In davan690/beech-publication-wr: Small mammal dynamics in NZ beech forests
# importing ris data and changing to bibtex structure
#makes ready for citr package
#Anthony
#feb2020
#set uni library correctly
# myPaths <- .libPaths("C:/Program Files/R/R-3.6.2/library")
# myPaths <- c(myPaths)
# .libPaths(myPaths) # add new path
# .libPaths()
################################ demo ########
## To cite bibliometrix in publications, please use:
## Aria, M. & Cuccurullo, C. (2017) bibliometrix: An R-tool for comprehensive science mapping analysis, Journal of Informetrics, 11(4), pp 959-975, Elsevier.
## http:\\www.bibliometrix.org
## To start with the shiny web-interface, please digit:
#import library
Sorting reference data {#dataref}
There are several packages I use in this analysis (bibliometrix, revtools,RefManageR). The overall workflow is focused around the development of a reference/resource in the overall database. This goes from raw data entry to unique bib entry with all the associated metadata and other bits. THe general steps are:
Step 1.
Import meta-data into mendeley database using one of these methods:
- webclipper
- bib entry
- manually
Step 2.
require(tidyverse)
##my data
#easiest way seems to be revtools
# jujst an idea
# revtools::read_bibliography(filename = "./data/mendeley/")
#for now have imported data as bibfile is the shiny app and saved as csv
dat_bib_beech <- read.csv("C://PhD/beech-publication-wr/_references/data/Bibliometrix-Export-File-2020-02-22.csv")
# length(names(M))
names(dat_bib_beech)
str(dat_bib_beech)
#manually reorder names
#to match example for shiny app
#quick fix
new_names <- c("AU", "TI", "DE_unknown", "DT", "DT2", "DI", "BE_unknown", "BN_unknown", "SN",
"PN", "PP", "PU", "VL", "BO", "DB", "PY", "TC","CR", "C1_unknown", "AU_UN", "SR_FULL", "SR")
fullNames_new <- c("Author", "TI", "DE_unknown", "DT", "DT2", "DI", "BE_unknown", "BN_unknown", "SN",
"PN", "PP", "PU", "VL", "BO", "DB", "PY", "TC","CR", "C1_unknown", "AU_UN", "SR_FULL", "SR")
names(dat_bib_beech) <- new_names
##Full number of references
#...
#Data wrangling
dat2 <- dat_bib_beech %>%
dplyr::select(-c(BN_unknown,BE_unknown,C1_unknown)) %>%
mutate(Publication_ID = seq(1:length(dat_bib_beech$TI)),
PrePrint = ifelse(DT == "PREPRINT", "Yes", "No"),
Tags_general = as.character(DE_unknown),
Author1 = as.character(AU),
Title = as.character(TI),
Publish_year = AU,
Document_type = DT2,
Contact_auth = gsub(",.*","",SR),
doi = DI,
pages = as.numeric(PP)) %>%
select(-c(TI,DE_unknown, DT, DT2, SR, DI)) %>%
as_tibble()
final_remove <- names(dat2)[1:13]
dat3 <- dat2 %>%
select(-c(final_remove))
Resources
Video tutorials
-
Video 1: Bibliometrics (17): The Biblioshiny App For Non-Coders | Bibliometrix R Package from Research HUB
-
Video 2: Bibliometrics (14): Another examle using Bibliometrix package of R
-
Basic Data
bibliometrix package
require(bibliometrix)
bibliometrix: An R-Tool for Comprehensive Science Mapping Analysis here.
##my data
#easiest way seems to be revtools
# jujst an idea
# revtools::read_bibliography(filename = "./data/mendeley/")
#for now have imported data as bibfile is the shiny app and saved as csv
dat_bib_beech <- read.csv("C://PhD/beech-publication-wr/_references/data/Bibliometrix-Export-File-2020-02-22.csv")
# length(names(M))
names(dat_bib_beech)
str(dat_bib_beech)
#manually reorder names
#to match example for shiny app
#quick fix
new_names <- c("AU", "TI", "DE_unknown", "DT", "DT2", "DI", "BE_unknown", "BN_unknown", "SN",
"PN", "PP", "PU", "VL", "BO", "DB", "PY", "TC","CR", "C1_unknown", "AU_UN", "SR_FULL", "SR")
fullNames_new <- c("Author", "TI", "DE_unknown", "DT", "DT2", "DI", "BE_unknown", "BN_unknown", "SN",
"PN", "PP", "PU", "VL", "BO", "DB", "PY", "TC","CR", "C1_unknown", "AU_UN", "SR_FULL", "SR")
names(dat_bib_beech) <- new_names
##Full number of references
#...
