_portfolio_template.qmd

---
execute:
  echo: false
  warnings: false
  message: false
  freeze: false
sidebar: true
---

<!-- Required R packages -->

```{r setup}
#| echo: false
#| message: false
source("R/setup.R")
if (params$collection == "oam") {
    oam <- hoaddata::oam_hybrid_jns |>
        dplyr::distinct(issn_l, esac_publisher = vertrag)
}
```

<!-- data preparation -->

```{r data prep}
#| echo: false
#| message: false
jn_ind_df <- hoaddata::jn_ind |>
    dplyr::mutate(cr_year = as.character(cr_year)) |>
    dplyr::mutate(cc = factor(
        cc,
        # Order by permissiveness
        levels = c(
            "CC BY",
            "CC BY-SA",
            "CC BY-NC",
            "CC BY-NC-SA",
            "CC BY-ND",
            "CC BY-NC-ND"
        )
    )) |>
    # Journal selection
    filter(issn_l %in% params$issn_l)

jn_aff_df <- hoaddata::jn_aff |>
    dplyr::mutate(cr_year = as.character(cr_year)) |>
    dplyr::mutate(cc = factor(
        cc,
        # Order by permissiveness
        levels = c(
            "CC BY",
            "CC BY-SA",
            "CC BY-NC",
            "CC BY-NC-SA",
            "CC BY-ND",
            "CC BY-NC-ND"
        )
    )) |>
    # Journal selection
    filter(issn_l %in% params$issn_l)
```

```{r ta_text}
#| echo: false
#| message: false
if (params$collection == "oam") {
    ta_text <- paste0("hybrid journals included in the German consortial transformative agreement **", params$publisher, "**")
} else {
    ta_text <- paste0("**", params$publisher, "**", " hybrid journals included in transformative agreements")
}
```

<!-- Teaser -->

The share of Open Access articles with a Creative Commons license in `r format(length(unique(jn_ind_df$issn_l)), big.mark = ",")` hybrid journals is as follows:


```{r}
#| echo: false
#| message: false
#| warning: false
#| results: asis
source("R/teaser.R")
basic_stat(jn_ind_df = jn_ind_df, jn_aff_df = jn_aff_df)
```

<small><sup>*</sup>Journal articles from lead authors based in Germany. Country affiliation data derived from OpenAlex.</small>

<!-- Creative Commons license prevalence-->

## Creative Commons licenses over time

Percentage of Open Access in `r ta_text` by Creative Commons license types as provided by Crossref.

```{r}
#| echo: false
#| message: false
#| warning: false
source("R/cc_over_year.R")
```

::: {.panel-tabset}

## Global

```{r cc_global_plot, message=FALSE}
cc_global_plot <- plot_cc_variants_by_year(cc_ind_global(jn_ind_df = jn_ind_df))
# Return SVG
girafe(
    ggobj = cc_global_plot,
    width_svg = 9,
    height_svg = 6 * 0.618,
    options = list(opts_tooltip(
        css = "background-color:white;
;font-size:1.15em;padding:10px;border-radius:5px;box-shadow: 0 0 10px 0 rgba(0, 0, 0, 0.5)",
        opacity = .95
    ),
    opts_toolbar(saveaspng = FALSE))
)
export_files(.data = cc_ind_global(jn_ind_df = jn_ind_df), .plot = cc_global_plot, width = 9, height = 6 * 0.618)
```

## Germany<sup>*</sup>

```{r cc_de_plot, message=FALSE}
cc_de_plot <- plot_cc_variants_by_year(cc_ind_de(jn_aff_df = jn_aff_df))
# Return SVG
girafe(
    ggobj = cc_de_plot,
    width_svg = 9,
    height_svg = 6 * 0.618,
    options = list(opts_tooltip(
        css = "background-color:white;
;font-size:1.15em;padding:10px;border-radius:5px;box-shadow: 0 0 10px 0 rgba(0, 0, 0, 0.5)",
        opacity = .95
    ),
    opts_toolbar(saveaspng = FALSE))
)
export_files(.data =  cc_ind_de(jn_aff_df = jn_aff_df), .plot = cc_de_plot,  width = 9, height = 6 * 0.618)
```

