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Chapter 2 code review #3

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Chapter 2 code review #3

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ebeef38
Review code for chapter 2
cforgaci Apr 10, 2024
571b322
Update review of ch2 code
cforgaci Apr 10, 2024
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96 changes: 52 additions & 44 deletions Part2_search_selection.R
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Original file line number Diff line number Diff line change
@@ -1,20 +1,26 @@
### Code to exemplify Part 2 with Xiaoxia's query

# Install and load packages ----
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I moved all package loading and installation to the beginning of the script. Packages are only installed if they are not present on the user's system.

## List pacakges used in the script
packages <- c("rscopus", "RefManageR", "dplyr", "stringr", "bibtex",
"revtools", "remotes", "igraph", "litsearchr",
"PRISMA2020", "PRISMAstatement")

## Load packages and install them if needed
for (package in packages) {
if (!require(package, character.only = TRUE)) {
if (package == "litsearchr") remotes::install_github("elizagrames/litsearchr", ref="main")
else install.packages(package)
}
}

# Section 1: Retrieve references from WoS and Scopus (Shuyu) ----

# Section 1: Retrieve references from WoS and Scopus (Shuyu)
# install and library packages for retrieving references from scopus
install.packages("rscopus")
library(rscopus)
install.packages("RefManageR")
library(RefManageR)
install.packages("dplyr")
library(dplyr)
install.packages("bibtex")
library(bibtex)

# Retrieving references from scopus:
# Set your API key, if you do not have, please go to the website of Elsevier Developer Portal: https://dev.elsevier.com/ to apply, and you will get the key.
options(elsevier_api_key = Your_scopus_api_key)
# Retrieving references from Scopus:
## Set API key by running Sys.setenv(Your_scopus_api_key = "YOUR_API_KEY_HERE")
## in the console. If you do not have an API key, get one from
## https://dev.elsevier.com/
options(elsevier_api_key = Sys.getenv("Your_scopus_api_key"))

# Set your research query
query <- "( ( ( TITLE ( govern* OR state OR decision-making OR policy-making OR stakeholder OR participat* ) ) AND ( TITLE-ABS-KEY ( impact OR outcome OR result OR differentiation OR consequence OR change OR transformation OR role ) ) ) OR ( TITLE-ABS-KEY ( governance W/0 ( mode OR model OR process ) ) ) ) AND
Expand All @@ -24,7 +30,8 @@ query <- "( ( ( TITLE ( govern* OR state OR decision-making OR policy-making OR
( LIMIT-TO ( DOCTYPE , \"ar\" ) ) AND
( LIMIT-TO ( LANGUAGE , \"English\" ) )"

# search on scopus if you get the api key, you can modify the max_count for each searching
# Search Scopus
## You can modify the max_count for each search
if (have_api_key()) {
res <- scopus_search(query = query, max_count = 200, count = 10)
search_results <- gen_entries_to_df(res$entries)
Expand Down Expand Up @@ -57,7 +64,7 @@ transposed_results_df <- t(results_df)
write.csv(transposed_results_df, "scopus_api_results.csv", row.names = FALSE)
df <- read.csv("scopus_api_results.csv")

# Example dataframe with additional fields
# Example data frame with additional fields
data <- data.frame(
Author = df$dc.creator,
Title = df$dc.title,
Expand All @@ -69,7 +76,7 @@ data <- data.frame(
DOI = df$prism.doi
)

# Convert the dataframe to a BibEntryList object
# Convert the data frame to a BibEntryList object
# Create a list of BibEntry objects
bib_entries <- lapply(1:nrow(data), function(i) {
BibEntry(
Expand All @@ -95,7 +102,6 @@ bib_text <- unlist(bib_texts, use.names = FALSE)
# Write BibTeX file
writeLines(bib_text, "scopus_references.bib")


# Retrieving references from web of science:
# wosr package is not working now? l tried many times with the username and password but could not connect to the server.

Expand Down Expand Up @@ -144,6 +150,9 @@ bib_data$Volume <- gsub("'", "", bib_data$Volume)
bib_data$Number <- gsub("'", "", bib_data$Number)
bib_data$Pages <- gsub("'", "", bib_data$Pages)

# Remove entries without a title
bib_data <- bib_data[bib_data$Title != "", ]

Comment on lines +153 to +155
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Hre I removed the entries without a title. That seems to have caused issues later in the BibEntry list.

# Create a list of BibEntry objects
# (l got problems that l cannot extract title from those cases:title="'Inner-city is not the place for social housing' - State-led gentrification in Lodz" and '"Freeways without futures": Urban highway removal in the United States and Spain as socio-ecological fix?' )
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Does my addition above solve this issue or is this something else?

bib_wos_entries <- lapply(1:nrow(bib_data), function(i) {
Expand Down Expand Up @@ -171,7 +180,6 @@ bib_wos_text <- unlist(bib_wos_texts, use.names = FALSE)
writeLines(bib_wos_text, "wos_references.bib")

# Method2: create bib file with multiple txt files
library(stringr)

# Function to read content from a text file and extract information
read_and_extract <- function(file_path) {
Expand Down Expand Up @@ -224,6 +232,9 @@ file_paths <- c("api_response_page1.txt", "api_response_page2.txt", "api_respons
# Read data from each file and combine them into one data frame
combined_data <- do.call(rbind, lapply(file_paths, read_and_extract))

# Remove entries without a title
combined_data <- combined_data[combined_data$Title != "", ]

Comment on lines +235 to +237
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Same as above, entries without title removed.

