title | author | date | output | editor_options | bibliography | csl | |||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Code and Data for: Reproduce to Validate: a Comprehensive Study on the Reproducibility of Economics Research |
|
2024-04-12 |
|
|
|
_readme/chicago-author-date.csl |
File prepared for Canadian Journal of Economics.
Herbert, Sylvérie; Kingi, Hautahi; Stanchi, Flavio; Vilhuber, Lars, 2024, "Replication Data and Code for: Reproduce to Validate: a Comprehensive Study on the Reproducibility of Economics Research", https://doi.org/10.5683/SP3/GJVVLI, Borealis, V1, UNF:6:KAT43A8y80Ct+4PyDB3XYw== [fileUNF]
The code in this replication package constructs the analysis file from the four data sources [@raw-data-2019; @openalex-data; @webofscience2018; @crossref-data]. The code is in R, but also uses public APIs to download some data. The replication package also includes PDF copies the survey used to query the replicators. The original Google Forms surveys cannot be exported.
All data are public, and can be redistributed. The key data [@raw-data-2019] are provided in a separate repository (https://doi.org/10.5281/zenodo.2639920), but are downloaded automatically. Data pulled via APIs are provided as of the date last downloaded, with no guarantees that the code to access the API still works.
- I certify that the author(s) of the manuscript have legitimate access to and permission to use the data used in this manuscript.
- I certify that the author(s) of the manuscript have documented permission to redistribute/publish the data contained within this replication package. Appropriate permission are documented in the LICENSE.txt file.
- Original data [@raw-data-2019] (not included) are licensed as CC-BY-NC-4.0.
- Data from @openalex-data are obtained under a CC0 Public Domain attribution.
- Data from @webofscience2018 are proprietary, but redistribution of small extracts is permitted.
- Data fom @crossref-data is "is open and available for reuse without restriction" (https://www.crossref.org/documentation/retrieve-metadata/)
All derivative data contained herein, if not otherwise encumbered, is available under a CC-BY-NC-4.0 license. Usage by commercial entities is permitted, reselling the data is not.
- All data are publicly available.
- Some data cannot be made publicly available.
- No data can be made publicly available.
Data Source | Filename | Provided |
---|---|---|
Kingi et al (2019) | ./data/replication_data/entryQ_pub.Rds | FALSE |
Kingi et al (2019) | ./data/replication_data/exitQ_pub.Rds | FALSE |
Kingi et al (2019) | ./data/replication_data/replication_list_pub.Rds | FALSE |
Crossref (2023) | ./data/crossref/crossref_aejdois.Rds | TRUE |
Crossref (2023) | ./data/crossref/crossref_info.csv | TRUE |
Crossref (2023) | ./data/crossref/crossref_info.Rds | TRUE |
OurResearch (2023) | ./data/openalex/citations-per-paper.Rds | TRUE |
OurResearch (2023) | ./data/openalex/openalex-aejae-authors.Rds | TRUE |
OurResearch (2023) | ./data/openalex/openalex-aejae.Rds | TRUE |
OurResearch (2023) | ./data/openalex/openalex-hindex.Rds | TRUE |
OurResearch (2023) | ./data/openalex/openalex-institutions-aejae.Rds | TRUE |
Reuters (2016), Clarivate (2018) and manual edits | ./data/h_index_data/h-index-assignment1.2019.csv | TRUE |
Reuters (2016), Clarivate (2018) and manual edits | ./data/h_index_data/h-index-assignment1.2019.xlsx | TRUE |
Generated during acquisition of Crossref data | ./data/crossref/crossref_timing.Rds | TRUE |
Generated for data quality audit purposes | ./data/crossref/audit-exp.xlsx | TRUE |
Hand-generated by authors based on AEA websites | ./data/crossref/issns.Rds | TRUE |
Generated from openAlex data | ./data/openalex/affiliations.csv | TRUE |
Hand-edited data to override or complement openAlex data | ./data/openalex/affiliation-impute.csv | TRUE |
Hand-edited data to override or complement openAlex data | ./data/openalex/affiliation-impute.xlsx | TRUE |
Machine-imputed institutions using auxiliary openAlex information | ./data/openalex/affiliations-imputed.Rds | TRUE |
Records to remove from extracted openAlex data | ./data/openalex/blacklist.xlsx | TRUE |
Procedural file to map short names to long variable names | ./data/auxiliary/mainOA-mapping.xlsx | TRUE |
The data were collected through the methods described in the paper. Data were collected over several years, and deposited at @raw-data-2019 in 2019, with replicator names replaced by random identifiers.