<small><sup>*</sup>Journal articles from lead authors based in Germany. Country affiliation data derived from OpenAlex.</small>

:::

## Publishing market

Hybrid journal portfolio analysis, showing publishing market shares in terms of total and Open Access article volume. Dashed lines represent median OA percentage (red) and median publication output (orange). Note that only hybrid journals included in transformative agreements are shown.

```{r}
#| echo: false
#| message: false
#| warning: false
# Data prep
if (params$collection == "oam") {
    oam <- hoaddata::oam_hybrid_jns |>
        dplyr::distinct(issn_l, esac_publisher = vertrag)
    source("R/oam_data_prep.R")
} else {
    source("R/data_prep.R")
}

my_df <- summarize_pubs(var_summary = c(cr_year, esac_publisher)) |>
    tidyr::complete(cr_year, esac_publisher, collection) |>
    mutate_if(is.numeric, ~ replace(., is.na(.), 0)) |>
    mutate(pub_col = ifelse(esac_publisher %in% params$publisher, "#0093C7", "#999999"))
```

::: {.panel-tabset}

```{r publishing_market}
#| echo: false
#| message: false
#| warning: false
source("R/pub_scatter.R")
```

## Global

```{r publishing_market_global}
#| echo: false
#| message: false
#| warning: false
plot_scatterplot(my_df, collection = "global")
my_df |>
  dplyr::filter(collection == "global") |>
  mutate(oa_prop = oa_articles / articles) |>
  export_files(.drop = c("pub_col"))
```
  
## Germany<sup>*</sup>

```{r publishing_market_de}
#| echo: false
#| message: false
#| warning: false
plot_scatterplot(my_df, collection = "de")

my_df |>
  dplyr::filter(collection == "de") |>
  mutate(oa_prop = oa_articles / articles) |>
  export_files(.drop = c("pub_col"))
```

<small><sup>*</sup>Journal articles from lead authors based in Germany. Country affiliation data derived from OpenAlex.</small>

:::

## Country view

This section shows how hybrid open access has been adopted in different parts of the world. The analysis is based on the country affiliation of lead authors. Lead authors are the first named authors of scholarly articles, who have typically conducted most of the research presented in the article, although the role of lead authors can vary across disciplines. We used OpenAlex as a data source to determine the affiliation of lead authors.

### Open Access in hybrid journals by country

Open Access uptake in hybrid journals with a Creative Commons license per country. Showing the Top 20 most productive countries in terms of articles published in `r ta_text` between 2017 and 2024. The analysis is based on lead author country affiliations.

::: column-body-outset
```{r country_top_20}
#| echo: false
#| message: false
#| warning: false
source("R/country_top_20.R")

ggiraph::girafe(
    ggobj = country_multiple_plot,
    width_svg = 9,
    height_svg = 7 * 0.618,
    options = list(opts_tooltip(
        css = "background-color:white;
;font-size:1.15em;padding:10px;border-radius:5px;box-shadow: 0 0 10px 0 rgba(0, 0, 0, 0.5)",
        opacity = .95
    ),
    opts_toolbar(saveaspng = FALSE))
)

export_files(
    .data = country_multiple_plot$data,
    .plot = country_multiple_plot,
    width = 9,
    height = 7 * 0.618,
    .drops = c("my_cols", "tooltip_text", ".group", "max_")
)
```
:::


### Country league

Publication volume and Open Access share per country in `r ta_text`. You can search for specific countries, and filter by publisher and publication year. The analysis is based on country-affiliations of lead authors.


```{r}
#| echo: false
#| message: false
#| warning: false
source("R/country_league.R")
```

```{r country_league}
htmltools::div(
    class = "agreement-tbl",
    htmltools::div(
        class = "filters",
        htmltools::div(
            class = "filter-input",
            filter_select(
                "filter_country",
                "Countries",
                shared_oa_country_df,
                ~country_name,
                multiple = TRUE
            )
        ),
        htmltools::div(
            class = "filter-input",
            filter_select(
                "filter_country_year",
                "Publication Year",
                shared_oa_country_df,
                ~cr_year,
                multiple = FALSE
            )
        )
    ),
    react_table_oa_country
)

export_files(
    .data = shared_oa_country_df$data(), 
    .drops = c("max_group", "max_all_group")
)
```


```{js,echo = FALSE}
 /* https://stackoverflow.com/a/66216595 */
$(document).ready(function() {
    document.getElementById("filter_country_year").getElementsByClassName("selectized")[0].selectize.setValue("2023", false);
});
```

## Open metadata

Open and comprehensive metadata is a key requirement of many transformative agreements. The following tables illustrate potential gaps in Crossref metadata for Open Access articles in hybrid journals included in transformative agreements.

