Load data

here::i_am("plots/citation-plot.qmd")

here() starts at /home/jferrer/proyectos/IUCN-RLE/RLE-publication-list

load(here::here("Rdata","CR-biblio-info.rda"))

Load library

library(plotly)

Loading required package: ggplot2

Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

    last_plot

The following object is masked from 'package:stats':

    filter

The following object is masked from 'package:graphics':

    layout

library(dplyr)

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

library(lubridate)

Attaching package: 'lubridate'

The following objects are masked from 'package:base':

    date, intersect, setdiff, union

library(stringr)
library(ggplot2)
library(tidyr)

plot

d <- ref.info$data %>% 
  select(doi, title, prefix, 
         short.container.title,
         container.title, issued, is.referenced.by.count) %>%
  mutate(
    title = str_remove_all(title, "<[a-z/]+>") %>% 
      str_replace_all("Red List of Ecosyste(ms|m)","RLE"),
    container.title = case_when(
      prefix %in% c("10.32942") ~ "EcoEvoRxiv",
      prefix %in% c("10.2305") ~ "IUCN",
      is.na(container.title) ~ prefix,
      TRUE ~ container.title),
    short.container.title = coalesce(short.container.title, container.title) %>%
      str_to_lower(),
    citations=as.numeric(is.referenced.by.count),
    date = case_when(
    nchar(issued) == 10 ~ ymd(issued),
    nchar(issued) == 7 ~ ym(issued),
    nchar(issued) == 4 ~ ym(sprintf("%s-01",issued))
  )) %>% mutate(
    short.container.title = str_replace_all(short.container.title,
                                            c("journal" = "j.",
                                              "annals" = "ann.",
                                              "association" = "assoc.",
                                              "geographers" = "geog.",
                                              "american" = "am."))
  )

Warning: There were 3 warnings in `mutate()`.
The first warning was:
ℹ In argument: `date = case_when(...)`.
Caused by warning:
!  32 failed to parse.
ℹ Run `dplyr::last_dplyr_warnings()` to see the 2 remaining warnings.

dim(d)

[1] 119   9

fig <- plot_ly(
  d, x = ~date, y = ~short.container.title,
  # Hover text:
  text = ~sprintf("title: %s<br>doi: %s<br>Issued: %s<br>Citations: %d", 
                  str_trunc(title,50), doi, issued, citations)
)
fig <- add_markers(fig, color = ~citations, size = ~citations)

layout(fig,
       title = "Citations per publication",
       xaxis = list(title="Issued (date)"),
       yaxis = list(title="Journal / Repository / Publisher")
       )

Warning: `line.width` does not currently support multiple values.

## Intro en https://poldham.github.io/abs/crossref.html
ref.info$data %>% count(subject, sort = TRUE)

# A tibble: 37 × 2
   subject                                                                     n
   <chr>                                                                   <int>
 1 Nature and Landscape Conservation,Ecology,Ecology, Evolution, Behavior…    22
 2 Ecology,Ecology, Evolution, Behavior and Systematics                       17
 3 <NA>                                                                       17
 4 Ecology,Ecology, Evolution, Behavior and Systematics,General Decision …     9
 5 Multidisciplinary                                                           8
 6 Nature and Landscape Conservation,Ecology, Evolution, Behavior and Sys…     8
 7 Nature and Landscape Conservation,Ecology,Global and Planetary Change       3
 8 Ecology, Evolution, Behavior and Systematics                                2
 9 General Environmental Science,Ecology,Environmental Chemistry,Global a…     2
10 Management, Monitoring, Policy and Law,Aquatic Science,Oceanography         2
# ℹ 27 more rows

ref.info$data %>% separate_longer_delim(subject, delim = ",") %>%
  count(subject=str_trim(subject), sort = TRUE) -> subjects  # output subjects

subjects %>%
  ggplot2::ggplot(aes(subject, n, fill = subject)) +
  geom_bar(stat = "identity", show.legend = FALSE) +
  coord_flip()