2017-12-27 412 views
1

我試圖使用tidyr :: separate()將一些免費(假的)文本分隔爲不同的列。如何使用正確的列名將文本分隔爲列

輸入:

structure(list(PathReportWhole = c("SP-37-2784518\nHospital: Random NHS Foundation Trust\nHospital Number: J6044658\nPatient Name: Jargon, Victoria\nDOB: 1943-10-13\nGeneral Practitioner: Dr. Martin, Marche\nDate received: 2009-11-11\nClinical Details: Ongoing antral gastritis despite treatment with PPI,Reflux sx.,High dyshagia OGD - fundic gastritis.,Chronic diarrhoea/colonic biopsies,Currently on steriod for IgG4 disease.,Food bolus obstruction.\n4 specimen. Nature of specimen: Nature of specimen as stated on pot = 'proximal body lesser curve polyps x4 ',Specimen A- Nature of specimen as stated on request form = 'GREATER CURVE ',Nature of specimen as stated on request form = 'Gastric polyp '\nMacroscopic description: 3 specimens collected the largest measuring 3 x 2 x 1 mm and the smallest 2 x 1 x 5 mm\nHistology: Two biopsies consist of small bowel mucosa and are within normal histological limits.\nDiagnosis: Distal transverse colon polyp excision:- tubular adenoma, low grade dysplasia.,Ileo-caecal valve, biopsies:.,Stomach antrum biopsies:- normal mucosa.,- Up to 34 eosinophils per high power field,Stomach, biopsy - Mild chronic inflammation.", 
"SP-50-4495875\nHospital: Random NHS Foundation Trust\nHospital Number: Y6417773\nPatient Name: Powell, Destiny\nDOB: 1946-12-29\nGeneral Practitioner: Dr. al-Safi, Lutfiyya\nDate received: 2008-06-15\nClinical Details: Quadrantic biopsies were taken at.,OGD - only 3cm sliding hiatus.\n7 specimen. Nature of specimen: Nature of specimen as stated on pot = 'RECTAL POLYPS X3 ',Nature of specimen as stated on pot = 'fundus polyps x4 ',Nature of specimen as stated on request form = 'DUODENAL BX ',Nature of specimen as stated on pot = 'Papilloma at 36 cm oesophagus ',a) Nature of specimen as stated on request form = 'D2 bx x 2' ,Nature of specimen as stated on pot = 'Oesophagus 26 cm '\nMacroscopic description: 4 specimens collected the largest measuring 4 x 4 x 4 mm and the smallest 5 x 3 x 1 mm\nHistology: modified giemsa stain.,These are biopsies of gastric mucosa ,There is no evidence of coeliac disease.,The nuclei are hyperchromatic,.,There is no granulomatous inflammation.,The appearances are in keeping with a reactive/chemical gastritis,features including basal layer hyperplasia and reactive nucelar changes with underlying.,These are two biopsies of squamous epithelium within normal limits,fibromuscularisation of the lamina propria and mild chronic inflammation.,These biopsies of columnar mucosa show focal acute inflammation, moderate chronic inflammation.\nDiagnosis: Rectum, polyp biopsy: - Tubular adenoma with mild dysplasia,- Raised intra-epithelial lymphocytes ,Duodenum, biopsies - within normal histological limits.,B GI biopsy - DISTAL OESOPHAGUS X2, MID OESO X3, PROX OESO X2.,Oesophagus, biopsies : - Minimal chronic inflammation,Sigmoid colon, polypectomy: - Tubular adenoma with moderate dysplasia,Oesophagus polyps biopsies:- 2 x papillomas.,Duodenum biopsies:- normal." 
)), .Names = "PathReportWhole", row.names = 1:2, class = "data.frame") 

目前,我使用的分隔符的特徵向量如下:

mywords<-c("Hospital Number","Patient Name:","DOB:","General Practitioner:",+ "Date received:","Clinical Details:","Macroscopic description:","Histology:","Diagnosis:") 

然後是功能如下(在自定義函數中使用,因爲最終我將單獨整理某些列):

Extractor2 <- function(dataframeIn, Column, delim) { 
    Column <- rlang::sym(Column) 
    dataframeIn <- data.frame(dataframeIn) 
    dataframeIn<-dataframeIn %>% tidyr::separate(!!Column, into = delim, 
              sep = paste(delim, collapse = "|")) 
    return(dataframeIn) 
} 

Extractor2(Mypath,"PathReportWhole",mywords) 

輸出:

