
HerbiTraits_Data = read.csv(filenames_list[which(grepl("_Data", filenames_list))])
HerbiTraits_Metadata = read.csv(filenames_list[which(grepl("_Metadata", filenames_list))])
HerbiTraits_References = read.csv(filenames_list[which(grepl("_References", filenames_list))])
## Create a blank workbook
OUT <- createWorkbook()
## Add sheets to the workbook
addWorksheet(OUT, "MetaData")
addWorksheet(OUT, "Data")
addWorksheet(OUT, "References")
## Write the data to the sheets
writeData(OUT, sheet = "MetaData", x = HerbiTraits_Metadata)
writeData(OUT, sheet = "Data", x = HerbiTraits_Data)
writeData(OUT, sheet = "References", x = HerbiTraits_References)
## Export the file
saveWorkbook(OUT, "/Data/Version_Dev/HerbiTraits_Dev/HerbiTraits_Dev.xlsx")
## Export the file
saveWorkbook(OUT, "./Data/Version_Dev/HerbiTraits_Dev/HerbiTraits_Dev.xlsx")
## Clear Working Memory
rm(list = ls())
## Check Working Directory
getwd()
## Load Data
herbitraits.data = read.csv("./data/Version_1/HerbiTraits_V1/HerbiTraits_Data_v1.csv")
herbitraits.references = read.csv("./data/Version_1/HerbiTraits_V1/HerbiTraits_References_v1.csv")
r format(Sys.time(), '%d %B %Y')
getwd()
getwd()
## Load Data
herbitraits.data = read.csv("./Data/Version_1/HerbiTraits_V1/HerbiTraits_Data_v1.csv")
## Load Data
herbitraits.data = read.csv("./Data/Version_1/HerbiTraits_V1/HerbiTraits_Data_v1.csv")
## Load Data
herbitraits.data = read.csv("../Data/Version_1/HerbiTraits_V1/HerbiTraits_Data_v1.csv")
## Load Data
herbitraits.data = read.csv("./Data/Version_1/HerbiTraits_V1/HerbiTraits_Data_v1.csv")
getwd()
/Users/au572919/Research/I_MegaPast2Future/HerbiTraits/Data/Version_1/HerbiTraits_V1/HerbiTraits_Data_v1.csv"
"Users/au572919/Research/I_MegaPast2Future/HerbiTraits/Data/Version_1/HerbiTraits_V1/HerbiTraits_Data_v1.csv"
read.csv("Users/au572919/Research/I_MegaPast2Future/HerbiTraits/Data/Version_1/HerbiTraits_V1/HerbiTraits_Data_v1.csv")
read.csv("Users/au572919/Research/I_MegaPast2Future/HerbiTraits/Data/Version_1/HerbiTraits_V1/HerbiTraits_Data_v1.csv")
file.exists("Users/au572919/Research/I_MegaPast2Future/HerbiTraits/Data/Version_1/HerbiTraits_V1/HerbiTraits_Data_v1.csv")
## Load Data
herbitraits.data = read.csv("./data/Version_1/HerbiTraits_V1/HerbiTraits_Data_v1.csv")
## Check Working Directory
getwd()
getwd()
## Check Working Directory
getwd()
setwd("/Users/au572919/Research/I_MegaPast2Future/HerbiTraits")
## Load Data
herbitraits.data = read.csv("./Data/Version_1/HerbiTraits_V1/HerbiTraits_Data_v1.csv")
## Check Working Directory
getwd()
setwd("/Users/au572919/Research/I_MegaPast2Future/HerbiTraits")
## Load Data
herbitraits.data = read.csv("./Data/Version_1/HerbiTraits_V1/HerbiTraits_Data_v1.csv")
## Clear Working Memory
rm(list = ls())
## Check Working Directory
getwd()
setwd("/Users/au572919/Research/I_MegaPast2Future/HerbiTraits")
## Load Data
herbitraits.data = read.csv("./Data/Version_1/HerbiTraits_V1/HerbiTraits_Data_v1.csv")
herbitraits.references = read.csv("./Data/Version_1/HerbiTraits_V1/HerbiTraits_References_v1.csv")
## Clear Working Memory
rm(list = ls())
## Check Working Directory
getwd()
setwd("/Users/au572919/Research/I_MegaPast2Future/HerbiTraits") # Change Directiory if needed
## Load Data
herbitraits.data = read.csv("./Data/Version_1/HerbiTraits_V1/HerbiTraits_Data_v1.csv")
herbitraits.references = read.csv("./Data/Version_1/HerbiTraits_V1/HerbiTraits_References_v1.csv")