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Peer review and preprint policies are unclear at most major journals

DOI

This repository holds code and data for the preprint Peer review and preprint policies are unclear at most major journals on bioRxiv.

Reproducible code

The whole analytic pipeline is reproducible through the drake package. Executing r_make("drake.R") will rebuild the analysis.

The pipeline is specified in the file R/plan.R. You can visualise the dependencies with the following code:

library(drake)
source("R/plan.R")

vis_drake_graph(plan)

A rendered version of the dependency graph is available under documentation/analysis_pipeline.png.

All packages that are used during the analysis are specified in R/packages.R. For the analysis files to render you will need to install the font "Hind" (for example from Google Fonts) and register it with extrafont. See the file load_fonts.R for specific instructions.

The basis for the paper is 02-analysis-writeup.Rmd (which is transformed into 02-analysis-writeup.html with the knitr package). Since writing the paper was a collaborative effort, we used a GoogleSheet to work on the manuscript. For this reason, the text in 02-analysis-writeup.html is not identical to the paper, but rather a first draft version. The code and figures are identical to the paper. Data for all figures has been exported to data/figures/.

Initial explorations can be found in 01-overview.html, as well as executing R/01-explore.R and R/02-explore-missings.R.

Code files

Core files for reproducing the analysis

Filename Purpose
drake.R Core file for building the analysis. Run with drake::r_make("drake.R").
R/plan.R Describes all inputs and outputs along with the functions processing them.
R/packages.R Lists and loads all packages relevant to the analysis.
R/plotting_functions.R Functions for plotting that are re-used in multiple places.
R/drake_functions.R Functions that wrap preprocessing tasks as outlined in plan.R.
R/correspondence_analysis_funs.R Functions for conducting and plotting the multiple correspondence analysis (Fig 2).
R/helpers.R General helper functions.

Additional files for scraping and exploring data

Filename Purpose
analysis-scripts/01-explore.R General exploratory graphs from early in the analysis.
analysis-scripts/02-explore-missings.R Exploration of missing values.
analysis-scripts/03-get-oa-status.R Matching the journals surveyed against the DOAJ to determine whether they are open access or not.
analysis-scripts/04-scrape-gs-fields.R Scraping h5-index and h5-median for all journals from GSM to fill in gaps in the initial data collection.
analysis-scripts/05-do-correspondence-analysis.R Script which records the steps taken while developing the multiple correspondence analysis for figure 2.
analysis-scripts/06-clean-coreview.R Script computing string-distances between co-review-policies to identify duplicates.
analysis-scripts/07-print-coreview-policies.Rmd Notebook that displays all co-review-policies so they can be printed out on paper for further inspection (finding duplicates).
analysis-scripts/08-upload-analysis.R Script used to upload the rendered analysis to GoogleDrive.

Data files

The original data file for the data we collected lives in a Google Sheet (A), which is available here: https://docs.google.com/spreadsheets/d/1WcvxxmDhaV3BwBiIfwC_nEAr6-EKCDD11R6eJ5vZElA/edit?usp=sharing

The original data from Google Scholar Metrics (GSM) on which journals are included, alongside data on their respective h5-index (B), is available here: https://docs.google.com/spreadsheets/d/1Dluo5DNWU4UrmwIZLzqcToioRdyZ1qc1EofAk4ypiW8/edit?usp=sharing

The files were downloaded as .csv and .xlsx for archival. The analysis builds on the .csv files, while the .xlsx files are supposed to preserve as much of the original formatting as possible, should the GoogleSheets become unavailable one day. These data, along with data which we scraped from GSM and the DOAJ, as well as a plain language description of the fields from (A) can be found in the data/raw directory.

Some data cleaning was necessary before conducting the analysis. The output of these operations are the files data/refined.csv and data/refined_w_areas.csv. The latter file contains more rows, since some journals belong to more than one area in GSM. Those journals have duplicate entries except for the column area which specifies the GSM area. All subsequent analysis is based on either of the two files (depending on whether area was considered or not). The files - along with other intermediate data-files - can be found in the directory data/transformed.

