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‎.gitignore

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.Rproj.user
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.Rhistory
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.RData
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.Ruserdata
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_targets/
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data/raw/results-survey.csv

‎README.md

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# Value dissonance in research(er) assessment: Individual and institutional priorities in review, promotion and tenure criteria related to research quality, quantity, openness and responsibility
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This repository holds code and data for the preprint "Value dissonance in research(er) assessment: Individual and institutional priorities in review, promotion and tenure criteria related to research quality, quantity, openness and responsibility".
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Not all raw data is shared, to avoid re-identification of participants. We
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provide a cleaned version of the data with qualitative answers and country
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information removed.
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## Reproducible code
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The analytic pipeline for generating tables and figures is reproducible through the
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`targets` package. Running `tar_make()` will rebuild all notebooks. The initial
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pipeline for data pre-processing involved multiple steps, however, they are not
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available for reproduction because we cannot openly share the original raw data.
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The pipeline is specified in the file `_targets.R`. You can visualise the
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dependencies with the following code:
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```r
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targets::tar_visnetwork()
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```
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All packages that are used during the analysis are specified in `R/packages.R`.
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For the analysis files to render you will need to install the font "Hind" (for
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example from [Google Fonts](https://fonts.google.com/)) and
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register it with
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[`extrafont`](https://cran.r-project.org/web/packages/extrafont/README.html).
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See the file `load_fonts.R` for specific instructions.
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### Code files
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The code to reproduce all values and figures can be found in five RMarkdown
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documents, located in the folder `analysis-notebooks`:
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- 01-demography.Rmd
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- 02-institutional-context.Rmd
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- 03-attitudes-towards-promotion-criteria.Rmd
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- 04-opinion-vs-practice.Rmd
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- 05-research-vs-policies.Rmd
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Rendered versions are available as `.md`-files (which are displayed on GitHub)
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or `.html` files which can be viewed locally.
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Note that this repository does not contain data necessary to reproduce
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`01-demography.Rmd`. To protect the identities of our participants, this data
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was removed from the public files.
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Further core files for the analysis pipeline's reproducibility are the following:
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|File name |Purpose |
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|:-------------------------------|:--------------------------------------------------------------------------|
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|_targets.R |Core file for building the analysis. Run with `targets::tar_make()`.|
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|R/packages.R |Lists all packages relevant to the analysis. |
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|R/functions.R |Functions that wrap preprocessing tasks as outlined in `_targets.R`.|
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|R/helpers.R |Some helper functions that are re-used throughout the analysis.|
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## Data description
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Procedures for collecting the data are outlined in the preprint.
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### Overview of data files
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|File name |Purpose |
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|:-------------------------------|:---------------------------------------------------------------------|
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|data/external/world_bank_country_classification.xlsx |Categorisations of countries into world regions. Obtained from the [World Bank](https://datahelpdesk.worldbank.org/knowledgebase/articles/906519-world-bank-country-and-lending-groups), and made available under CC-BY.|
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|data/processed/shareable_data.csv|This is the main data file that underlies the analysis. A description of variables is provided in the next file.|
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|data/processed/var_overview.csv |Provides full column names as key-value pairs for the abbreviated column names from the main data file.|
