---
title: "Get pubmed data"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Get pubmed data}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

## Introduction

This vignette demonstrates how to retrieve citation data from PubMed using:

- `get_pubmed_count()` — to retrieve the total count of articles matching a term.
- `get_pubmed_by_year()` — to get article counts by publication year.

These functions are part of the `risk.assessr` package.

DISCLAIMER: This feature only works if you choose a good R package name.

---

## Setting Your PubMed API Key

To increase request limits and improve stability, you can use an NCBI API key.

```{r api-key-example, eval = FALSE}
# Replace with your actual API key
options(pubmed.api_key = "your_actual_ncbi_api_key")

```

---

## Load Required Libraries

```{r setup}
library(risk.assessr)
library(ggplot2)

package_name <- "limma"
```

---

## Total Number of Articles Matching a Term

```{r, message=FALSE, warning=FALSE, eval=FALSE}
pubmed_count <- get_pubmed_count(package_name)
pubmed_count
```

---

## Number of Articles by Year

```{r, message=FALSE, warning=FALSE, eval=FALSE}
citation_data <- get_pubmed_by_year(package_name, years_back = 20)
citation_data
```

---

## Plotting the Article Trend Over Time

```{r, message=FALSE, warning=FALSE, echo=FALSE, eval=FALSE}
ggplot(citation_data, aes(x = Year, y = Count)) +
  geom_col(fill = "steelblue") +
  labs(
    title = "PubMed Articles per Year",
    subtitle = paste("Search term:", package_name),
    x = "Publication Year",
    y = "Number of Articles"
  ) +
  theme_minimal()
```