Overview of data files

Raw data files

Filename Purpose
data/raw/TRANSPOSE landscape study - round 3 - Raw.csv Raw data of the landscape scan on 171 journals. Conducted with the data collection instrument.
data/raw/Compiled_Landscape study journals list - G_ALL_dedup.csv Data from GSM on journals and their respective ranking within the overall top 100 and top 20 per subject area. Retrieved on 2018-10-13.
data/raw/data_collection_instrument.csv This file preserves the instrument used when collecting data on journals.
data/raw/gs_scraped_total.csv All journals listed in GSM as of 2019-06-18, including h5-index and h5-median. This file was generated via the script analysis-scripts/04-scrape-gs-fields.R
data/raw/oa_data.csv Data on open access status of all journals surveyed. Generated via analysis-scripts/04-get-oa-status.R

Transformed data files

Filename Purpose
data/transformed/refined.csv Cleaned data from our landscape scan, joined with data from GSM. This file is the basis for the analysis presented in our paper.
data/transformed/refined_w_areas.csv This file is identical to refined.csv, except for the additional variable "area" which holds data on the subject category from GSM. Since some journals appear in multiple categories, this file has more rows (193) than refined.csv (which has 171 rows on 171 journals).
data/transformed/var_overview.csv Plain language descriptions of the variables in data/raw/TRANSPOSE landscape study - round 3 - Raw.csv.
data/transformed/coreview-policies.csv String distances between different coreview policies for detecting duplicates. Produced via analysis-scripts/06-clean-coreview.R
data/transformed/journals_with_missing_categories.csv List of journals for which no subject category from GSM is available in data/raw/Compiled_Landscape study journals list - G_ALL_dedup.csv. The missing data for these journals is taken from data/raw/gs_scraped_total.csv.
data/transformed/policies.txt A plain language file containing the raw text of the journals' policies on coreviewing.

Further resources

You can find more information on the drake package here: https://books.ropensci.org/drake/

Package versions used

The analysis was last rendered with the following package versions:

─ Session info ─────────────────────────────────────────
 setting  value                       
 version  R version 4.0.2 (2020-06-22)
 os       Windows 10 x64              
 system   x86_64, mingw32             
 ui       RStudio                     
 language (EN)                        
 collate  German_Austria.1252         
 ctype    German_Austria.1252         
 tz       Europe/Berlin               
 date     2020-07-04                    