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|data/processed/labels_expanded.csv |Small file used to generate lables for some of the figures.|
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|data/processed/disciplines_lookup.xlsx |Manual mapping of respondents' disciplines to disciplines from Web of Science.|
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## Further resources
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You can find more information on the `targets` package here:
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https://books.ropensci.org/targets/
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## Package versions used
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The analysis was last rendered with the following package versions:
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```r
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sessioninfo::session_info()
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─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
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setting value
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version R version 4.2.2 (2022-10-31 ucrt)
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os Windows 10 x64 (build 19045)
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system x86_64, mingw32
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ui RStudio
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language (EN)
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collate German_Austria.utf8
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ctype German_Austria.utf8
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tz Europe/Berlin
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date 2022-12-20
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rstudio 2022.12.0+353 Elsbeth Geranium (desktop)
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pandoc 2.19.2 @ C:/Users/tklebel/AppData/Local/Programs/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
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─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
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package * version date (UTC) lib source
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ash 1.0-15 2015-09-01 [1] CRAN (R 4.2.0)
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assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.2.1)
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backports 1.4.1 2021-12-13 [1] CRAN (R 4.2.0)
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base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.2.0)
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base64url 1.4 2018-05-14 [1] CRAN (R 4.2.1)
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boot 1.3-28 2021-05-03 [2] CRAN (R 4.2.2)
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broom 1.0.1 2022-08-29 [1] CRAN (R 4.2.1)
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ca * 0.71.1 2020-01-24 [1] CRAN (R 4.2.2)
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cachem 1.0.6 2021-08-19 [1] CRAN (R 4.2.1)
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callr 3.7.3 2022-11-02 [1] CRAN (R 4.2.2)
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cellranger 1.1.0 2016-07-27 [1] CRAN (R 4.2.1)
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checkmate 2.1.0 2022-04-21 [1] CRAN (R 4.2.1)
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class 7.3-20 2022-01-16 [2] CRAN (R 4.2.2)
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cli 3.4.0 2022-09-08 [1] CRAN (R 4.2.1)
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clisymbols 1.2.0 2017-05-21 [1] CRAN (R 4.2.2)
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cluster 2.1.4 2022-08-22 [2] CRAN (R 4.2.2)
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codetools 0.2-18 2020-11-04 [2] CRAN (R 4.2.2)
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colorspace 2.0-3 2022-02-21 [1] CRAN (R 4.2.1)
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corrplot * 0.92 2021-11-18 [1] CRAN (R 4.2.2)
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crayon 1.5.2 2022-09-29 [1] CRAN (R 4.2.2)
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data.table 1.14.4 2022-10-17 [1] CRAN (R 4.2.2)
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DBI 1.1.3 2022-06-18 [1] CRAN (R 4.2.1)
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dbplyr 2.2.1 2022-06-27 [1] CRAN (R 4.2.1)
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deldir 1.0-6 2021-10-23 [1] CRAN (R 4.2.1)
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DescTools * 0.99.47 2022-10-22 [1] CRAN (R 4.2.2)
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devtools 2.4.5 2022-10-11 [1] CRAN (R 4.2.1)
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digest 0.6.30 2022-10-18 [1] CRAN (R 4.2.2)
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dplyr * 1.0.10 2022-09-01 [1] CRAN (R 4.2.1)
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e1071 1.7-12 2022-10-24 [1] CRAN (R 4.2.2)
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ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.2.1)
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evaluate 0.18 2022-11-07 [1] CRAN (R 4.2.2)
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Exact 3.2 2022-09-25 [1] CRAN (R 4.2.1)
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expm 0.999-6 2021-01-13 [1] CRAN (R 4.2.2)
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extrafont * 0.18 2022-04-12 [1] CRAN (R 4.2.0)
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extrafontdb 1.0 2012-06-11 [1] CRAN (R 4.2.0)
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fansi 1.0.3 2022-03-24 [1] CRAN (R 4.2.1)
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fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.1)
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forcats * 0.5.2 2022-08-19 [1] CRAN (R 4.2.1)
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foreign 0.8-83 2022-09-28 [2] CRAN (R 4.2.2)
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Formula 1.2-4 2020-10-16 [1] CRAN (R 4.2.0)
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fs 1.5.2 2021-12-08 [1] CRAN (R 4.2.1)
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gargle 1.2.1 2022-09-08 [1] CRAN (R 4.2.1)
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gdtools 0.2.4 2022-02-14 [1] CRAN (R 4.2.1)
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generics 0.1.3 2022-07-05 [1] CRAN (R 4.2.1)
