--- title: "Overview" author: - "Matthias Grenié" - "Hugo Gruson" date: "2020-03-05" output: rmarkdown::html_vignette vignette: > %\VignetteIndexEntry{Overview} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} --- ## Query Journal Data **NOTE:** SHERPA/RoMEO data is released under the [Creative Commons Attribution-NonCommercial-ShareAlike 2.5 (CC BY-NC-SA 2.5) license](https://creativecommons.org/licenses/by-nc-sa/2.5/). A suggestion of citation is included in `rromeo` via `citation("rromeo")` The SHERPA/RoMEO database contains information on the archival policies of academic journals and publishers. Some journals let you archive a version of a submitted manuscript or book chapter (= preprint) before it's reviewed, some also let you archive the peer-reviewed but not formatted version (= postprint) and some even let you archive the peer-reviewed **and** formatted version of the manuscript (= pdf or publisher's version). The goal of `rromeo` is to make this database accessible through R. ### Query using ISSN Let's try to access summary data using the ISSN of a journal: ```r library(rromeo) rr_journal_issn("1947-6264") ``` ``` ## title provided_issn issn romeocolour preprint ## 1 A Critical Introduction to Media and Communication Theory 1947-6264 1947-6264 yellow can ## postprint pdf pre_embargo post_embargo pdf_embargo ## 1 restricted restricted 12 months 12 months ``` From this we see that the archival of the preprint is permitted while some restrictions apply for both postprint and pdf version of the manuscript. The restrictions are visible in the `*_embargo` field: the authors have to wait 12 months after publication before archiving postprint and formatted manuscript. **Nota Bene**: the `rr_journal_issn()` function can use either the paper edition ISSN of the journal or the ISSN of the electronic version of the journal (e-ISSN or ESSN) which may differ ### Query by Journal Title We can also search journal by names using `rr_journal_find()` the first argument `name` is the string to look for and the second argument `qtype` defines the way to match. If we want to look at journals that have the word `Biostatistics` in their title we can use the following code: ```r rr_journal_find("Biostatistics", qtype = "contains") ``` ``` ## 17 journals match your query terms. ``` ``` ## Only titles and ISSNs of journals returned. Get more information using `rr_journal_name()` ``` ``` ## title provided_issn issn ## 1 American Journal of Biostatistics 1948-9889 ## 2 Annals of Biometrics and Biostatistics 2374-0116 ## 4 Austin Biometrics and Biostatistics 2378-9840 ## 5 Biometrics & biostatistics international journal ## 6 Biostatistics 1465-4644 ## 7 Biostatistics -Basel- 1527-2486 ## 8 Biostatistics, bioinformatics and biomathematics 0976-1594 ## 9 Edorium Journal of Biostatistics ## 10 Enliven: Biostatistics and Metrics ## 11 Epidemiology Biostatistics and Public Health 2282-2305 ## 12 International Journal of Biostatistics 1557-4679 ## 13 International journal of clinical biostatistics and biometrics ## 14 Journal of Biometrics and Biostatistics 2155-6180 ## 15 Journal of epidemiology and biostatistics 1359-5229 ## 16 JP journal of biostatistics 0973-5143 ## 17 Monographs in Epidemiology and Biostatistics 0740-0845 ``` `rr_journal_find()` will only return the list of titles and ISSN. You can then use this list to select the exact journal you are looking for (in this case, it is recommended to use the ISSN). Alternatively, you may want to get data for all those journals. To achieve this, you need to use the function `rr_journal_name()` which uses a similar syntax to `rr_journal_find()`: ```r res <- rr_journal_name("Biostatistics", qtype = "contains") ``` ``` ## 17 journals match your query terms. ``` ``` ## Recursively fetching data from each journal. This may take some time... ``` ```r tail(res, 3) ``` ``` ## title provided_issn issn romeocolour preprint postprint ## 14 Journal of epidemiology and biostatistics 1359-5229 1359-5229 ## 15 JP journal of biostatistics 0973-5143 0973-5143 ## 16 Monographs in Epidemiology and Biostatistics 0740-0845 0740-0845 yellow can restricted ## pdf pre_embargo post_embargo pdf_embargo ## 14 ## 15 ## 16 unclear 12 months ``` The query may run for