─ Packages ─────────────────────────────────────────────
 package       * version  date       lib source                             
 ash             1.0-15   2015-09-01 [1] CRAN (R 4.0.0)                     
 assertthat      0.2.1    2019-03-21 [1] CRAN (R 4.0.0)                     
 backports       1.1.8    2020-06-17 [1] CRAN (R 4.0.2)                     
 base64enc       0.1-3    2015-07-28 [1] CRAN (R 4.0.0)                     
 base64url       1.4      2018-05-14 [1] CRAN (R 4.0.0)                     
 blob            1.2.1    2020-01-20 [1] CRAN (R 4.0.0)                     
 bookdown      * 0.20     2020-06-23 [1] CRAN (R 4.0.2)                     
 broom           0.5.6    2020-04-20 [1] CRAN (R 4.0.0)                     
 ca            * 0.71.1   2020-01-24 [1] CRAN (R 4.0.2)                     
 callr           3.4.3    2020-03-28 [1] CRAN (R 4.0.0)                     
 cellranger      1.1.0    2016-07-27 [1] CRAN (R 4.0.0)                     
 cli             2.0.2    2020-02-28 [1] CRAN (R 4.0.0)                     
 clisymbols      1.2.0    2017-05-21 [1] CRAN (R 4.0.2)                     
 colorspace      1.4-1    2019-03-18 [1] CRAN (R 4.0.0)                     
 crayon          1.3.4    2017-09-16 [1] CRAN (R 4.0.0)                     
 curl            4.3      2019-12-02 [1] CRAN (R 4.0.0)                     
 DBI             1.1.0    2019-12-15 [1] CRAN (R 4.0.0)                     
 dbplyr          1.4.4    2020-05-27 [1] CRAN (R 4.0.0)                     
 desc            1.2.0    2018-05-01 [1] CRAN (R 4.0.0)                     
 devtools        2.3.0    2020-04-10 [1] CRAN (R 4.0.0)                     
 digest          0.6.25   2020-02-23 [1] CRAN (R 4.0.0)                     
 dplyr         * 1.0.0    2020-05-29 [1] CRAN (R 4.0.0)                     
 drake         * 7.12.4   2020-06-29 [1] CRAN (R 4.0.2)                     
 ellipsis        0.3.1    2020-05-15 [1] CRAN (R 4.0.0)                     
 extrafont       0.17     2014-12-08 [1] CRAN (R 4.0.0)                     
 extrafontdb     1.0      2012-06-11 [1] CRAN (R 4.0.0)                     
 fansi           0.4.1    2020-01-08 [1] CRAN (R 4.0.0)                     
 farver          2.0.3    2020-01-16 [1] CRAN (R 4.0.0)                     
 fastmap         1.0.1    2019-10-08 [1] CRAN (R 4.0.2)                     
 fastmatch     * 1.1-0    2017-01-28 [1] CRAN (R 4.0.0)                     
 filelock        1.0.2    2018-10-05 [1] CRAN (R 4.0.0)                     
 forcats       * 0.5.0    2020-03-01 [1] CRAN (R 4.0.0)                     
 formatR         1.7      2019-06-11 [1] CRAN (R 4.0.2)                     
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 generics        0.0.2    2018-11-29 [1] CRAN (R 4.0.0)                     
 ggalt         * 0.4.0    2017-02-15 [1] CRAN (R 4.0.2)                     
 ggchicklet    * 0.5.0    2020-06-25 [1] local                              
 ggforce         0.3.2    2020-06-23 [1] CRAN (R 4.0.2)                     
 ggplot2       * 3.3.2    2020-06-19 [1] CRAN (R 4.0.2)                     
 ggraph        * 2.0.3    2020-05-20 [1] CRAN (R 4.0.2)                     
 ggrepel         0.8.2    2020-03-08 [1] CRAN (R 4.0.2)                     
 ggridges      * 0.5.2    2020-01-12 [1] CRAN (R 4.0.2)                     
 glue            1.4.1    2020-05-13 [1] CRAN (R 4.0.0)                     
 graphlayouts    0.7.0    2020-04-25 [1] CRAN (R 4.0.2)                     
 gridExtra       2.3      2017-09-09 [1] CRAN (R 4.0.0)                     
 gtable          0.3.0    2019-03-25 [1] CRAN (R 4.0.0)                     
 haven           2.3.1    2020-06-01 [1] CRAN (R 4.0.0)                     
 highr           0.8      2019-03-20 [1] CRAN (R 4.0.0)                     
 hms             0.5.3    2020-01-08 [1] CRAN (R 4.0.0)                     
 hrbrmisc      * 0.2.0    2020-07-01 [1] Github (hrbrmstr/hrbrmisc@ebb928c) 
 htmltools       0.5.0    2020-06-16 [1] CRAN (R 4.0.0)                     
 htmlwidgets     1.5.1    2019-10-08 [1] CRAN (R 4.0.0)                     
 httpuv          1.5.4    2020-06-06 [1] CRAN (R 4.0.2)                     
 httr            1.4.1    2019-08-05 [1] CRAN (R 4.0.0)                     
 igraph        * 1.2.5    2020-03-19 [1] CRAN (R 4.0.0)                     
 janeaustenr     0.1.5    2017-06-10 [1] CRAN (R 4.0.2)                     
 janitor       * 2.0.1    2020-04-12 [1] CRAN (R 4.0.2)                     
 jsonlite        1.7.0    2020-06-25 [1] CRAN (R 4.0.2)                     
 KernSmooth      2.23-17  2020-04-26 [2] CRAN (R 4.0.2)                     
 knitr           1.29     2020-06-23 [1] CRAN (R 4.0.2)                     
 labelled        2.5.0    2020-06-17 [1] CRAN (R 4.0.2)                     
 later           1.1.0.1  2020-06-05 [1] CRAN (R 4.0.0)                     
 lattice         0.20-41  2020-04-02 [2] CRAN (R 4.0.2)                     
