---
title: "Core SCI Journal List For Chinese Academics in Biology & Medicine"
author: "Weibin Huang"
date: "`r Sys.Date()`"
output:
  prettydoc::html_pretty:
    theme: architect
    toc: TRUE
    toc_depth: 3
    highlight: github
    math: katex
    keep_md: false
---


```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, warning = FALSE, comment = '')
```

# Packages

```{r}
packages_needed <- c("dplyr","plyr","readxl","readr","stringr")

if (!requireNamespace("pacman", quietly = TRUE)){
  install.packages("pacman")
  library(pacman)
} else {
  library(pacman)
}
  
for(i in packages_needed){p_load(char=i)}
```

# Data

Load JCR information data:

```{r}
# 来自微信公众号: 生信小课堂
j <- read_xlsx('raw/2022IF.xlsx', na = c("", "N/A"), col_types = c( "text", "text","text", "text",  "numeric",  "numeric",  "numeric",  "numeric")) %>% 
  arrange(category, desc(IF)) %>% 
  as.data.frame()
str(j)
```


# Filtering

All Journals listed in Pubmed:

```{r}
issn_avail <- read_delim('raw/List of All Journals in Pubmed.txt', delim  = '\t') %>% 
  as.matrix() %>% as.character() %>% 
  .[grepl('issn',., ignore.case = T)] %>% 
  str_extract(.,pattern = '[0-9|X]{4}[-][0-9|X]{4}') %>%
  unique(.[!is.na(.)])
```

Warning journals in bioMed

> https://earlywarning.fenqubiao.com/#/zh-cn/early-warning-journal-list-2021

```{r}

issn_warn <- c(
  # BioFactors
  '0951-6433',
  
  # Frontiers in Cell and Developmental Biology
  '2296-634X',
  
  # Pharmazie
  '0031-7144',
  
  # Molecular Therapy-Nucleic Acids
  '2162-2531',
  
  # Experimental and Molecular Pathology
  '0014-4800',
  
  # Journal of Cellular and Molecular Medicine
  '1582-1838',
  
  # Molecular Medicine Reports
  '1791-2997',
  
  # Journal of International Medical Research
  '0300-0605',
  
  # Journal of Cancer
  '1837-9664',
  
  # Aging-US
  '1945-4589',
  
  # OncoTargets and Therapy,
  '1178-6930',
  
  # Cancer Management and Research
  '1179-1322',
  
  # World Journal of Clinical Cases
  '2307-8960',
  
  # Annals of Palliative Medicine
  '2224-5820'
  
)
```

ISSN available in Pubmed: 

```{r}
j$ISSN <- apply(
  as.matrix(j[c('issn', 'eissn')]), 
  1, 
  function(x){
    x2 <- x[x %in% issn_avail]
    if(length(x2) == 0){
      return(NA)
    } else if(length(x2) == 1) {
      return(x2)
    } else {
      return(x2[1])
    }
})

```

Target journals:

```{r}

# Filters
target_biomed <- read.table('raw/SCI category_Biology&Medicine.txt')[,1] %>% 
  as.character() %>% 
  paste0(.,collapse = '|')
target_other <- 'MULTIDISCIPLINARY SCIENCES' # Nature/Science等杂志
target_sci <- 'SSCI|SCIE'

# Target
j_biomed <- filter(
  
  j,
  
  # Not a Warning journal in Chinese Academy of Sciences Ranking
  !ISSN %in% issn_warn,
  
  # With availble Impact factor
  !is.na(IF),
  
  # With ISSN in Pubmed
  !is.na(ISSN),
  
  # IF>=5 And Q1/Q2; IF < 5 And Q1
  (IF>=5 & grepl('Q1|Q2', category) & !grepl('Q3|Q4', category)) | (IF < 5 & grepl('Q1', category) & !grepl('Q2|Q3|Q4', category)), 
  
  # Area in Biology/Medicine/Multidisciprinary
  grepl(target_biomed, category) | grepl(target_other, category),
  
  # As a SSCI/SCIE journal
  grepl(target_sci, category)
  
) %>% arrange(desc(IF))

```

Have a look at the target journals:

```{r}
head(j_biomed[c('journal_name', 'ISSN', 'IF')], n=10)

```

# ISSN

## IF>=15

```{r}
j_biomed_15 <- filter(j_biomed, IF>=15)
j_biomed_15$ISSN %>% paste0(.,collapse = '|')
```


## 15>IF>=10


```{r}
j_biomed_10 <- filter(j_biomed, IF<15, IF>=10)
j_biomed_10$ISSN %>% paste0(.,collapse = '|')
```


## 10>IF>=7


```{r}
j_biomed_7 <- filter(j_biomed, IF<10, IF>=7)
j_biomed_7$ISSN %>% paste0(.,collapse = '|')
```

## 7>IF>=6


```{r}
j_biomed_6 <- filter(j_biomed, IF<7, IF>=6)
j_biomed_6$ISSN %>% paste0(.,collapse = '|')
```


## 6>IF>=5.5


```{r}
j_biomed_5.5 <- filter(j_biomed, IF<6, IF>=5.5)
j_biomed_5.5$ISSN %>% paste0(.,collapse = '|')
```


## 5.5>IF>=5

```{r}
j_biomed_5 <- filter(j_biomed, IF<5.5, IF>=5)
j_biomed_5$ISSN %>% paste0(.,collapse = '|')

```

## IF<5

```{r}
j_biomed_m5 <- filter(j_biomed, IF<5)
j_biomed_m5$ISSN %>% paste0(.,collapse = '|')

```