endometriosis.Rmd

---
title: "endometriosis"
output: html_notebook
---

```{r}
library(europepmc)
```


```{r}
endometriosis_articlesPerTotalArticles <- europepmc::epmc_hits_trend(query = "endometriosis", period = 1980:2018)

endometriosis_articlesPerTotalArticles

# View(endometriosis_articlesPerTotalArticles)

xlsx::write.xlsx(endometriosis_articlesPerTotalArticles, here::here("data/endometriosis_articlesPerTotalArticles.xlsx")
)

```


```{r}
library(ggplot2)
ggplot(endometriosis_articlesPerTotalArticles, aes(year, query_hits / all_hits)) + 
  geom_point() + 
  geom_line() +
  xlab("Year published") + 
  ylab("Proportion of Endometriois \n articles in Europe PMC")
```

---


```
("endometriosis" AND "inflammation") AND (SRC:"MED")
```


```{r}
dvcs <- c('("endometriosis" AND "inflammation") AND (SRC:"MED")', '("endometriosis" AND "infertility") AND (SRC:"MED")', '("endometriosis" AND "fertility") AND (SRC:"MED")' , '("endometriosis") AND (SRC:"MED")'
          )
```


```{r}
my_df <- purrr::map_df(dvcs, function(x) {
  # get number of publications with indexed reference lists
  refs_hits <- 
    europepmc::epmc_hits_trend(x, period = 1980:2018, synonym = FALSE)$query_hits
  # get hit count querying for code repositories 
  europepmc::epmc_hits_trend(x, period = 1980:2018, synonym = FALSE) %>% 
    dplyr::mutate(query_id = x) %>%
    dplyr::mutate(refs_hits = refs_hits) %>%
    dplyr::select(year, all_hits, refs_hits, query_hits, query_id)
}) 
my_df
```


```{r}
## Recoding my_df$query_id into my_df$Query
my_df$Query <- recode(my_df$query_id,
               "(\"endometriosis\" AND \"inflammation\") AND (SRC:\"MED\")" = "endometriosis AND inflammation",
               "(\"endometriosis\" AND \"infertility\") AND (SRC:\"MED\")" = "endometriosis AND infertility",
               "(\"endometriosis\" AND \"fertility\") AND (SRC:\"MED\")" = "endometriosis AND fertility",
               "(\"endometriosis\") AND (SRC:\"MED\")" = "endometriosis")
my_df$Query <- factor(my_df$Query)

```

```{r}
library(ggplot2)
ggplot(my_df, aes(x = year, 
                  y = query_hits / all_hits,
                  group = Query, 
                  color = Query)) + 
  geom_point() + 
  geom_line() +
  xlab("Year published") + 
  ylab("Proportion of articles in PubMed \n Data from: Europe PMC") +
  theme(legend.position = "bottom",
        legend.direction = "vertical")
```

```{r}
library(ggplot2)
ggplot(my_df, aes(x = year, 
                  y = scales::percent(query_hits / all_hits, accuracy = 0.02),
                  group = Query, 
                  color = Query)) + 
  geom_point() + 
  geom_line() +
  xlab("Year published") + 
  ylab("Proportion of articles in PubMed \n Data from: Europe PMC") +
  theme(legend.position = "bottom",
        legend.direction = "vertical")
```



```{r}
library(ggplot2)
ggplot(my_df, aes(factor(year), query_hits / refs_hits, group = query_id, 
                  color = query_id)) +
  geom_line(size = 1, alpha = 0.8) +
  geom_point(size = 2) +
  scale_color_brewer(name = "Query", palette = "Set1")+
  xlab("Year published") +
  ylab("Proportion of articles in PubMed \n Data from: Europe PMC")
```

























---



```{r}
library("handlr")
deneme <- handlr::bibtex_reader("data/europepmc_endometriosisinflammation.bib")

# handlr::citeproc_writer(deneme)

# handlr::codemeta_writer(deneme)


jsonlite::write_json(handlr::codemeta_writer(deneme, pretty = FALSE), path = "data/europepmc_endometriosisinflammation.json")