 lifecycle       0.2.0    2020-03-06 [1] CRAN (R 4.0.0)                     
 lubridate       1.7.9    2020-06-08 [1] CRAN (R 4.0.0)                     
 magrittr        1.5      2014-11-22 [1] CRAN (R 4.0.0)                     
 maps            3.3.0    2018-04-03 [1] CRAN (R 4.0.2)                     
 MASS            7.3-51.6 2020-04-26 [2] CRAN (R 4.0.2)                     
 Matrix          1.2-18   2019-11-27 [2] CRAN (R 4.0.2)                     
 memoise         1.1.0    2017-04-21 [1] CRAN (R 4.0.0)                     
 mime            0.9      2020-02-04 [1] CRAN (R 4.0.0)                     
 miniUI          0.1.1.1  2018-05-18 [1] CRAN (R 4.0.2)                     
 modelr          0.1.8    2020-05-19 [1] CRAN (R 4.0.0)                     
 munsell         0.5.0    2018-06-12 [1] CRAN (R 4.0.0)                     
 nlme            3.1-148  2020-05-24 [2] CRAN (R 4.0.2)                     
 patchwork     * 1.0.1    2020-06-22 [1] CRAN (R 4.0.2)                     
 pillar          1.4.4    2020-05-05 [1] CRAN (R 4.0.0)                     
 pkgbuild        1.0.8    2020-05-07 [1] CRAN (R 4.0.0)                     
 pkgconfig       2.0.3    2019-09-22 [1] CRAN (R 4.0.0)                     
 pkgload         1.1.0    2020-05-29 [1] CRAN (R 4.0.0)                     
 plyr            1.8.6    2020-03-03 [1] CRAN (R 4.0.0)                     
 polyclip        1.10-0   2019-03-14 [1] CRAN (R 4.0.0)                     
 prettyunits     1.1.1    2020-01-24 [1] CRAN (R 4.0.0)                     
 processx        3.4.2    2020-02-09 [1] CRAN (R 4.0.0)                     
 progress        1.2.2    2019-05-16 [1] CRAN (R 4.0.0)                     
 proj4           1.0-10   2020-03-02 [1] CRAN (R 4.0.0)                     
 promises        1.1.1    2020-06-09 [1] CRAN (R 4.0.0)                     
 prompt          1.0.0    2020-07-01 [1] Github (gaborcsardi/prompt@b332c42)
 ps              1.3.3    2020-05-08 [1] CRAN (R 4.0.0)                     
 purrr         * 0.3.4    2020-04-17 [1] CRAN (R 4.0.0)                     
 questionr     * 0.7.1    2020-05-26 [1] CRAN (R 4.0.2)                     
 R6              2.4.1    2019-11-12 [1] CRAN (R 4.0.0)                     
 RColorBrewer  * 1.1-2    2014-12-07 [1] CRAN (R 4.0.0)                     
 Rcpp            1.0.4.6  2020-04-09 [1] CRAN (R 4.0.0)                     
 readODS       * 1.6.7    2018-11-26 [1] CRAN (R 4.0.2)                     
 readr         * 1.3.1    2018-12-21 [1] CRAN (R 4.0.0)                     
 readxl          1.3.1    2019-03-13 [1] CRAN (R 4.0.0)                     
 remotes         2.1.1    2020-02-15 [1] CRAN (R 4.0.0)                     
 reprex          0.3.0    2019-05-16 [1] CRAN (R 4.0.0)                     
 rlang           0.4.6    2020-05-02 [1] CRAN (R 4.0.0)                     
 rprojroot       1.3-2    2018-01-03 [1] CRAN (R 4.0.0)                     
 rstudioapi      0.11     2020-02-07 [1] CRAN (R 4.0.0)                     
 Rttf2pt1        1.3.8    2020-01-10 [1] CRAN (R 4.0.0)                     
 rvest           0.3.5    2019-11-08 [1] CRAN (R 4.0.0)                     
 scales          1.1.1    2020-05-11 [1] CRAN (R 4.0.0)                     
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 snakecase       0.11.0   2019-05-25 [1] CRAN (R 4.0.2)                     
 SnowballC       0.7.0    2020-04-01 [1] CRAN (R 4.0.0)                     
 storr           1.2.1    2018-10-18 [1] CRAN (R 4.0.0)                     
 stringi         1.4.6    2020-02-17 [1] CRAN (R 4.0.0)                     
 stringr       * 1.4.0    2019-02-10 [1] CRAN (R 4.0.0)                     
 testthat        2.3.2    2020-03-02 [1] CRAN (R 4.0.0)                     
 tibble        * 3.0.1    2020-04-20 [1] CRAN (R 4.0.0)                     
 tidygraph       1.2.0    2020-05-12 [1] CRAN (R 4.0.2)                     
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 tidyselect      1.1.0    2020-05-11 [1] CRAN (R 4.0.0)                     
 tidytext      * 0.2.4    2020-04-17 [1] CRAN (R 4.0.2)                     
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 tweenr          1.0.1    2018-12-14 [1] CRAN (R 4.0.2)                     
 txtq            0.2.3    2020-06-23 [1] CRAN (R 4.0.2)                     
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 viridis         0.5.1    2018-03-29 [1] CRAN (R 4.0.2)                     
 viridisLite   * 0.3.0    2018-02-01 [1] CRAN (R 4.0.0)                     
 visdat        * 0.5.3    2019-02-15 [1] CRAN (R 4.0.2)                     
 whisker         0.4      2019-08-28 [1] CRAN (R 4.0.0)                     
 withr           2.2.0    2020-04-20 [1] CRAN (R 4.0.0)                     
 xfun            0.15     2020-06-21 [1] CRAN (R 4.0.2)                     
 xml2            1.3.2    2020-04-23 [1] CRAN (R 4.0.0)                     
 xtable          1.8-4    2019-04-21 [1] CRAN (R 4.0.2)