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ggalt * 0.4.0 2017-02-15 [1] CRAN (R 4.2.2)
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ggchicklet * 0.5.0 2022-12-13 [1] local
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ggplot2 * 3.4.0 2022-11-04 [1] CRAN (R 4.2.2)
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ggrepel 0.9.2 2022-11-06 [1] CRAN (R 4.2.2)
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gld 2.6.6 2022-10-23 [1] CRAN (R 4.2.2)
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glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.1)
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googledrive 2.0.0 2021-07-08 [1] CRAN (R 4.2.1)
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googlesheets4 1.0.1 2022-08-13 [1] CRAN (R 4.2.1)
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gridExtra 2.3 2017-09-09 [1] CRAN (R 4.2.1)
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gtable 0.3.1 2022-09-01 [1] CRAN (R 4.2.1)
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haven 2.5.1 2022-08-22 [1] CRAN (R 4.2.1)
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Hmisc 4.7-2 2022-11-18 [1] CRAN (R 4.2.2)
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hms 1.1.2 2022-08-19 [1] CRAN (R 4.2.1)
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hrbrthemes * 0.8.0 2020-03-06 [1] CRAN (R 4.2.1)
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htmlTable 2.4.1 2022-07-07 [1] CRAN (R 4.2.2)
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htmltools 0.5.3 2022-07-18 [1] CRAN (R 4.2.1)
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htmlwidgets 1.5.4 2021-09-08 [1] CRAN (R 4.2.1)
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httpuv 1.6.6 2022-09-08 [1] CRAN (R 4.2.1)
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httr 1.4.4 2022-08-17 [1] CRAN (R 4.2.1)
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igraph 1.3.5 2022-09-22 [1] CRAN (R 4.2.2)
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interp 1.1-3 2022-07-13 [1] CRAN (R 4.2.2)
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janitor * 2.1.0 2021-01-05 [1] CRAN (R 4.2.2)
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jpeg 0.1-10 2022-11-29 [1] CRAN (R 4.2.2)
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jsonlite 1.8.3 2022-10-21 [1] CRAN (R 4.2.2)
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KernSmooth 2.23-20 2021-05-03 [2] CRAN (R 4.2.2)
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knitr 1.40 2022-08-24 [1] CRAN (R 4.2.1)
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later 1.3.0 2021-08-18 [1] CRAN (R 4.2.1)
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lattice 0.20-45 2021-09-22 [2] CRAN (R 4.2.2)
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latticeExtra 0.6-30 2022-07-04 [1] CRAN (R 4.2.2)
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lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.2.2)
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lmom 2.9 2022-05-29 [1] CRAN (R 4.2.0)
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lubridate 1.9.0 2022-11-06 [1] CRAN (R 4.2.2)
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magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.1)
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maps 3.4.1 2022-10-30 [1] CRAN (R 4.2.2)
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MASS 7.3-58.1 2022-08-03 [2] CRAN (R 4.2.2)
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Matrix 1.5-3 2022-11-11 [1] CRAN (R 4.2.2)
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memoise 2.0.1 2021-11-26 [1] CRAN (R 4.2.1)
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mime 0.12 2021-09-28 [1] CRAN (R 4.2.0)
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miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.2.1)
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modelr 0.1.10 2022-11-11 [1] CRAN (R 4.2.2)
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munsell 0.5.0 2018-06-12 [1] CRAN (R 4.2.1)
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mvtnorm 1.1-3 2021-10-08 [1] CRAN (R 4.2.0)
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nnet 7.3-18 2022-09-28 [2] CRAN (R 4.2.2)
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patchwork * 1.1.2 2022-08-19 [1] CRAN (R 4.2.1)
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pillar 1.8.1 2022-08-19 [1] CRAN (R 4.2.1)
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pkgbuild 1.3.1 2021-12-20 [1] CRAN (R 4.2.1)
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pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.1)
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pkgload 1.3.1 2022-10-28 [1] CRAN (R 4.2.1)
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png 0.1-8 2022-11-29 [1] CRAN (R 4.2.2)
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prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.2.1)
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processx 3.8.0 2022-10-26 [1] CRAN (R 4.2.2)
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profvis 0.3.7 2020-11-02 [1] CRAN (R 4.2.1)
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proj4 1.0-12 2022-11-30 [1] CRAN (R 4.2.2)
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promises 1.2.0.1 2021-02-11 [1] CRAN (R 4.2.1)
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prompt 1.0.1 2021-03-12 [1] CRAN (R 4.2.1)
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proxy 0.4-27 2022-06-09 [1] CRAN (R 4.2.2)
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ps 1.7.2 2022-10-26 [1] CRAN (R 4.2.2)
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purrr * 0.3.5 2022-10-06 [1] CRAN (R 4.2.2)
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R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.1)
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RColorBrewer 1.1-3 2022-04-03 [1] CRAN (R 4.2.0)
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Rcpp 1.0.9 2022-07-08 [1] CRAN (R 4.2.1)
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readr * 2.1.3 2022-10-01 [1] CRAN (R 4.2.2)
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readxl 1.4.1 2022-08-17 [1] CRAN (R 4.2.1)
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remotes 2.4.2 2021-11-30 [1] CRAN (R 4.2.1)
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reprex 2.0.2 2022-08-17 [1] CRAN (R 4.2.1)
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rlang 1.0.6 2022-09-24 [1] CRAN (R 4.2.2)