```


```{r}
z <- system.file("data/europepmc_endometriosisinflammation.bib", package = "handlr")
x <- HandlrClient$new(x = z)
x$read("bibtex")
x$write("citeproc")
```











---

```{r}
endometriosis_articles1 <- europepmc::epmc_hits_trend(query = "endometriosis AND fertility", period = 1980:2018)

endometriosis_articles1

# View(endometriosis_articlesPerTotalArticles)

xlsx::write.xlsx(endometriosis_articlesPerTotalArticles, here::here("data/endometriosis_articlesPerTotalArticles.xlsx")
)

```







```{r}
library(ggplot2)
ggplot(endometriosis_articlesPerTotalArticles, aes(year, query_hits / all_hits)) + 
  geom_point() + 
  geom_line() +
  xlab("Year published") + 
  ylab("Proportion of Endometriois \n articles in Europe PMC")
```





---

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5031306/


```{r}
knitcitations::citep("10.1186/s12905-016-0336-0")
```



vosviewer

---

# Bibliometrix Package Analysis Last 10 year Endometriosis

## Search PubMed

```
"endometriosis"[MeSH Major Topic] AND "english and humans"[Filter] AND ("2009/03/10"[PDat] : "2019/03/07"[PDat])
```


```{r Search PubMed download xml Last 10 year Endometriosis, eval=FALSE, include=FALSE}
myTerm <- rstudioapi::terminalCreate(show = FALSE)
rstudioapi::terminalSend(
    myTerm,
    "esearch -db pubmed -query \"endometriosis[MeSH Major Topic] AND english and humans[Filter] AND (2009/03/10[PDat] : 2019/03/07[PDat]) \" -datetype PDAT -mindate 1800 -maxdate 3000 | \ efetch -format xml > data/endometriosis/Last10YearEndometriosis.xml \n"
)
Sys.sleep(1)
repeat {
    Sys.sleep(0.1)
    if (rstudioapi::terminalBusy(myTerm) == FALSE) {
        print("Code Executed")
        break
    }
}

file.info(here::here("data/endometriosis/Last10YearEndometriosis.xml"))$ctime
```



```{r extract pmid doi from xml Last 10 year Endometriosis, message=FALSE, warning=FALSE}
myTerm <- rstudioapi::terminalCreate(show = FALSE)
rstudioapi::terminalSend(
myTerm,
"xtract -input data/endometriosis/Last10YearEndometriosis.xml -pattern PubmedArticle -tab \"|\" -sep \";\" -def \"NA\" -element MedlineCitation/PMID -block ArticleId -if ArticleId@IdType -equals doi -element ArticleId > data/endometriosis/Last10YearEndometriosis.csv \n"
)
Sys.sleep(1)
repeat {
Sys.sleep(0.1)
if (rstudioapi::terminalBusy(myTerm) == FALSE) {
print("Code Executed")
break
}
}
```


```{r read extracted data Last 10 year Endometriosis}
library(readr)
Last10YearEndometriosis <- read_delim(here::here("data/endometriosis/Last10YearEndometriosis.csv"), 
    "|",
    escape_double = FALSE,
    col_names = FALSE, 
    trim_ws = TRUE)
# View(Last10YearEndometriosis)

names(Last10YearEndometriosis) <- c("PMID", "DOI")

```


```{r WOS search file write PMID DOI with OR Last 10 year Endometriosis}

PMID_List <- paste0("PMID=(", Last10YearEndometriosis$PMID[!is.na(Last10YearEndometriosis$PMID)], ") OR")
# DOI_List <- paste0("DO=(", Last10YearEndometriosis$DOI[!is.na(Last10YearEndometriosis$DOI)], ") OR")


write(PMID_List,
      here::here("data/endometriosis/Last10YearEndometriosis_pmid_ListforWOS.txt")
)

# write(DOI_List,
#       here::here("data/NeurosurgeryFromTurkey_doi_ListforWOS.txt")
# )

```




```{r}
library(tidyverse)
library(bibliometrix)
bibliometrix::biblioshiny()
```