#Data wrangling
dat2 <- dat_bib_beech %>%
select(-c(BN_unknown,BE_unknown,C1_unknown)) %>%
mutate(Publication_ID = seq(1:length(dat_bib_beech$TI)),
PrePrint = ifelse(DT == "PREPRINT", "Yes", "No"),
Tags_general = as.character(DE_unknown),
Author1 = as.character(AU),
Title = as.character(TI),
Publish_year = AU,
Document_type = DT2,
Contact_auth = gsub(",.*","",SR),
doi = DI,
pages = as.numeric(PP)) %>%
select(-c(TI,DE_unknown, DT, DT2, SR, DI)) %>%
as_tibble()
final_remove <- names(dat2)[1:13]
dat3 <- dat2 %>%
select(-c(final_remove))
needs to be sorted...
this is the respondant I think...
#feb2020
# dat2$Contact_auth <- gsub(",.*","",dat2$SR)
# str(dat2)
# names(dat2)
#group_by(Title)
# %>%
# summarise_all()
# unique(dat2$Title)
#unique id
# max(dat2$Publication_ID)
#number of referenced pre-prints
table(dat2$PrePrint)
#what are theses???
# unique(dat2$Tags_general)
#save modified data
write.csv(dat2, "C://PhD/beech-publication-wr/_references/data/v2_RCode_output.csv")
#run bib shiny again and import new v2 csv file
# bibliometrix::
# ?biblioshiny()
# dat2 == data_setLocations
#data from locations etc
# data_setLocations <- revtools::read_bibliography("./data/v1_RCode_output.csv")
#bibliography from data resource
dat_full_tidy_approach <- revtools::read_bibliography("C://PhD/beech-publication-wr/_references/Beech_forests.bib") %>%
mutate(Publication_ID = seq(1,174,1)) %>%
full_join(dat2, by = "Publication_ID")
#amazing?
# revtools::as.bibliography(dat_full_tidy_approach)
# glimpse(dat_full_tidy_approach)
#manual for now
dat_full_tidy_approach$date[1] <- "2017"
#for all dates with year first
dat_full_tidy_approach$date <- gsub("-.*","",dat_full_tidy_approach$date)
dat_tidy1 <- dat_full_tidy_approach %>%
mutate(year = as.factor(date))
Modified data
#read in modified bib data
dat2 <- read.csv("C://PhD/beech-publication-wr/_references/data/v2_RCode_output.csv")
# kableExtra::kable(head(dat2))
revtools package
require(revtools)
Simple example
#nah but help notes
library(revtools)
# import data
file_location <- system.file(
"extdata",
"avian_ecology_bibliography.ris",
package = "revtools")
x <- read_bibliography(file_location)
# generate then locate some 'fake' duplicates
x_duplicated <- rbind(x, x[1:5,])
x_check <- find_duplicates(x_duplicated)
# returns a vector of potential matches
x_check
revtools::extract_unique_references(x_duplicated, find_duplicates(x_duplicated))
# ?find_duplicates
revtools::find_duplicates(data = dat_tidy1)
#list for referencing short keys
# revtools::print.bibliography(dat_tidy1)
Using shiny too
write_bibliography(dat_tidy1, "C://PhD/beech-publication-wr/_references/data/test_out2.ris", format = "ris")
write_bibliography(dat_tidy1, "C://PhD/beech-publication-wr/_references/data/test_out2.ris", format = "ris")
write_bibliography(dat_tidy1, "C://PhD/beech-publication-wr/_references/data/test_out2.bib", format = "bib")
?write_bibliography
#page count...
ggplot(data = dat_tidy1, aes(x = year, y = pages.x)) +
geom_point()
#reference dates
table(dat_tidy1$year)
write.csv(dat_tidy1, "C://PhD/beech-publication-wr/_references/data/revtools_dataframe_structure.csv")
#demo
# vignette("revtools")
#print titles to check first
#manual changing in case of accident
#feb2020
#what sort of grammar is actually important?