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rmarkdown 2.18 2022-11-09 [1] CRAN (R 4.2.2)
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rootSolve 1.8.2.3 2021-09-29 [1] CRAN (R 4.2.0)
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rpart 4.1.19 2022-10-21 [2] CRAN (R 4.2.2)
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rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.1)
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Rttf2pt1 1.3.11 2022-10-08 [1] CRAN (R 4.2.1)
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rvest 1.0.3 2022-08-19 [1] CRAN (R 4.2.1)
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scales 1.2.1 2022-08-20 [1] CRAN (R 4.2.1)
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sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.1)
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shiny 1.7.3 2022-10-25 [1] CRAN (R 4.2.2)
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snakecase 0.11.0 2019-05-25 [1] CRAN (R 4.2.2)
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stringi 1.7.8 2022-07-11 [1] CRAN (R 4.2.1)
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stringr * 1.4.1 2022-08-20 [1] CRAN (R 4.2.1)
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survival 3.4-0 2022-08-09 [2] CRAN (R 4.2.2)
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systemfonts 1.0.4 2022-02-11 [1] CRAN (R 4.2.1)
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tarchetypes * 0.7.2 2022-10-31 [1] CRAN (R 4.2.2)
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targets * 0.14.0 2022-11-01 [1] CRAN (R 4.2.2)
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tibble * 3.1.8 2022-07-22 [1] CRAN (R 4.2.1)
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tidylog * 1.0.2 2020-07-03 [1] CRAN (R 4.2.2)
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tidyr * 1.2.1 2022-09-08 [1] CRAN (R 4.2.1)
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tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.2.2)
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tidyverse * 1.3.2 2022-07-18 [1] CRAN (R 4.2.1)
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timechange 0.1.1 2022-11-04 [1] CRAN (R 4.2.2)
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tzdb 0.3.0 2022-03-28 [1] CRAN (R 4.2.1)
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urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.2.1)
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usethis 2.1.6 2022-05-25 [1] CRAN (R 4.2.1)
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utf8 1.2.2 2021-07-24 [1] CRAN (R 4.2.1)
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vctrs 0.5.0 2022-10-22 [1] CRAN (R 4.2.2)
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withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.1)
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xfun 0.34 2022-10-18 [1] CRAN (R 4.2.2)
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xml2 1.3.3 2021-11-30 [1] CRAN (R 4.2.1)
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xtable 1.8-4 2019-04-21 [1] CRAN (R 4.2.1)
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yaml 2.3.6 2022-10-18 [1] CRAN (R 4.2.1)
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[1] C:/Users/tklebel/AppData/Local/R/win-library/4.2
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[2] C:/Program Files/R/R-4.2.2/library
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────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
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```
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‎RPT-survey-analysis.Rproj

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Version: 1.0
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RestoreWorkspace: Default
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SaveWorkspace: Default
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AlwaysSaveHistory: Default
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EnableCodeIndexing: Yes
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UseSpacesForTab: Yes
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NumSpacesForTab: 2
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Encoding: UTF-8
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RnwWeave: Sweave
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LaTeX: pdfLaTeX
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AutoAppendNewline: Yes
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StripTrailingWhitespace: Yes

‎_targets.R

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library(targets)
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library(tarchetypes)
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source("R/functions.R")
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source("R/helpers.R")
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options(tidyverse.quiet = TRUE)
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# ggchicklet is not available from CRAN
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# install.packages("ggchicklet", repos = "https://cinc.rud.is")
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tar_option_set(packages = c("scales", "tidyverse", "ggchicklet", "hrbrthemes",
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"janitor"))
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owner <- FALSE # set this to FALSE if you are not Thomas Klebel
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if (owner) {
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# full pipeline for original data
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list(
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tar_target(
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raw_data_file,
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"data/raw/results-survey.csv",
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format = "file"
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),
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tar_target(
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recoded_disciplines_file,
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"data/processed/disciplines_lookup.xlsx",
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format = "file"
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),
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tar_target(
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wb_file,
