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Add Graphs for general snowball search
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@rkrug
rkrug committed May 24, 2024
1 parent 3fa0c0e commit dec6841
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82,162 changes: 82,162 additions & 0 deletions IPBES_TCA_Ch3_clusters.html
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185 changes: 154 additions & 31 deletions snowball.qmd → IPBES_TCA_Ch3_clusters.qmd
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Original file line number Diff line number Diff line change
Expand Up @@ -18,16 +18,13 @@ params:
gdm_path: !expr file.path('data', 'gdm')
---

# Back to [Readme](https://IPBES-Data.github.io/IPBES_BBA_Ch4_Snowball_Pilot_1/)

Waiting for new key-papers

# Setup
```{r}
#| label: setup
#|
if (!exists("params")) {
params <- rmarkdown::yaml_front_matter("snowball.qmd")$params
params <- rmarkdown::yaml_front_matter("IPBES_TCA_Ch3_clusters.qmd")$params
}
knitr::opts_chunk$set(message = NA)
Expand All @@ -36,11 +33,14 @@ library(IPBES.R)
library(openalexR)
library(dplyr)
library(readxl)
library(arrow)
library(tibble)
# library(dplyr)
# library(knitr)
library(networkD3)
library(webshot)
library(tictoc)
library(patchwork)
Expand Down Expand Up @@ -110,6 +110,15 @@ cluster <- lapply(
)
names(cluster) <- paste0("cluster_", 1:6)
approach_colors <- c(
"#D46746",
"#E69A6A",
"#E6C540",
"#B5C788",
"#2DB3B0",
"#A693B5"
)
```

# Verification of key papers
Expand Down Expand Up @@ -370,6 +379,43 @@ toc()

# Create Graphs

## Create Static Citation Network Graph of the General Corpus

```{r}
#| label: openalex_graph
## | |
no <- list.files("figures", pattern = "snowball_cited", full.names = TRUE) |>
length()
if (no < 4) {
snowball <- file.path("data", "snowball.rds") |>
readRDS()
key_works_au <- file.path("data", "key_works.rds") |>
readRDS() |>
IPBES.R::abbreviate_authors()
key_works_id <- names(key_works_au)
key_works_cit <- Map(function(au, id) c(cit = au, id = id), key_works_au, key_works_id)
names(key_works_cit) <- NULL
snowball$nodes$cited_by_count_by_year <- snowball$nodes$cited_by_count / (2024 - snowball$nodes$publication_year)
snowball_p <- snowball
for (i in seq_along(key_works_cit)) {
snowball_p$nodes$id[snowball_p$nodes$id %in% key_works_cit[[i]]["id"]] <- key_works_cit[[i]]["cit"]
snowball_p$edges$from[snowball_p$edges$from %in% key_works_cit[[i]]["id"]] <- key_works_cit[[i]]["cit"]
snowball_p$edges$to[snowball_p$edges$to %in% key_works_cit[[i]]["id"]] <- key_works_cit[[i]]["cit"]
}
IPBES.R::plot_snowball(snowball_p, name = "snowball", path = "figures")
rm(snowball_p)
}
```

## Create Static Citation Network Graph of the S1 Corpus

Only S1 corpus of S1 can be graphed due to the size of the S2 corpus.
Expand Down Expand Up @@ -594,6 +640,35 @@ toc()


# Results

## Network Graph of General Snowball Search

![Cited by count](figures/snowball_cited_by_count.png)

To download the highres graph, please [click here](figures/snowball_cited_by_count.pdf).

```{r}
#| label: general_snowball_nodes_data
#|
data <- readRDS(file.path("data", "snowball.rds"))[["nodes"]]
data$author_abbr <- IPBES.R::abbreviate_authors(data)
data$doi <- paste0("<a href=\'", data$doi, "\' target='_blank'>", gsub("https://doi.org/", "", data$doi), "</a>")
data |>
dplyr::select(
id,
doi,
author_abbr,
title,
cited_by_count,
ab
) |>
IPBES.R::table_dt()
```