#feb2020
dat_full_tidy_approach$title[1] <- c("Confronting the risks of large-scale invasive species control")
dat_full_tidy_approach$title[2] <- c("Unexpected consequences of control: Competitive vs. Predator release in a four-species assemblage of invasive mammals")
RefManageR package
##########################ON old way I was working with it but not anymore.....####################
require(revtools)
##raw import
#should be bib but dont have one
dat <- readFiles("C://PhD/beech-publication-wr/Beech-forests.bib")
dat_ris <- readFiles("C://PhD/beech-publication-wr/_references/data/Beech_forests.ris")
#working with ris
# str(dat)
#
M <- convert2df(dat, dbsource = "scopus", format = "plaintext")
names(M)
head(M)
M_scop <- convert2df(dat, dbsource = "scopus", format = "bibtex")
#
M_webof_Sci <- convert2df(dat, dbsource = "isi", format = "bibtex")
require(tidyverse)
glimpse(M_webof_Sci)
head(M_webof_Sci[22])
glimpse(M_scop)
summary(M_webof_Sci)
# dat_lits <-
require(RefManageR)
#run shiny app locally
# needs other packages above too
# bibliometrix::biblioshiny()
#demo
# vignette("bibliometrix-vignette")
davan690/beech-publication-wr documentation built on March 29, 2020, 11:09 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
# importing ris data and changing to bibtex structure #makes ready for citr package #Anthony #feb2020 #set uni library correctly # myPaths <- .libPaths("C:/Program Files/R/R-3.6.2/library") # myPaths <- c(myPaths) # .libPaths(myPaths) # add new path # .libPaths() ################################ demo ######## ## To cite bibliometrix in publications, please use: ## Aria, M. & Cuccurullo, C. (2017) bibliometrix: An R-tool for comprehensive science mapping analysis, Journal of Informetrics, 11(4), pp 959-975, Elsevier. ## http:\\www.bibliometrix.org ## To start with the shiny web-interface, please digit: #import library
Sorting reference data {#dataref}
There are several packages I use in this analysis (bibliometrix, revtools,RefManageR). The overall workflow is focused around the development of a reference/resource in the overall database. This goes from raw data entry to unique bib entry with all the associated metadata and other bits. THe general steps are:
Step 1.
Import meta-data into mendeley database using one of these methods: - webclipper - bib entry - manually
Step 2.
require(tidyverse) ##my data #easiest way seems to be revtools # jujst an idea # revtools::read_bibliography(filename = "./data/mendeley/") #for now have imported data as bibfile is the shiny app and saved as csv dat_bib_beech <- read.csv("C://PhD/beech-publication-wr/_references/data/Bibliometrix-Export-File-2020-02-22.csv") # length(names(M)) names(dat_bib_beech) str(dat_bib_beech) #manually reorder names #to match example for shiny app #quick fix new_names <- c("AU", "TI", "DE_unknown", "DT", "DT2", "DI", "BE_unknown", "BN_unknown", "SN", "PN", "PP", "PU", "VL", "BO", "DB", "PY", "TC","CR", "C1_unknown", "AU_UN", "SR_FULL", "SR") fullNames_new <- c("Author", "TI", "DE_unknown", "DT", "DT2", "DI", "BE_unknown", "BN_unknown", "SN", "PN", "PP", "PU", "VL", "BO", "DB", "PY", "TC","CR", "C1_unknown", "AU_UN", "SR_FULL", "SR") names(dat_bib_beech) <- new_names ##Full number of references #... #Data wrangling dat2 <- dat_bib_beech %>% dplyr::select(-c(BN_unknown,BE_unknown,C1_unknown)) %>% mutate(Publication_ID = seq(1:length(dat_bib_beech$TI)), PrePrint = ifelse(DT == "PREPRINT", "Yes", "No"), Tags_general = as.character(DE_unknown), Author1 = as.character(AU), Title = as.character(TI), Publish_year = AU, Document_type = DT2, Contact_auth = gsub(",.*","",SR), doi = DI, pages = as.numeric(PP)) %>% select(-c(TI,DE_unknown, DT, DT2, SR, DI)) %>% as_tibble() final_remove <- names(dat2)[1:13] dat3 <- dat2 %>% select(-c(final_remove))
Resources
Video tutorials
-
Video 1: Bibliometrics (17): The Biblioshiny App For Non-Coders | Bibliometrix R Package from Research HUB
-
Video 2: Bibliometrics (14): Another examle using Bibliometrix package of R
Basic Data
bibliometrix package
require(bibliometrix)
bibliometrix: An R-Tool for Comprehensive Science Mapping Analysis here.
##my data #easiest way seems to be revtools # jujst an idea # revtools::read_bibliography(filename = "./data/mendeley/") #for now have imported data as bibfile is the shiny app and saved as csv dat_bib_beech <- read.csv("C://PhD/beech-publication-wr/_references/data/Bibliometrix-Export-File-2020-02-22.csv") # length(names(M)) names(dat_bib_beech) str(dat_bib_beech) #manually reorder names #to match example for shiny app #quick fix new_names <- c("AU", "TI", "DE_unknown", "DT", "DT2", "DI", "BE_unknown", "BN_unknown", "SN", "PN", "PP", "PU", "VL", "BO", "DB", "PY", "TC","CR", "C1_unknown", "AU_UN", "SR_FULL", "SR") fullNames_new <- c("Author", "TI", "DE_unknown", "DT", "DT2", "DI", "BE_unknown", "BN_unknown", "SN", "PN", "PP", "PU", "VL", "BO", "DB", "PY", "TC","CR", "C1_unknown", "AU_UN", "SR_FULL", "SR") names(dat_bib_beech) <- new_names ##Full number of references #... #Data wrangling dat2 <- dat_bib_beech %>% select(-c(BN_unknown,BE_unknown,C1_unknown)) %>% mutate(Publication_ID = seq(1:length(dat_bib_beech$TI)), PrePrint = ifelse(DT == "PREPRINT", "Yes", "No"), Tags_general = as.character(DE_unknown), Author1 = as.character(AU), Title = as.character(TI), Publish_year = AU, Document_type = DT2, Contact_auth = gsub(",.*","",SR), doi = DI, pages = as.numeric(PP)) %>% select(-c(TI,DE_unknown, DT, DT2, SR, DI)) %>% as_tibble() final_remove <- names(dat2)[1:13] dat3 <- dat2 %>% select(-c(final_remove))
needs to be sorted... this is the respondant I think...