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"data/external/world_bank_country_classification.xlsx",
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format = "file"
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),
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tar_target(
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label_file,
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"data/processed/labels_expanded.csv",
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format = "file"
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),
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tar_target(
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var_overview,
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create_var_overview(raw_data_file)
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),
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tar_target(
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raw_data,
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read_csv(raw_data_file, col_names = FALSE, skip = 1)
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),
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tar_target(
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expanded_labels,
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read_csv(label_file, col_types = "cc")
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),
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tar_target(
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recoded_disciplines,
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readxl::read_excel(recoded_disciplines_file, na = "NA")
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),
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tar_target(
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wb_countries,
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read_clean_wb_countries(wb_file)
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),
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tar_target(
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clean_data,
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clean_raw_data(raw_data, wb_countries) %>%
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merge_disciplines(recoded_disciplines)
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),
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tar_target(
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shareable_data,
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clean_data %>%
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select(-X12, -X16, -X89) # remove country and institution information
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),
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tar_target(
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share_data,
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write_csv(shareable_data, "data/processed/shareable_data.csv")
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),
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tar_render(demographics, "analysis-notebooks/01-demography.Rmd"),
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tar_render(institutional_context, "analysis-notebooks/02-institutional-context.Rmd"),
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tar_render(attitudes, "analysis-notebooks/03-attitudes-towards-promotion-criteria.Rmd"),
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tar_render(opinion_vs_practice, "analysis-notebooks/04-opinion-vs-practice.Rmd"),
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tar_render(research_vs_policy, "analysis-notebooks/05-research-vs-policies.Rmd"))
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} else {
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# abbreviated target pipeline for publicly shared data
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list(
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tar_target(
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survey_file,
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"data/processed/shareable_data.csv",
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format = "file"
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),
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tar_target(
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shareable_data,
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read_csv(survey_file)
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),
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tar_target(
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var_overview_file,
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"data/processed/var_overview.csv",
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format = "file"
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),
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tar_target(
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var_overview,
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read_csv(var_overview_file, col_types = "cc")
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),
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tar_target(
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label_file,
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"data/processed/labels_expanded.csv",
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format = "file"
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),
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tar_target(
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expanded_labels,
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read_csv(label_file, col_types = "cc")
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),
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tar_render(institutional_context, "analysis-notebooks/02-institutional-context.Rmd"),
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tar_render(attitudes, "analysis-notebooks/03-attitudes-towards-promotion-criteria.Rmd"),
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tar_render(opinion_vs_practice, "analysis-notebooks/04-opinion-vs-practice.Rmd"),
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tar_render(research_vs_policy, "analysis-notebooks/05-research-vs-policies.Rmd")
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)
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}
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