### License metadata gaps

**`r params$publisher`**: Comparison of open licence metadata in Crossref with Unpaywall via OpenAlex per year. You can compare global metrics with metrics only for articles by lead authors based in Germany. In addition to Crossref licence information, Unpaywall also analyses publisher websites to determine whether an article has been published under an open content licence. More Open Access articles derived from Crossref may indicate a delay between metadata changes and Unpaywall-indexing, while more Open Access articles identified by Unpaywall suggest that publishers have not deposited licensing metadata in Crossref for all articles.

::: {.panel-tabset}

## Global 

```{r cr_upw_global}
#| echo: false
#| message: false
#| warning: false
source("R/cr_upw.R")
cr_upw_global_plot <- cr_upw_plot(cr_upw_data = hoaddata::cr_upw, params$issn_l, my_cat = "Global")

ggiraph::girafe(
    ggobj = cr_upw_global_plot,
    width_svg = 9,
    height_svg = 6 * 0.618,
    options = list(
        opts_tooltip(
            css = "background-color:white;
;font-size:1.15em;padding:10px;border-radius:5px;box-shadow: 0 0 10px 0 rgba(0, 0, 0, 0.5)",
            opacity = .95
        ),
        opts_toolbar(saveaspng = FALSE)
    )
)

export_files(
    .data = cr_upw_data(hoaddata::cr_upw, params$issn_l, my_cat = "Global") |>
        dplyr::mutate(oa_share = value / article_total) |>
        dplyr::rename(oa_articles = value),
    .plot = cr_upw_global_plot,
    width = 9,
    height = 6 * 0.618,
    .drops = c("my_cols", "tooltip_text", ".group", "max_")
)
```

## Germany<sup>*</sup>


```{r cr_upw_de}
#| echo: false
#| message: false
#| warning: false
cr_upw_de_plot <- cr_upw_plot(cr_upw_data = hoaddata::cr_upw, params$issn_l, my_cat = "Germany")

ggiraph::girafe(
    ggobj = cr_upw_de_plot,
    width_svg = 9,
    height_svg = 6 * 0.618,
    options = list(
        opts_tooltip(
            css = "background-color:white;
;font-size:1.15em;padding:10px;border-radius:5px;box-shadow: 0 0 10px 0 rgba(0, 0, 0, 0.5)",
            opacity = .95
        ),
        opts_toolbar(saveaspng = FALSE)
    )
)

export_files(
    .data = cr_upw_data(hoaddata::cr_upw, params$issn_l, my_cat = "Germany") |>
        dplyr::mutate(oa_share = value / article_total) |>
        dplyr::rename(oa_articles = value),
    .plot = cr_upw_de_plot,
    width = 9,
    height = 6 * 0.618,
    .drops = c("my_cols", "tooltip_text", ".group", "max_")
)
```

<small><sup>*</sup>Journal articles from lead authors based in Germany. Country affiliation data derived from OpenAlex.</small>

:::