Data Source | Filename | Provided |
---|---|---|
Kingi et al (2019) | ./data/replication_data/entryQ_pub.Rds | FALSE |
Kingi et al (2019) | ./data/replication_data/exitQ_pub.Rds | FALSE |
Kingi et al (2019) | ./data/replication_data/replication_list_pub.Rds | FALSE |
Crossref were extracted as needed to obtain bibliographic information (author names, article titles, publication dates) [@crossref-data], using the rcrossref
package to query the API `. The database itself is free to access. More information about it can be read in @crossref-paper . Note that data can and is updated, so running the query again
Data Source | Filename | Provided |
---|---|---|
Crossref (2023) | ./data/crossref/crossref_aejdois.Rds | TRUE |
Crossref (2023) | ./data/crossref/crossref_info.csv | TRUE |
Crossref (2023) | ./data/crossref/crossref_info.Rds | TRUE |
Generated during acquisition of Crossref data | ./data/crossref/crossref_timing.Rds | TRUE |
Generated for data quality audit purposes | ./data/crossref/audit-exp.xlsx | TRUE |
Hand-generated by authors based on AEA websites | ./data/crossref/issns.Rds | TRUE |
Data were accessed in 2023 to increase the time series covered by the bibliometric analysis [@openalex-data]. The openAlex database is described in @openalex2022. OpenAlex data are accessed via an API, and computed statistics, such as the h-index, are limited to the past 10 years. We therefore had to recompute some numbers. We also saved our extract, as future extracts may have different numbers, due to improvements in entity disambiguation (author names) and other factors outside of our control.
Not all data elements are complete in the openAlex data. We output data for various quality checks, and did manual research to "impute" attributes such as affiliations. All "overrides" are captured in a separate file.
Thus, the openAlex data has (a) the raw data as downloaded; (b) the problematic data, as output for manual review (c) the edited/imputed data as used to complement the downloaded data.
Data Source | Filename | Provided |
---|---|---|
OurResearch (2023) | ./data/openalex/citations-per-paper.Rds | TRUE |
OurResearch (2023) | ./data/openalex/openalex-aejae-authors.Rds | TRUE |
OurResearch (2023) | ./data/openalex/openalex-aejae.Rds | TRUE |
OurResearch (2023) | ./data/openalex/openalex-hindex.Rds | TRUE |
OurResearch (2023) | ./data/openalex/openalex-institutions-aejae.Rds | TRUE |
Generated from openAlex data | ./data/openalex/affiliations.csv | TRUE |
Hand-edited data to override or complement openAlex data | ./data/openalex/affiliation-impute.csv | TRUE |
Hand-edited data to override or complement openAlex data | ./data/openalex/affiliation-impute.xlsx | TRUE |
Machine-imputed institutions using auxiliary openAlex information | ./data/openalex/affiliations-imputed.Rds | TRUE |
Records to remove from extracted openAlex data | ./data/openalex/blacklist.xlsx | TRUE |
The bibliometric information, in particular on h-index, was originally extracted from Web of Science [@WebofScience;@webofscience2018], and was used in the early working papers [@kingi2018;@herbert2021]. In response to referee comments, the primary bibliometric analysis shifted to the use of openAlex data (described next). OpenAlex data is compared to WoS data in the appendix.
WoS is proprietary data and requires a subscription. We accessed the interface thanks to Cornell's subscription.
Data were manually extracted from the WoS web interface, with RAs following guidance on what data to extract (see data/h_index_data/README.md
). The collated data is provided in XLSX and CSV formats.
Data Source | Filename | Provided |
---|---|---|
Reuters (2016), Clarivate (2018) and manual edits | ./data/h_index_data/h-index-assignment1.2019.csv | TRUE |
Reuters (2016), Clarivate (2018) and manual edits | ./data/h_index_data/h-index-assignment1.2019.xlsx | TRUE |
Procedural file to map short names to long variable names | ./data/auxiliary/mainOA-mapping.xlsx | TRUE |
-
The replication package contains one or more programs to install all dependencies and set up the necessary directory structure.
-
R version 4.2.2 (2022-10-31) on x86_64, linux-gnu
- Docker image is used (see appendix), with system libraries defined by the relevant image (rocker/verse:4.2.2) (optional, but recommended)
- RSPM (now Posit Package Manager, PPM) is used, set to 2022-11-22. All libraries are installed from that time-stamped repository.
