## ----include=FALSE, echo=FALSE, results='hide', eval=TRUE--------------------- # Declarations base_epm_ver <- '3.0' stab_epm_ver <- '3.1.3' this_epm_ver <- '3.1.3' # pre-load libs and data library(easyPubMed) data("epm_samples") # Collect custom f(x) rebuild_uili <- epm_samples$fx$rebuild_uili rebuild_li <- epm_samples$fx$rebuild_li rebuild_df <- epm_samples$fx$rebuild_df fabricate_epm_obj <- epm_samples$fx$fabricate_epm_obj slice_epm_obj_to_special <- epm_samples$fx$slice_epm_obj_to_special # Collect data blca_2018 <- epm_samples$bladder_cancer_2018 blca_40y <- epm_samples$bladder_cancer_40y # Fabricate objects (vignette version) epm <- fabricate_epm_obj(blca_2018$demo_data_03) epm_xmpl_01 <- slice_epm_obj_to_special(epm, mode = 1) epm_xmpl_02 <- slice_epm_obj_to_special(epm, mode = 2) epm_xmpl_03 <- fabricate_epm_obj(blca_2018$demo_data_04) epm_xmpl_04 <- fabricate_epm_obj(blca_40y$demo_data_01) epm_xmpl_06 <- fabricate_epm_obj(blca_2018$demo_data_02) epm_xmpl_07 <- fabricate_epm_obj(blca_2018$demo_data_05) ## ----inst__0001, include = TRUE, echo = TRUE, eval = FALSE-------------------- # install.packages("easyPubMed") ## ----inst___04, include = TRUE, echo = TRUE, eval = FALSE--------------------- # devtools::install_github("dami82/easyPubMed") ## ----eval=FALSE, include=TRUE, echo=TRUE-------------------------------------- # # Load library # library(easyPubMed) # # # Define Query String # my_query <- '"bladder cancer"[Ti] AND "2018"[PDAT]' # # # Submit the Query # epm <- epm_query(my_query) # # # Retrieve Records (xml format) # epm <- epm_fetch(epm, format = 'xml') # # # Extract Information # epm <- epm_parse(epm) # # # All results are stored in an easyPubMed object. # epm ## ----echo=FALSE, include=TRUE, results='markup', eval=TRUE-------------------- epm ## ----include=TRUE, results='markup', eval=TRUE, echo=TRUE--------------------- job_meta <- get_epm_meta(x = epm) head(job_meta) ## ----results='markup'--------------------------------------------------------- raw_records <- get_epm_raw(epm) # elements are named after the corresponding PMIDs head(names(raw_records)) # elements include raw PubMed records first_record <- raw_records[[1]] # Show excerpt (from record #1) cat(substr(first_record, 1, 1200)) ## ----results='markup'--------------------------------------------------------- proc_data <- get_epm_data(epm) # show an excerpt (first 6 records, selected columns) slctd_fields <- c('pmid', 'doi', 'jabbrv', 'year', 'month', 'day') head(proc_data[, slctd_fields]) ## ----------------------------------------------------------------------------- # Get PMIDs all_pmids <- get_epm_uilist(epm) # Show excerpt head(all_pmids) ## ----results='markup', message=FALSE, warning=FALSE--------------------------- # Article Title (including new-line chars) my_title <- "Role of gemcitabine and cisplatin as neoadjuvant chemotherapy in muscle invasive bladder cancer: Experience over the last decade." # Unpolished title string cat(my_title) # Clean the title my_title <- gsub('[[:space:]]+', ' ', my_title) # Clean title string cat(my_title) ## ----results='hide', message=FALSE, warning=FALSE, eval=FALSE, include=TRUE, echo=TRUE---- # # Query and fetch # epm_xmpl_01 <- epm_query_by_fulltitle(fulltitle = my_title) # epm_xmpl_01 <- epm_fetch(epm_xmpl_01) # epm_xmpl_01 ## ----results='markup', message=FALSE, warning=FALSE, eval=TRUE, include=TRUE, echo=FALSE---- epm_xmpl_01 ## ----results='markup', message=FALSE, warning=FALSE, eval=FALSE, include=TRUE, echo=TRUE---- # my_pmids <- c('31572460', '31511849', '31411998') # # epm_xmpl_02 <- epm_query_by_pmid(pmids = my_pmids) # epm_xmpl_02 <- epm_fetch(epm_xmpl_02) # epm_xmpl_02 ## ----results='markup', message=FALSE, warning=FALSE, eval=TRUE, include=TRUE, echo=FALSE---- epm_xmpl_02 ## ----results='markup', message=FALSE, warning=FALSE, eval=FALSE, include=TRUE, echo=TRUE---- # # Define Query String # my_query <- '"bladder cancer"[Ti] AND "2018"[PDAT]' # # # Submit the Query # epm_xmpl_03 <- epm_query(my_query) # # # Retrieve Records (request 'medline' format!) # epm_xmpl_03 <- epm_fetch(epm_xmpl_03, format = 'medline') # # # Get records # xmpl_03_raw <- get_epm_raw(epm_xmpl_03) # # # Elements are named after the corresponding PMIDs # head(names(xmpl_03_raw)) ## ----results='markup', message=FALSE, warning=FALSE, eval=TRUE, include=TRUE, echo=FALSE---- xmpl_03_raw <- get_epm_raw(epm_xmpl_03) head(names(xmpl_03_raw)) ## ----results='markup', message=FALSE, warning=FALSE--------------------------- # Elements include raw PubMed records first_record <- xmpl_03_raw[[1]] # Show an Excerpt (record n. 12, first 18 lines) cat(head(first_record, n=20), sep = '\n') ## ----eval=FALSE, echo=TRUE, include=TRUE-------------------------------------- # # Define Query String # blca_query <- '"bladder cancer"[Ti] AND ("1980"[PDAT]:"2020"[PDAT])' # # # Submit the Query # epm_xmpl_04 <- epm_query(blca_query) # # # Retrieve Records (medline format) # epm_xmpl_04 <- epm_fetch(epm_xmpl_04) # # # Parse all records # epm_xmpl_04 <- epm_parse(epm_xmpl_04) # # # Show Object # epm_xmpl_04 ## ----eval=TRUE, echo=FALSE, include=TRUE, results='markup'-------------------- # Show Object epm_xmpl_04 ## ----include=TRUE, echo=TRUE, eval=FALSE-------------------------------------- # # Define Query String # my_query <- '"bladder cancer"[Ti] AND "2018"[PDAT]' # # # Submit the Query # epm_xmpl_05 <- epm_query(my_query) # # # Retrieve Records # epm_xmpl_05 <- epm_fetch(epm_xmpl_05, write_to_file = TRUE) # # # Check if file exists # dir(pattern = '^easypubmed') ## ----echo=FALSE, include=TRUE, results='markup', eval=TRUE-------------------- print('easypubmed_job_202311201513_batch_01.txt') ## ----eval=FALSE, echo=TRUE, include=TRUE-------------------------------------- # # Import XML records from saved file # epm_xmpl_06 <- epm_import_xml(x = 'easypubmed_job_202311201513_batch_01.txt') # # # Show Object # epm_xmpl_06 ## ----eval=TRUE, echo=FALSE, include=TRUE, results='markup'-------------------- epm_xmpl_06 ## ----eval=FALSE, echo=TRUE, include=TRUE-------------------------------------- # my_query <- '"bladder cancer"[Ti] AND "2018"[PDAT]' # # # Submit the Query # epm_xmpl_07 <- epm_query(my_query) # # # Retrieve Records # epm_xmpl_07 <- epm_fetch(epm_xmpl_07) # # # Parse (custom params) # epm_xmpl_07 <- epm_parse(epm_xmpl_07, # max_authors = 3, compact_output = TRUE, # max_references = 5, ref_id_type = 'pmid') # # # Request parsed data # epm_data <- get_epm_data(epm_xmpl_07) # # # Columns of interest # cols_of_int <- c('pmid', 'doi', 'authors', 'jabbrv', 'year', 'references') # # # Show an excerpt # head(epm_data[, cols_of_int]) ## ----eval=TRUE, echo=FALSE, include=TRUE, results='markup'-------------------- epm_data <- get_epm_data(epm_xmpl_07) # Columns of interest cols_of_int <- c('pmid', 'doi', 'authors', 'jabbrv', 'year', 'references') # Show an excerpt head(epm_data[, cols_of_int]) ## ----message = FALSE, warning = FALSE, eval=TRUE------------------------------ sessionInfo()