#feb2020 # dat2$Contact_auth <- gsub(",.*","",dat2$SR) # str(dat2) # names(dat2) #group_by(Title) # %>% # summarise_all() # unique(dat2$Title) #unique id # max(dat2$Publication_ID) #number of referenced pre-prints table(dat2$PrePrint) #what are theses??? # unique(dat2$Tags_general) #save modified data write.csv(dat2, "C://PhD/beech-publication-wr/_references/data/v2_RCode_output.csv")
#run bib shiny again and import new v2 csv file # bibliometrix:: # ?biblioshiny() # dat2 == data_setLocations #data from locations etc # data_setLocations <- revtools::read_bibliography("./data/v1_RCode_output.csv") #bibliography from data resource dat_full_tidy_approach <- revtools::read_bibliography("C://PhD/beech-publication-wr/_references/Beech_forests.bib") %>% mutate(Publication_ID = seq(1,174,1)) %>% full_join(dat2, by = "Publication_ID") #amazing? # revtools::as.bibliography(dat_full_tidy_approach) # glimpse(dat_full_tidy_approach) #manual for now dat_full_tidy_approach$date[1] <- "2017" #for all dates with year first dat_full_tidy_approach$date <- gsub("-.*","",dat_full_tidy_approach$date) dat_tidy1 <- dat_full_tidy_approach %>% mutate(year = as.factor(date))
Modified data
#read in modified bib data dat2 <- read.csv("C://PhD/beech-publication-wr/_references/data/v2_RCode_output.csv") # kableExtra::kable(head(dat2))
revtools package
require(revtools)
Simple example
#nah but help notes library(revtools) # import data file_location <- system.file( "extdata", "avian_ecology_bibliography.ris", package = "revtools") x <- read_bibliography(file_location) # generate then locate some 'fake' duplicates x_duplicated <- rbind(x, x[1:5,]) x_check <- find_duplicates(x_duplicated) # returns a vector of potential matches x_check revtools::extract_unique_references(x_duplicated, find_duplicates(x_duplicated)) # ?find_duplicates revtools::find_duplicates(data = dat_tidy1) #list for referencing short keys # revtools::print.bibliography(dat_tidy1)
Using shiny too
write_bibliography(dat_tidy1, "C://PhD/beech-publication-wr/_references/data/test_out2.ris", format = "ris") write_bibliography(dat_tidy1, "C://PhD/beech-publication-wr/_references/data/test_out2.ris", format = "ris") write_bibliography(dat_tidy1, "C://PhD/beech-publication-wr/_references/data/test_out2.bib", format = "bib") ?write_bibliography #page count... ggplot(data = dat_tidy1, aes(x = year, y = pages.x)) + geom_point() #reference dates table(dat_tidy1$year) write.csv(dat_tidy1, "C://PhD/beech-publication-wr/_references/data/revtools_dataframe_structure.csv") #demo # vignette("revtools") #print titles to check first #manual changing in case of accident #feb2020 #what sort of grammar is actually important? #feb2020 dat_full_tidy_approach$title[1] <- c("Confronting the risks of large-scale invasive species control") dat_full_tidy_approach$title[2] <- c("Unexpected consequences of control: Competitive vs. Predator release in a four-species assemblage of invasive mammals")
RefManageR package
##########################ON old way I was working with it but not anymore.....#################### require(revtools) ##raw import #should be bib but dont have one dat <- readFiles("C://PhD/beech-publication-wr/Beech-forests.bib") dat_ris <- readFiles("C://PhD/beech-publication-wr/_references/data/Beech_forests.ris") #working with ris # str(dat) # M <- convert2df(dat, dbsource = "scopus", format = "plaintext") names(M) head(M) M_scop <- convert2df(dat, dbsource = "scopus", format = "bibtex") # M_webof_Sci <- convert2df(dat, dbsource = "isi", format = "bibtex") require(tidyverse) glimpse(M_webof_Sci) head(M_webof_Sci[22]) glimpse(M_scop) summary(M_webof_Sci) # dat_lits <-
require(RefManageR) #run shiny app locally # needs other packages above too # bibliometrix::biblioshiny() #demo # vignette("bibliometrix-vignette")
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