Libraries are defined in |
---|
global-libraries.R |
programs/libraries.R |
readme-libraries.R |
text/libraries.R |
Only directly loaded libraries are cited. For all libraries used in the runtime environment, see the Appendix.
Package | Version | Citation |
---|---|---|
base | 4.2.2 | @base |
devtools | 2.4.5 | @devtools |
fastDummies | 1.6.3 | @fastDummies |
knitr | 1.42 | @knitr2014; @knitr2015; @knitr2023 |
openalexR | 1.2.2.9999 | @openalexR |
rcrossref | 1.2.0 | @rcrossref |
remotes | 2.4.2 | @remotes |
reshape2 | 1.4.4 | @reshape2 |
rmarkdown | 2.20 | @rmarkdown2018; @rmarkdown2020; @rmarkdown2023 |
rprojroot | 2.0.3 | @rprojroot |
tidyverse | 2.0.0 | @tidyverse |
- Random seed is set at line _____ of program ______
- No Pseudo random generator is used in the analysis described here.
Note that re-running the API queries (turned off by default) will generate different data, which is likely to affect the regression output.
Approximate time needed to reproduce the analyses on a standard (CURRENT YEAR) desktop machine (when not running API queries):
- <10 minutes
- 10-60 minutes
- 1-2 hours
- 2-8 hours
- 8-24 hours
- 1-3 days
- 3-14 days
- > 14 days
API queries can take a long time, are not guaranteed to work, and are not guaranteed to return the same results. All API queries are stored as of the last run, and made available in the replication package.
Approximate storage space needed:
-
< 25 MBytes
-
25 MB - 250 MB
-
250 MB - 2 GB
-
2 GB - 25 GB
-
25 GB - 250 GB
-
> 250 GB
-
Not feasible to run on a desktop machine, as described below.
The code was last run on
- OS: "openSUSE Leap 15.5"
- Processor: AMD Ryzen 9 3900X 12-Core Processor, 24 cores
- Memory available: 31GB memory
- Docker version 24.0.7-ce, build 311b9ff0aa93
- R version 4.2.2 (2022-10-31) on x86_64, linux-gnu
as well as a Macbook with 16GB of memory. At least one program failed when run with less than 16GB of memory.
Each numbered R program can be run independently, in the sequence implied by the numbering scheme.
A convenience bash main script (run.sh
) to run all programs is provided in the root of the project, and will run all data cleaning and analysis programs.
Of note, several programs leverage APIs, which can yield different results, and might take long time. The programs will detect previously downloaded data files, and skip the download part if those files are present. To start with a fresh download, delete the following files:
- /home/rstudio/data/crossref/crossref_info.Rds - Crossref extract.
- /home/rstudio/text/includes/Replication_write.bib - bibtex file of articles analyzed
- /home/rstudio/data/openalex/openalex-aejae.Rds - extract of articles analyzed from openAlex
- /home/rstudio/data/openalex/openalex-aejae-authors.Rds - bibliometric information from openAlex on all the authors of articles analyzed
- /home/rstudio/data/crossref/crossref_aejdois.Rds - bibliographic information from Crossref for later analysis
Internet access is required to run the programs,
- to download the key input files [@raw-data-2019]
- when re-running queries to the APIs
The programs can be run without internet access if manually downloaded files from https://doi.org/10.5281/zenodo.2639920 are placed into dataloc
.
The code (all files ending in .R
, .Rmd
, and .sh
) is licensed under a BSD license. See LICENSE.txt for details.
If using Docker image on Linux or macOS system:
- run
start_rstudio.sh
and connect to https://localhost:8787 - in the "Terminal" of the RStudio app, run
bash ./run.sh
or equivalently,
- in the terminal of a computer with Docker installed, run
bash ./run_docker.sh ./run.sh
Alternative ways to run this (these were not tested):
- optionally, before running project code, run
Rscript -e "renv::init()"
(on Windows,Rscript.exe -e "renv::init()"
) to isolate the project libraries from your system (assumesrenv
is installed, see renv). - Using the same R version as described above, run each program individually as desired, in the order indicated above.