# Create a list of BibEntry objects
bib_entries <- lapply(1:nrow(combined_data), function(i) {
BibEntry(
Expand All @@ -249,16 +260,9 @@ bib_text <- unlist(bib_texts, use.names = FALSE)
# Write BibTeX file
writeLines(bib_text, "wos_references.bib")

# Section 2: Combine tables, deduplicate references and summarise (Kyri?)
library(revtools)

# Section 3: Suggest new keywords (Clementine)
# Section 2: Combine tables, deduplicate references and summarise (Kyri?) ----

# install.packages("remotes")
# library(remotes)
# install_github("elizagrames/litsearchr", ref="main")
library(litsearchr)
library(igraph)
# Section 3: Suggest new keywords (Clementine) ----
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I so not have the data for this section, so I cannot run it.


#Import .bib or .ris database

Expand Down Expand Up @@ -322,14 +326,8 @@ litsearchr::write_search(grouped,
verbose = TRUE,
closure = "left")

# Section 4: build PRISMA figure (Xiaoxia)
library(PRISMA2020)


## ----prisma--------------------------------------------------------------
#install.packages("PRISMAstatement")
library(PRISMAstatement)

# Section 4: build PRISMA figure (Xiaoxia) ----
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I think this section is unnecessarily long. It would be enough to show a full example with all/most customisation and refer the reader to the package documentation.

## Prisma
prisma(found = 750,
found_other = 123,
no_dupes = 776,
Expand All @@ -341,7 +339,10 @@ prisma(found = 750,
quantitative = 319,
width = 800, height = 800)

## ----prismadupesbox------------------------------------------------------ Ideally, you will stick closely to the PRISMA statement, but small deviations are common. PRISMAstatement gives the option of adding a box which simply calculates the number of duplicates removed.
## Prismadupesbox
### Ideally, you will stick closely to the PRISMA statement, but small deviations
### are common. PRISMAstatement gives the option of adding a box which simply
### calculates the number of duplicates removed.
prisma(found = 750,
found_other = 123,
no_dupes = 776,
Expand All @@ -353,24 +354,29 @@ prisma(found = 750,
quantitative = 319,
extra_dupes_box = TRUE)

## ----labels-------------------------------------------------------------- You can also change the labels, but you will have to insert the number for any label you chang
## Labels
### You can also change the labels, but you will have to insert the number for
### any label you change
prisma(1000, 20, 270, 270, 10, 260, 20, 240, 107,
labels = list(found = "FOUND", found_other = "OTHER"))

## ----errors and warnings-------------------------------------------------
## Errors and warnings
tryCatch(
prisma(1, 2, 3, 4, 5, 6, 7, 8, 9),
error = function(e) e$message)

prisma(1000, 20, 270, 270, 10, 260, 19, 240, 107,
width = 100, height = 100)

prisma(1000, 20, 270, 270, 269, 260, 20, 240, 107,
width = 100, height = 100)

## ----font_size-----------------------------------------------------------
## Font size
prisma(1000, 20, 270, 270, 10, 260, 20, 240, 107, font_size = 6)
prisma(1000, 20, 270, 270, 10, 260, 20, 240, 107, font_size = 60)

## ----prismadpi1, fig.cap="just set width and height"---------------------
## Prismadpi1,
### just set width and height
prisma(found = 750,
found_other = 123,
no_dupes = 776,
Expand All @@ -382,7 +388,8 @@ prisma(found = 750,
quantitative = 319,
width = 200, height = 200)

## ----prismadpi2, fig.cap="same width and height but DPI increased to 300"----
## Prismadpi2
### same width and height but DPI increased to 300
prisma(found = 750,
found_other = 123,
no_dupes = 776,
Expand All @@ -395,7 +402,8 @@ prisma(found = 750,
width = 200, height = 200,
dpi = 300)

## ----prismadpi3, fig.cap="same width and height but DPI decreased to 36"----
## Prismadpi3
### same width and height but DPI decreased to 36
prisma(found = 750,
found_other = 123,
no_dupes = 776,
Expand All @@ -408,7 +416,7 @@ prisma(found = 750,
width = 200, height = 200,
dpi = 36)

## ----prismapdf, echo = TRUE, eval = FALSE--------------------------------
## Prismapdf
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@cforgaci cforgaci Apr 10, 2024 •
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Can this section be removed?

# prsm <- prisma(found = 750,
# found_other = 123,
# no_dupes = 776,
Expand Down