longer but it gives you all the information on all returned journals. You can also use other type of name matching with other options for `qtype`, for example when `qtype = "starts"` the query string have to begin the title of the journal: ```r rr_journal_name("Biostatistics", qtype = "starts") ``` ``` ## 3 journals match your query terms. ``` ``` ## Recursively fetching data from each journal. This may take some time... ``` ``` ## title provided_issn issn romeocolour preprint ## 1 Biostatistics 1465-4644 1465-4644 green can ## 2 Biostatistics -Basel- 1527-2486 1527-2486 ## 3 Biostatistics, bioinformatics and biomathematics 0976-1594 0976-1594 ## postprint pdf pre_embargo post_embargo pdf_embargo ## 1 can cannot ## 2 ## 3 ``` While using `qtype = exact` the title of the journal should match exactly the used string: ```r rr_journal_name("Biostatistics", qtype = "exact") ``` ``` ## title provided_issn issn romeocolour preprint postprint pdf pre_embargo post_embargo ## 1 Biostatistics 1465-4644 green can can cannot ## pdf_embargo ## 1 ``` ## Query Publisher Data Not only can `rromeo` query journals archival policies but it can do the same for publishers. Indeed the SHERPA/RoMEO database contains much information on publishers' policies, with many ways to retrieve the information. ### Query by Publisher's Name With `rr_publisher_name()` you can query publishers' information using the name of the publishers. The first argument `name` is the string to match publisher's names the second argument `qtype` gives the type of matching: ```r rr_publisher_name(name = "Oxford", qtype = "all") ``` ``` ## romeoid publisher alias romeocolour preprint ## 1 2632 Oxford Brookes University blue cannot ## 2 1892 Oxford Centre for Hebrew and Jewish Studies blue unclear ## 3 986 Oxford University Anthropological Society green can ## 4 55 Oxford University Press OUP yellow can ## 5 2072 University of Oxford, Oxford Uehiro Centre for Practical Ethics green can ## postprint pdf ## 1 can can ## 2 can cannot ## 3 can can ## 4 restricted unclear ## 5 can can ``` When `qtype = "all"` the publishers' names should contain all the words, in any order, included in provided string: ```r rr_publisher_name(name = "Oxford University", qtype = "all") ``` ``` ## romeoid publisher alias romeocolour preprint ## 1 2632 Oxford Brookes University blue cannot ## 2 986 Oxford University Anthropological Society green can ## 3 55 Oxford University Press OUP yellow can ## 4 2072 University of Oxford, Oxford Uehiro Centre for Practical Ethics green can ## postprint pdf ## 1 can can ## 2 can can ## 3 restricted unclear ## 4 can can ``` While when `qtype = "exact"` the publishers' names should contain all the words in the same order as provided in the string: ```r rr_publisher_name(name = "Oxford University", qtype = "exact") ``` ``` ## romeoid publisher alias romeocolour preprint postprint pdf ## 1 986 Oxford University Anthropological Society green can can can ## 2 55 Oxford University Press OUP yellow can restricted unclear ``` Finally, when `qtype = "any"` publishers' names can contain any words of the provided string. ### Query by RoMEO's ID The first column of publishers' policies data frame returned by `rromeo` is named `romeoid` it corresponds to the identifier used by SHERPA/RoMEO to identify publishers in a unique way: ```r rr_publisher_id(id = 55) ``` ``` ## romeoid publisher alias romeocolour preprint postprint pdf ## 1 55 Oxford University Press OUP yellow can restricted unclear ``` ### Query by Country or Region You can also query publishers information based on the country they are in using their two-letters ISO codes (see `?rr_publisher_country` for more information): ```r rr_publisher_country(country = "IR") ``` ``` ## romeoid publisher alias ## 1 1936 Acta Advances in Agricultural Sciences ## 2 2786 Avicenna Journals Advancements in Science ## 3 1556 Azad University, Mahlkesi Branch, Mechanical Engineering Department ## 4 2741 Geodynamics Research International Bulletin ## 5 2159 International Journal of Management, Accounting and Economics ## 6 1823 Islamic Azad University, Najafabad Branch ## 7 1745 Islamic Azad University, Shahreza Branch ## 8 1726 Islamic Press ## 9 1742 Jahan Elm Institute of Higher Education ## 10 1414 Kerman University of Medical Sciences ## 11 1867 Oboor Publishing Group ## 12 3078 Shahid Sadoughi University of Medical Sciences ## 13 2084 Shefa Neuroscience Research Center ## 14 1362 Shiraz University ## 15 1753 Society of Diabetic Nephropathy Prevention ## 16 2922 Tabriz University of Medical Sciences ## 17 1208 Tehran University of Medical Sciences ## 18 2845 University of Maragheh, Department of Mathematics ## romeocolour preprint postprint pdf ## 1 blue cannot can can ## 2 green can can can ## 3 blue cannot cannot can ## 4 blue cannot cannot can ## 5 green can can can ## 6 blue cannot can can ## 7 blue unclear can can ## 8 blue cannot cannot can ## 9 blue unclear can can ## 10 blue cannot can can ## 11 green can can can ## 12 yellow can restricted restricted ## 13 green can can can ## 14 blue cannot can can ## 15 blue cannot cannot can ## 16 blue cannot can can ## 17 green can can can ## 18 green can can can ``` It is also possible to query publisher's information on a specific region or continent using `rr_publisher_continent()` (see the help page for the list of available regions): ```r rr_publisher_continent(continent = "Australasia") ``` ``` ## romeoid publisher ## 1 1514 ANU Press ## 2 1853 ANZAMEMS ## 3 959 ARRB Group ## 4 736 Association of Occupational Science ## 5 222 Auckland University of Technology, School of Communication Studies, Pacific Media Centre ## 6 2343 Australasian Association for Information Systems ## 7 1358 Australasian Medical Journal ## 8 220 Australasian Society for Computers in Learning in Tertiary Education ## 9 98 Australian Academic Press ## 10 518 Australian Accoustical Society ## 11 638 Australian Clearinghouse for Youth Studies ## 12 97 Australian Computer Society Inc ## 13 1813 Australian International Academic Centre ## 14 255 Australian Library and Information Association ## 15 248 Australian Mathematical Society ## 16 151 Australian Physiotherapy Association ## 17 161 Australian Psychological Society ## 18 383 Australian Rock Art Research Association ## 19 290 Australian Society of Anaesthetists ## 20 2420 Bareknuckle Books ## 21 150 College of Intensive Care Medicine of Australia and New Zealand ## 22 160 CSIRO Publishing ## 23 553 e-Content Management ## 24 550 Early Childhood Australia ## 25 2501 Edith Cowan University ## 26 2453 EMAJ ## 27 571 Field Naturalists Club of Victoria ## 28 626 Griffith University, Griffith Law School, Socio-Legal Research Centre ## 29 1928 Infinity Press ## 30 1026 Institute of Foresters of Australia ## 31 557 International Association for Statistics Education ## 32 3226 LexisNexis Australia ## 33 163 Libertas Academica ## 34 745 Macquarie University, Department of International Communication ## 35 284 Magnolia Press ## 36 1397 Mathematics Education Research Group of Australasia ## 37 1310 Melbourne University, Law Review Association ## 38 665 Monash University ePress ## 39 2471 New Zealand Ecological Society ## 40 2472 New Zealand Institute of Forestry ## 41 598 New Zealand Medical Association ## 42 623 New Zealand Nurses Organisation ## 43 666 New Zealand Society of Animal Production ## 44 2134 Outdoor Council of Australia ## 45 670 Python Papers ## 46 2755 Queensland University of Technology ## 47 2385 Queensland University of Technology, Faculty of Law ## 48 581 RMIT Publishing ## 49 1767 Royal New Zealand College of General Practitioners ## 50 264 Royal Society of New Zealand ## 51 1329 Royal Society of Victoria ## 52 1432 SETScholars ## 53 3041 Studies in Material Thinking ## 54 3016 Sydney Law School ## 55 164 Thomson Reuters ## 56 1946 UTS ePRESS ## 57 2532 Western Australian Institutes for Educational Research ## 58 380 World Institute for Engineering and Technology Education ## alias romeocolour preprint ## 1 green can ## 2 Australian and New Zealand Association for Medieval and Early Modern Studies green can ## 3 blue cannot ## 4 white cannot ## 5 blue cannot ## 6 AAIS green can ## 7 green can ## 8 ascilite green can ## 9 blue cannot ## 10 white cannot ## 11 green can ## 12 green can ## 13 AIAC green can ## 14 blue unclear ## 15 yellow can ## 16 blue cannot ## 17 white unclear ## 18 white cannot ## 19 white cannot ## 20 green can ## 21 white cannot ## 22 green can ## 23 green