Filename | Note |
---|---|
./global-libraries.R | Defines libraries used globally in various pieces (text, analysis, and documentation) |
./pathconfig.R | Defines various relative paths |
./programs/_footnotes.R | Functions for displaying various table footnotes. |
./programs/_read_analysis_data.R | Function to read analysis data used in various programs |
./programs/01_download_replication_data.R | Download the Replication Lab data from Zenodo. |
./programs/02_get_crossref.R | Old program to get Crossref info on articles. May no longer work. |
./programs/04_clean_replicationlist.R | Various cleaning steps applied to the Replication Lab data. |
./programs/06_gen_hindex_list.R | Used to generate the task list to query Web of Science. Used once, for reference only. |
./programs/07_readclean_hindex_list.R | Read the generated and hand-collated data from Web of Science. |
./programs/08_get_crossref_bibs.R | Old program to get Crossref info for bib files for all the articles. May no longer be functional. |
./programs/25_prepare_sample.R | Uses downloaded data and generates the analysis sample |
./programs/30_results1.R | Original analysis, now only used for appendix tables. |
./programs/31_results2.R | Original analysis, now only used for appendix tables. |
./programs/40_supplementary1.R | New query to Crossref, creation of table_article_selection.tex. |
./programs/41_supplementary2.R | Query to openAlex for all articles and their subsequent citations. |
./programs/42_prepare_authors.R | Query to openAlex for author and institution information |
./programs/43_supplementary4.R | Processes the author and institution information, completing missing information |
./programs/44_supplementary_hindex.R | Re-computes the h-index per author and year |
./programs/45_supplementary_authexp.R | This program primarily handles computing academic age of author |
./programs/46_prepare_analysis.R | Combine the various pieces into a single analysis file for the bibliometric analysis. |
./programs/47_prepare_mainOA.R | Add additional pieces to the analysis |
./programs/48_mainOA_authorpaper_stats.R | Summary statistics: Papers and authors |
./programs/49_assignments.R | Summary statistics: Assignments |
./programs/50_analysis_openAlex.R | Core analysis |
./programs/51_analysis_Poisson.R | Poisson models |
./programs/52_robustess_standarderrors.R | Robust standard errors |
./programs/99_zz_info.R | System information |
./programs/config.R | Basic configuration |
./programs/libraries.R | All libraries used |
./text/libraries.R | Additional libraries (possibly no longer relevant, kept for robustness) |
The provided code reproduces:
- All numbers provided in text in the paper
- All tables and figures in the paper
- Selected tables and figures in the paper, as explained and justified below.
The code also produces numerous tables which were not included in the paper. Note that following a request from copy-editors, all tables used in the paper were subsumed into the main document. Earlier versions used \input
statements in LaTeX.
Table number | Program | LaTeX file |
---|---|---|
1 | programs/40_supplementary1.R | text/includes/table_article_selection.tex |
2 | NA | No code |
3 | programs/30_results1.R | text/includes/table_data_availability.tex |
4 | programs/30_results1.R | text/includes/table_data_prog.tex |
5 | programs/30_results1.R | text/includes/table_difficult.tex |
6 | programs/30_results1.R | text/includes/table_doc.tex |
7 | programs/31_results2.R | text/includes/table_results_both.tex |
8 | programs/31_results2.R | text/includes/table_reason.tex |
9 | programs/31_results2.R | text/analysis/table_code.tex |
10 | programs/31_results2.R | text/analysis/table_reg1.tex |
11 | programs/48_mainOA_authorpaper_stats.R | text/analysis/table_metrics_OA.tex |
12 | programs/48_mainOA_authorpaper_stats.R | text/analysis/table_reg_probit_0_full.tex |
13 | programs/48_mainOA_authorpaper_stats.R | text/analysis/table_ratios.tex |
14 | programs/50_analysis_openAlex.R | text/analysis/table_reg2OA.tex |
15 | programs/50_analysis_openAlex.R | text/analysis/table_arcreg3OA.tex |
16 | programs/50_analysis_openAlex.R | text/analysis/table_arcregpost12OA.tex |
17 | programs/50_analysis_openAlex.R | text/analysis/table_arcreg3OA4.tex |
A1 | programs/49_assignments.R | text/includes/table_assignments.tex |
A2 | programs/30_results1.R | text/includes/table_absence.tex |
A3 | programs/31_results2.R | text/includes/table_results_by_year.tex |
A4 | programs/48_mainOA_authorpaper_stats.R | text/analysis/table_reg_probit_0_fullpartial.tex |
A5 | programs/48_mainOA_authorpaper_stats.R | text/analysis/table_metrics_OA_app0.tex |
A6 | programs/31_results2.R | text/analysis/table_metrics.tex |
A7 | programs/48_mainOA_authorpaper_stats.R | text/analysis/table_metrics_OA_wos.tex |
A8 | programs/50_analysis_openAlex.R | text/analysis/table_stassessed.tex |
A9 | programs/50_analysis_openAlex.R | text/analysis/table_stattempted.tex |
A10 | programs/50_analysis_openAlex.R | text/analysis/table_reg3OA.tex |
A11 | programs/50_analysis_openAlex.R | text/analysis/table_logreg3OA.tex |
A12 | programs/51_analysis_Poisson.R | text/analysis/table_poissonreg.tex |
A13 | programs/50_analysis_openAlex.R | text/analysis/table_arcreg3OA_partial.tex |
A14 | programs/50_analysis_openAlex.R | text/analysis/table_reg3OA_partial.tex |
A15 | programs/50_analysis_openAlex.R | text/analysis/table_logreg3OA_partial.tex |
A16 | programs/51_analysis_Poisson.R | text/analysis/table_poissonreg_partial.tex |
A17 | programs/50_analysis_openAlex.R | text/analysis/table_arcregpost12OA_partial.tex |
This README based on the template created by @template-readme.