### Crossref metadata coverage

This table shows the proportion of Crossref metadata that is publicly available for Open Access articles in hybrid journals included in transformative agreements. Publishers can use Crossref to share information about [Text and Data Mining (TDM)](https://www.crossref.org/blog/evolving-our-support-for-text-and-data-mining/ ), authors [(ORCID)](https://orcid.org/) and [funding](https://www.crossref.org/community/funders/). They can also open up [abstracts](https://i4oa.org/) and [reference lists](https://i4oc.org/) through Crossref.


```{r crossref_md_coverage}
#| echo: false
#| message: false
#| warning: false
source("R/open_md.R")
# Should be done in hoaddata
md_tmp <- hoaddata::cr_md |>
    tidyr::complete(cr_year, issn_l, cat) |>
    mutate_all(~ ifelse(is.na(.), 0, .))

my_df <- shared_open_md_df(.data = md_tmp, issn_l = params$issn_l, publisher = params$publisher)

htmltools::div(
    class = "agreement-tbl",
    # filters,
    htmltools::div(
        class = "filters",
        htmltools::div(
            class = "filter-input",
            filter_select(
                "filter_open_md_cat_input",
                "Global / Germany",
                my_df,
                ~cat,
                multiple = FALSE
            )
        ),
    ),
    # table
    open_md_react(
        my_df
    )
)

export_files(.data =  my_df$data())
```

```{js,echo = FALSE}
 /* https://stackoverflow.com/a/66216595 */
$(document).ready(function() {
    document.getElementById("filter_open_md_cat_input").getElementsByClassName("selectized")[0].selectize.setValue("Global", false);
});
```

## Journal table

**`r params$publisher`**: This table presents the publication volume and Open Access share by  hybrid journal between 2017 and 2024, comparing global metrics with metrics only for articles by lead authors based in Germany. Charts show the yearly Open Access share. You can search for journals or select a table header to sort by journal name or a metric.

::: column-body-outset


```{r}
#| echo: false
#| message: false
#| warning: false
my_df <- summarize_pubs(var_summary = c(cr_year, issn_l)) |>
    filter(issn_l %in% params$issn_l) |>
    tidyr::complete(cr_year, issn_l, collection) |>
    mutate_if(is.numeric, ~ replace(., is.na(.), 0))
```

```{r journal_indicators}
#| echo: false
#| message: false
#| warning: false
source("R/journal_tbl.R")
htmltools::div(
    class = "agreement-tbl",
    journal_listing
)

export_files(.data =  my_df)
```

:::

<small>Dashboard last compiled on `r format(Sys.time(), '%d %B, %Y')`.</small>

```{css}
.my-tbl {
  margin: 0 auto;
  width: 575px;
}
.tbl-header {
  margin: 18px 0;
  font-size: 1.25em;
}
.filters {
  display: flex;
  flex-wrap: wrap;
  margin-top: 4px;
  margin-bottom: 24px;
  margin-left: auto;
  margin-right: auto;
}
.filter-input {
  margin-top: 4px;
  margin-left: 32px;
  flex: 1;
  max-width: 250px;
}
.filter-input label {
  color: hsl(0, 0%, 45%);
  font-weight: 700;
  font-size: 13px;
  letter-spacing: 0.4px;
  text-transform: uppercase;
}
.group-header {
  font-weight: 700;
  font-size: 14px;
  letter-spacing: 0.4px;
  text-transform: uppercase;
}
.filter-input select,
.filter-input input[type="search"] {
  padding: 0 6px;
  height: 32px;
}
.filter-input input[type="search"] {
  /* Reset Bootstrap 3 styles */
  -webkit-appearance: searchfield;
}
.filter-input input[type="search"]::-webkit-search-cancel-button {
  /* Reset Bootstrap 3 styles */
  -webkit-appearance: searchfield-cancel-button;
}
.followers-tbl a {
  color: inherit;
}
.header {
  border-bottom: 2px solid #555;
  font-size: 14px;
  font-weight: bold;
  text-transform: uppercase;
}
.header:hover {
  background-color: #eee;
}
/* Highlight headers when sorting */
.header:hover,
.header[aria-sort="ascending"],
.header[aria-sort="descending"] {
  background-color: rgba(236, 236, 237, 1);
}
.agreement-footer {
  margin: 18px 0;
  font-size: 10px;
  }
  
.agreement-tbl {
  margin: 18px 0;
  font-size: 14px;
}
.bar-cell {
  display: flex;
  align-items: center;
}
.number {
  font-family: monospace;
  font-size: 14px;
  white-space: pre;
}
.label {
  font-size: 14px;
  white-space: pre;
}
.bar-chart {
  flex-grow: 1;
  margin-left: 6px;
  height: 14px;
}
.bar {
  height: 100%;
}
.border-left {
  border-left: 1px solid #b5b5b5;
}
.name {
  font-weight: 900;
}
```