## Graphs and Maps

The following interactions are possible in the interactive graphs:
Expand Down Expand Up @@ -825,7 +900,7 @@ plot_chord <- function(
"cluster_2" ~ "Knowledge co-creation",
"cluster_3" ~ "Systems",
"cluster_4" ~ "Inner Transformation",
"cluster_5" ~ "Empowerrment",
"cluster_5" ~ "Empowerment",
"cluster_6" ~ "Structural"
)
colnames(m) <- dplyr::case_match(
Expand All @@ -834,18 +909,18 @@ plot_chord <- function(
"cluster_2" ~ "Knowledge co-creation",
"cluster_3" ~ "Systems",
"cluster_4" ~ "Inner Transformation",
"cluster_5" ~ "Empowerrment",
"cluster_5" ~ "Empowerment",
"cluster_6" ~ "Structural"
)
groupColors <- c(
"#D46746",
"#E69A6A",
"#E6C540",
"#B5C788",
"#2DB3B0",
"#A693B5"
)
# groupColors <- c(
# "#D46746",
# "#E69A6A",
# "#E6C540",
# "#B5C788",
# "#2DB3B0",
# "#A693B5"
# )
# groupColors <- c(
# grDevices::rgb(red = .87, green = 0.45, blue = 0.33),
Expand All @@ -862,7 +937,7 @@ plot_chord <- function(
showTicks = showTicks,
type = "directional", ,
margin = margin,
groupColors = groupColors,
groupColors = approach_colors,
...
)
return(cd)
Expand Down Expand Up @@ -972,6 +1047,14 @@ nodes <- data.frame(
data$Theory |> unique()
)
)
nodes$group <- c(
paste0(1:6, "."),
rep(
"theory",
nrow(nodes) - length(approach_colors)
)
)
links <- lapply(
2:7,
Expand Down Expand Up @@ -1002,45 +1085,85 @@ links <- lapply(
as.numeric(),
target = as.numeric(target) - 1,
value = 1
) |>
dplyr::filter(
!is.na(level)
)
library(networkD3)
library(webwidgets)
library(webshot)
links$level <- as.character(links$level)
my_color <- 'd3.scaleOrdinal() .domain(["1", "2", "1.", "2.", "3.", "4.", "5.", "6.", "theory"]) .range(["red", "blue", "#D46746", "#E69A6A", "#E6C540", "#B5C788", "#2DB3B0", "#A693B5", "lightgrey"])'
##########
bn <- file.path("figures", "approaches_theories_1")
sankeyNetwork(
Links = links |> dplyr::filter(level == 1),
LinkGroup = "level",
Nodes = nodes,
Source = "source",
Target = "target",
NodeGroup = "group",
Source = "target",
Target = "source",
Value = "value",
NodeID = "name"
NodeID = "name",
colourScale = my_color,
sinksRight = FALSE
) |>
htmlwidgets::saveWidget(
file = paste0(bn, ".html"),
selfcontained = TRUE
saveNetwork(
file = paste0(bn, ".html"),
selfcontained = TRUE
)
webshot::webshot(
url = paste0(bn, ".html"),
file = paste0(bn, ".pdf")
)
unlink(paste0(bn, "_files"), recursive = TRUE)
##########
bn <- file.path("figures", "approaches_theories_2")
sankeyNetwork(
Links = links |> dplyr::filter(level == 2),
LinkGroup = "level",
Nodes = nodes,
NodeGroup = "group",
Source = "target",
Target = "source",
Value = "value",
NodeID = "name",
colourScale = my_color,
sinksRight = FALSE
) |>
saveNetwork(
file = paste0(bn, ".html"),
selfcontained = TRUE
)
webshot::webshot(
url = paste0(bn, ".html"),
file = paste0(bn, ".pdf")
)
unlink(paste0(bn, "_files"), recursive = TRUE)
bn <- file.path("figures", "approaches_theories_1_2")
sankeyNetwork(
Links = links |> dplyr::filter(!is.na(level)),
LinkGroup = "level",
Nodes = nodes,
Source = "source",
Target = "target",
NodeGroup = "group",
Source = "target",
Target = "source",
Value = "value",
NodeID = "name"
NodeID = "name",
colourScale = my_color,
sinksRight = FALSE
) |>
htmlwidgets::saveWidget(
file = paste0(bn, ".html"),
selfcontained = TRUE
)
saveNetwork(
file = paste0(bn, ".html"),
selfcontained = TRUE
)
unlink(paste0(bn, "_files"), recursive = TRUE)
webshot::webshot(
url = paste0(bn, ".html"),
file = paste0(bn, ".pdf")
Expand Down
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6 changes: 3 additions & 3 deletions figures/approaches_theories_1.html
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Expand Up @@ -1595,9 +1595,9 @@
</head>
<body style="background-color: white;">
<div id="htmlwidget_container">
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