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## os Ubuntu 22.04.2 LTS
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## tz Etc/UTC
## date 2024-03-16
## pandoc 2.19.2 @ /usr/local/bin/ (via rmarkdown)
##
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## skimr * 2.1.4 2022-04-15 [1] RSPM (R 4.2.0)
## stargazer * 5.2.3 2022-03-04 [1] RSPM (R 4.2.0)
## stringi 1.7.12 2023-01-11 [1] RSPM (R 4.2.0)
## stringr * 1.5.0 2022-12-02 [1] RSPM (R 4.2.0)
## tibble 3.2.0 2023-03-08 [1] RSPM (R 4.2.0)
## tictoc * 1.1 2022-09-03 [1] RSPM (R 4.2.0)
## tidyr * 1.3.0 2023-01-24 [1] RSPM (R 4.2.0)
## tidyselect 1.2.0 2022-10-10 [1] RSPM (R 4.2.0)
## tzdb 0.3.0 2022-03-28 [1] RSPM (R 4.2.0)
## urlchecker 1.0.1 2021-11-30 [1] RSPM (R 4.2.0)
## usethis * 2.1.6 2022-05-25 [1] RSPM (R 4.2.0)
## utf8 1.2.3 2023-01-31 [1] RSPM (R 4.2.0)
## vctrs 0.5.2 2023-01-23 [1] RSPM (R 4.2.0)
## withr 2.5.0 2022-03-03 [1] RSPM (R 4.2.0)
## xfun 0.37 2023-01-31 [1] RSPM (R 4.2.0)
## xml2 1.3.3 2021-11-30 [1] RSPM (R 4.2.0)
## xtable * 1.8-4 2019-04-21 [1] RSPM (R 4.2.0)
## zoo 1.8-11 2022-09-17 [1] RSPM (R 4.2.0)
##
## [1] /usr/local/lib/R/site-library
## [2] /usr/local/lib/R/library
##
## ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
## _
## platform x86_64-pc-linux-gnu
## arch x86_64
## os linux-gnu
## system x86_64, linux-gnu
## status
## major 4
## minor 2.2
## year 2022
## month 10
## day 31
## svn rev 83211
## language R
## version.string R version 4.2.2 (2022-10-31)
## nickname Innocent and Trusting
## FROM rocker/verse:4.2.2
##
## RUN apt-get update \
## && DEBIAN_FRONTEND=noninteractive apt-get install -y \
## locales \
## libcurl4-openssl-dev \
## libssl-dev \
## imagemagick \
## libmagick++-dev \
## gsfonts \
## pandoc \
## libicu-dev \
## libtcl8.6 \
## libtk8.6 \
## && rm -rf /var/lib/apt/lists/* \
## && localedef -i en_US -c -f UTF-8 -A /usr/share/locale/locale.alias en_US.UTF-8
## RUN apt-get update \
## && DEBIAN_FRONTEND=noninteractive apt-get install -y \
## texlive-latex-recommended texlive-latex-base texlive-binaries texlive-latex-extra\
## texlive-humanities texlive-bibtex-extra biber \
## && rm -rf /var/lib/apt/lists/* \
## && localedef -i en_US -c -f UTF-8 -A /usr/share/locale/locale.alias en_US.UTF-8
##
## COPY global-libraries.R install1.R
## COPY programs/libraries.R install2.R
## COPY text/libraries.R install3.R
## COPY readme-libraries.R install4.R
##
## RUN cat install?.R > install.R && Rscript install.R