pmxml into a dataframe?

[bbanzai88]

Hi,

Fantastic package!! I ran the following code:

PMIDs<-unique(pm_subset$pubmed_id)

pmxml <- fetch_pubmed_data_by_PMID(PMIDs)

How do I turn pmxml into a dataframe?

Thank you!!

tom

[rempsyc]

@bbanzai88 the solution is to use the table_articles_byAuth() function, as demonstrated in the reprex below:

library(easyPubMed)

d.fls <- batch_pubmed_download(pubmed_query_string = "2019[yr] AND Basic and clinical neuroscience [Journal]")
#> [1] "PubMed data batch 1 / 1 downloaded..."

my_df <- table_articles_byAuth(d.fls)
#> Processing PubMed data .................................................. done!

str(my_df)
#> 'data.frame':    337 obs. of  14 variables:
#>  $ pmid     : chr  "37323961" "37323961" "37323961" "37313020" ...
#>  $ doi      : chr  "10.32598/bcn.2021.3341.1" "10.32598/bcn.2021.3341.1" "10.32598/bcn.2021.3341.1" "10.32598/bcn.2021.1422.1" ...
#>  $ title    : chr  "Evaluation of the Relationship Between Celiac Disease and Refractory Epilepsy in Patients Referring to Imam Kho"| __truncated__ "Evaluation of the Relationship Between Celiac Disease and Refractory Epilepsy in Patients Referring to Imam Kho"| __truncated__ "Evaluation of the Relationship Between Celiac Disease and Refractory Epilepsy in Patients Referring to Imam Kho"| __truncated__ "Chondroitinase ABC Administration in Locomotion Recovery After Spinal Cord Injury: A Systematic Review and Meta-analysis." ...
#>  $ abstract : chr  "Celiac disease can be associated with other diseases, including neurological disorders. In this study, the rela"| __truncated__ "Celiac disease can be associated with other diseases, including neurological disorders. In this study, the rela"| __truncated__ "Celiac disease can be associated with other diseases, including neurological disorders. In this study, the rela"| __truncated__ "The present systematic review and meta-analysis aims to conduct a comprehensive and complete search of electron"| __truncated__ ...
#>  $ year     : chr  "2023" "2023" "2023" "2023" ...
#>  $ month    : chr  "06" "06" "06" "06" ...
#>  $ day      : chr  "17" "17" "17" "15" ...
#>  $ jabbrv   : chr  "Basic Clin Neurosci" "Basic Clin Neurosci" "Basic Clin Neurosci" "Basic Clin Neurosci" ...
#>  $ journal  : chr  "Basic and clinical neuroscience" "Basic and clinical neuroscience" "Basic and clinical neuroscience" "Basic and clinical neuroscience" ...
#>  $ keywords : chr  "Celiac disease; Epilepsy; Refractory; Transglutaminase" "Celiac disease; Epilepsy; Refractory; Transglutaminase" "Celiac disease; Epilepsy; Refractory; Transglutaminase" "Animal; Chondroitinase ABC; Locomotion; Spinal cord injuries" ...
#>  $ lastname : chr  "Mollazadeh" "Nazarbaghi" "Pashaei" "Yousefifard" ...
#>  $ firstname: chr  "Hanieh" "Surena" "Mohammad Reza" "Mahmoud" ...
#>  $ address  : chr  "Patient Safety Research Center, Clinical Research Institute, Urmia University of Medical Sciences, Urmia, Iran" "Department of Internal Medicine, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran" "Department of Internal Medicine Gastroenterology and Hepatology Section, Urmia University of Medical Sciences, Urmia, Iran" "Department of Physiology, Researcher at Physiology Research Center, School of Medicine, Iran University of Medi"| __truncated__ ...
#>  $ email    : chr  NA NA NA NA ...

^{Created on 2023-06-18 with reprex v2.0.2}

Please close this issue if this solves your problem. Thanks.