dami82
commented
5 years ago Since version 2.11, easyPubMed does not use the XML library for processing PubMed records anymore. Therefore, functions such as fetch_pubmed_data() and others return character-class objects (strings which include XML tags) instead of XMLInternalDocument-class objects. This is clearly stated in the vignette that comes with the package (try: vignette("getting_started_with_easyPubMed")). If you absolutely need to get an XMLInternalDocument object, you can roll back to version 2.9 (available here, on GitHub, aka "dev version of the package"), or you can use XML or a similar library to cast the XML string returned by fetch_pubmed_data().
hi when I try the codes of "Retrieving and Processing PubMed Records using easyPubMed": >my_abstracts_xml <- fetch_pubmed_data(my_entrez_id)
sessionInfo() R version 3.5.2 (2018-12-20) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
locale: [1] LC_COLLATE=Chinese (Simplified)_China.936 [2] LC_CTYPE=Chinese (Simplified)_China.936
[3] LC_MONETARY=Chinese (Simplified)_China.936 [4] LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.936
attached base packages: [1] stats graphics grDevices utils
[5] datasets methods base
other attached packages: [1] XML_3.98-1.19 kableExtra_1.0.1 [3] dplyr_0.7.8 easyPubMed_2.12
loaded via a namespace (and not attached): [1] Rcpp_1.0.0 pillar_1.3.1
[3] compiler_3.5.2 bindr_0.1.1
[5] tools_3.5.2 digest_0.6.18
[7] evaluate_0.12 tibble_2.0.1
[9] viridisLite_0.3.0 pkgconfig_2.0.2
[11] rlang_0.3.1 rstudioapi_0.9.0 [13] yaml_2.2.0 xfun_0.4
[15] bindrcpp_0.2.2 httr_1.4.0
[17] stringr_1.4.0 knitr_1.21
[19] xml2_1.2.0 hms_0.4.2
[21] webshot_0.5.1 tidyselect_0.2.5 [23] glue_1.3.0 R6_2.3.0
[25] rmarkdown_1.11 pacman_0.5.0
[27] readr_1.3.1 purrr_0.3.0
[29] magrittr_1.5 scales_1.0.0
[31] htmltools_0.3.6 assertthat_0.2.0 [33] rvest_0.3.2 colorspace_1.4-0 [35] stringi_1.2.4 munsell_0.5.0
[37] crayon_1.3.4