My objective was to make a list of ecological questions and methods that are addressed in these papers. I ended up with more than 5000 papers. The bibliometric and text analyses were somehow useful, but I needed to dig a bit deeper to achieve the objective. Here how I did.
First, I isolated the methodological journals. To do so, I focused the search on journals that had published more than 10 papers about capture-recapture over the last 10 years:
library(tidyverse)
raw_dat <- read_csv(file = 'crdat.csv')## Parsed with column specification:
## cols(
## title = col_character(),
## keywords = col_character(),
## journal = col_character(),
## authors = col_character(),
## abstract = col_character()
## )
raw_dat %>%
group_by(journal) %>%
filter(n() > 10) %>%
ungroup() %>%
count(journal)## # A tibble: 107 x 2
## journal n
## <chr> <int>
## 1 AFRICAN JOURNAL OF ECOLOGY 15
## 2 AFRICAN JOURNAL OF MARINE SCIENCE 21
## 3 AMERICAN MIDLAND NATURALIST 11
## 4 AMERICAN NATURALIST 14
## 5 AMPHIBIA-REPTILIA 20
## 6 ANIMAL BEHAVIOUR 11
## 7 ANIMAL CONSERVATION 25
## 8 ANNALS OF APPLIED STATISTICS 18
## 9 AQUATIC CONSERVATION-MARINE AND FRESHWATER ECOSYSTEMS 17
## 10 ARDEA 12
## # … with 97 more rows
By inspecting the list, I ended up with these journals:
methods <- raw_dat %>%
filter(journal %in% c('BIOMETRICS',
'ECOLOGICAL MODELLING',
'JOURNAL OF AGRICULTURAL BIOLOGICAL AND ENVIRONMENTAL STATISTICS',
'METHODS IN ECOLOGY AND EVOLUTION',
'ANNALS OF APPLIED STATISTICS',
'ENVIRONMENTAL AND ECOLOGICAL STATISTICS'))The number of papers published in each of them was:
methods %>%
count(journal)## # A tibble: 6 x 2
## journal n
## <chr> <int>
## 1 ANNALS OF APPLIED STATISTICS 18
## 2 BIOMETRICS 45
## 3 ECOLOGICAL MODELLING 26
## 4 ENVIRONMENTAL AND ECOLOGICAL STATISTICS 20
## 5 JOURNAL OF AGRICULTURAL BIOLOGICAL AND ENVIRONMENTAL STATISTICS 33
## 6 METHODS IN ECOLOGY AND EVOLUTION 77
Now I exported the 219 papers published in these methodological journals in a csv file:
raw_dat %>%
filter(journal %in% c('BIOMETRICS',
'ECOLOGICAL MODELLING',
'JOURNAL OF AGRICULTURAL BIOLOGICAL AND ENVIRONMENTAL STATISTICS',
'METHODS IN ECOLOGY AND EVOLUTION',
'ANNALS OF APPLIED STATISTICS',
'ENVIRONMENTAL AND ECOLOGICAL STATISTICS')) %>%
write_csv('papers_in_methodological_journals.csv')The next step was to annotate this file to determine the methods used. I’m afraid R cannot help, and I had to do it by hand. I read the >200 titles and abstracts and added my tags in an extra column. Took me 2 hours or so. The task was cumbersome but very interesting. I enjoyed seeing what my colleagues have been working on. There were a few papers that I didn't know the existence of, and several others that I was pleased to spot again. The results are in this file.
By focusing the annotation on the methodological journals, I ignored all the methodological papers that had been published in other non-methodological journals like, among others, Ecology, Journal of Applied Ecology, Conservation Biology and Plos One which welcome methods. I address this issue below. In brief, I scanned the corpus of ecological papers and tagged all methodological papers (126 in total); I moved them to the file of methodological papers and added a column to keep track of the paper original (methodological vs ecological corpus).
Second, I isolated the ecological journals. To do so, I focused the search on journals that had been published more than 50 papers about capture-recapture over the last 10 years, and I excluded the methodological journals
ecol <- raw_dat %>%
filter(!journal %in% c('BIOMETRICS',
'ECOLOGICAL MODELLING',
'JOURNAL OF AGRICULTURAL BIOLOGICAL AND ENVIRONMENTAL STATISTICS',
'METHODS IN ECOLOGY AND EVOLUTION',
'ANNALS OF APPLIED STATISTICS',
'ENVIRONMENTAL AND ECOLOGICAL STATISTICS')) %>%
group_by(journal) %>%
filter(n() > 50) %>%
ungroup()
ecol %>%
count(journal, sort = TRUE)## # A tibble: 16 x 2
## journal n
## <chr> <int>
## 1 PLOS ONE 219
## 2 JOURNAL OF WILDLIFE MANAGEMENT 170
## 3 ECOLOGY AND EVOLUTION 116
## 4 ECOLOGY 101
## 5 BIOLOGICAL CONSERVATION 99
## 6 JOURNAL OF ANIMAL ECOLOGY 80
## 7 JOURNAL OF MAMMALOGY 73
## 8 JOURNAL OF APPLIED ECOLOGY 72
## 9 NORTH AMERICAN JOURNAL OF FISHERIES MANAGEMENT 65
## 10 POPULATION ECOLOGY 60
## 11 CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES 55
## 12 WILDLIFE RESEARCH 55
## 13 FISHERIES RESEARCH 54
## 14 OECOLOGIA 54
## 15 TRANSACTIONS OF THE AMERICAN FISHERIES SOCIETY 54
## 16 JOURNAL OF INSECT CONSERVATION 51
ecol %>%
nrow()## [1] 1378
ecol %>%
write_csv('papers_in_ecological_journals.csv')Again, I inspected the papers one by one. Took me several hours as there were >1000 papers (remember I moved the 126 methodological papers I found in ecological journals to the methodological corpus)! I mainly focused my reading on the titles. I didn't annotate the papers.