can ## 24 white unclear ## 25 blue cannot ## 26 green can ## 27 blue unclear ## 28 blue cannot ## 29 green can ## 30 white cannot ## 31 IASE blue unclear ## 32 blue unclear ## 33 green can ## 34 white unclear ## 35 white cannot ## 36 blue unclear ## 37 blue cannot ## 38 yellow can ## 39 yellow can ## 40 yellow can ## 41 white cannot ## 42 blue cannot ## 43 white unclear ## 44 blue unclear ## 45 blue unclear ## 46 green can ## 47 green can ## 48 green can ## 49 blue cannot ## 50 yellow can ## 51 white cannot ## 52 green can ## 53 blue unclear ## 54 blue cannot ## 55 Professional blue cannot ## 56 green can ## 57 blue cannot ## 58 WIETE white cannot ## postprint pdf ## 1 can ## 2 can can ## 3 can cannot ## 4 restricted cannot ## 5 can can ## 6 can can ## 7 can ## 8 can can ## 9 can cannot ## 10 cannot ## 11 can restricted ## 12 can ## 13 can can ## 14 can ## 15 cannot restricted ## 16 cannot can ## 17 restricted cannot ## 18 restricted ## 19 restricted ## 20 can can ## 21 cannot cannot ## 22 can cannot ## 23 can cannot ## 24 unclear ## 25 can can ## 26 can can ## 27 can can ## 28 can can ## 29 can can ## 30 restricted restricted ## 31 can ## 32 can restricted ## 33 can can ## 34 unclear ## 35 cannot cannot ## 36 cannot can ## 37 can can ## 38 cannot ## 39 restricted restricted ## 40 restricted restricted ## 41 cannot restricted ## 42 cannot can ## 43 restricted ## 44 cannot can ## 45 can ## 46 can can ## 47 can can ## 48 can cannot ## 49 can can ## 50 restricted cannot ## 51 cannot cannot ## 52 can can ## 53 cannot can ## 54 cannot can ## 55 can ## 56 can can ## 57 can can ## 58 cannot ``` ### Query by RoMEO colour RoMEO assigns a colour depending on the different policies of publishers. | RoMEO colour | Archiving policy | |:-------------|:--------------------------------------------------------| | `green` | can archive preprint, postprint and publisher's version | | `blue` | can archive postprint **or** publisher's version | | `yellow` | can archive preprint | | `white` | archiving not formally supported | (Table taken from ) You can query journals using this classification with the function `rr_romeo_colour()`: ```r rr_romeo_colour(romeo_colour = "green") ``` In this example vignette we do not run the query because it can run for quite long as it returns the policies of all publishers of the given colour (you can see the numbers of publishers in each category in the following web page ). ## Setting up an API key SHERPA/RoMEO lets you make 500 queries per day per IP address for free. If you get past this limit you will get the following error: ``` You have exceeded the free use limit of 500 requests per day. To go beyond this limit you should register for a free API key available at http://www.sherpa.ac.uk/romeo/apiregistry.php ``` We encourage you to register for a **free** API key at the above-mentioned address. To provide your API key to `rromeo` you can: 1. provide it as a character string as the `key` arguments of `rromeo` functions as `rr_*(..., key = "my_key_as_a_string")`, we **do not recommend** this method as your API key will be available from your history; 1. you can define the variable `SHERPAROMEO_KEY` in an `.Renviron` file in your working directory, the file should contain the following line `SHERPAROMEO_KEY=my_key_without_quotes`; 1. you can also define the variable `SHERPAROMEO_KEY` in an `.Rprofile` file in your working directory, the file should contain the following line `SHERPAROMEO_KEY="my_key_with_quotes"`. ## Visualization Example `rromeo` can be quite useful in bibliometric studies to report on archival policies. For example, we can now have a quick visual overview of the policies of journals in a given field from the results obtained in a query: ```r library(ggplot2) theme_set(theme_minimal()) stacked_res <- stack(res[, 4:6]) ggplot(stacked_res, aes(x = ind, fill = values)) + geom_bar() + labs(x = NULL, subtitle = "Archiving Policies of Journals with 'Biostatistics' in their title") ``` ![plot of chunk bar_graph](bar_graph-1.png) ```r ggplot(res, aes(x = "a", fill = romeocolour)) + geom_bar() + coord_polar("y") + labs(x = NULL, subtitle = "RoMEO colours of Journals with 'Biostatistics' in their title") ``` ![plot of chunk pie_chart](pie_chart-1.png)