'data.frame': 2 obs. of 18 variables: 
$ Hospital Number   : chr "SP-37-2784518\nHospital: Random NHS Foundation Trust\n" "SP-50-4495875\nHospital: Random NHS Foundation Trust\n" 
$ Patient Name:   : chr ": J6044658\n" ": Y6417773\n" 
$ DOB:     : chr " Jargon, Victoria\n" " Powell, Destiny\n" 
$ General Practitioner: : chr " 1943-10-13\n" " 1946-12-29\n" 
$ Date received:   : chr " Dr. Martin, Marche\n" " Dr. al-Safi, Lutfiyya\n" 
$ Clinical Details:  : chr " 2009-11-11\n" " 2008-06-15\n" 
$ Macroscopic description:: chr " Ongoing antral gastritis despite treatment with PPI,Reflux sx.,High dyshagia OGD - fundic gastritis.,Chronic "| __truncated__ " Quadrantic biopsies were taken at.,OGD - only 3cm sliding hiatus.\n7 specimen. Nature of specimen: Nature of"| __truncated__ 
$ Histology:    : chr " 3 specimens collected the largest measuring 3 x 2 x 1 mm and the smallest 2 x 1 x 5 mm\n" " 4 specimens collected the largest measuring 4 x 4 x 4 mm and the smallest 5 x 3 x 1 mm\n" 
$ Diagnosis:    : chr " Two biopsies consist of small bowel mucosa and are within normal histological limits.\n" " modified giemsa stain.,These are biopsies of gastric mucosa ,There is no evidence of coeliac disease.,The nuc"| __truncated__ 
$ HospitalNumber   : chr " J6044658\n" " Y6417773\n" 
$ PatientName    : chr " Jargon, Victoria\n" " Powell, Destiny\n" 
$ DOB      : chr " 1943-10-13\n" " 1946-12-29\n" 
$ GeneralPractitioner  : chr " Dr\n Martin, Marche\n" " Dr\n al-Safi, Lutfiyya\n" 
$ Dateofprocedure   : Date, format: "2009-11-11" "2008-06-15" 
$ ClinicalDetails   : chr " Ongoing antral gastritis despite treatment with PPI,Reflux sx\n,High dyshagia OGD - fundic gastritis\n,Chroni"| __truncated__ " Quadrantic biopsies were taken at\n,OGD - only 3cm sliding hiatus\n\n7 specimen\n Nature of specimen: Nature"| __truncated__ 
$ Macroscopicdescription : chr " 3 specimens collected the largest measuring 3 x 2 x 1 mm and the smallest 2 x 1 x 5 mm\n" " 4 specimens collected the largest measuring 4 x 4 x 4 mm and the smallest 5 x 3 x 1 mm\n" 
$ Histology    : chr " Two biopsies consist of small bowel mucosa and are within normal histological limits\n\n" " modified giemsa stain\n,These are biopsies of gastric mucosa ,There is no evidence of coeliac disease\n,The n"| __truncated__ 
$ Diagnosis    : chr " Distal transverse colon polyp excision:- tubular adenoma, low grade dysplasia\n,Ileo-caecal valve, biopsies:\"| __truncated__ " Rectum, polyp biopsy: - Tubular adenoma with mild dysplasia,- Raised intra-epithelial lymphocytes ,Duodenum, "| __truncated__ 
NULL 

問題:

的問題是,列似乎是由一個被移位,使得下Patient Name:數據例如應該在Hospital Number和之下根據Patient Name:等。我想這是因爲列名是以'停止'分隔符命名的。我怎樣才能改變這一點,而不必添加一些引用移動列名的亂碼?

回答

1

我認爲在列中添加一個空列名可能會起作用?

Extractor2 <- function(dataframeIn, Column, delim) { 
    Column <- rlang::sym(Column) 
    dataframeIn <- data.frame(dataframeIn) 
    dataframeIn<-dataframeIn %>% tidyr::separate(!!Column, into = c("added_name",delim), 
     sep = paste(delim, collapse = "|")) 
    return(dataframeIn) 
} 

這將返回

'data.frame': 2 obs. of 10 variables: 
$ added_name    : chr "FdSP-37-2784518\nHospital: Random NHS Foundation Trust\n" "SP-50-4495875\nHospital: Random NHS Foundation Trust\n" 
$ Hospital Number   : chr ": J6044658\n" ": Y6417773\n" 
$ Patient Name:   : chr " Jargon, Victoria\n" " Powell, Destiny\n" 
$ DOB:     : chr " 1943-10-13\n" " 1946-12-29\n" 
$ General Practitioner: : chr " Dr. Martin, Marche\n" " Dr. al-Safi, Lutfiyya\n" 
$ Date received:   : chr " 2009-11-11\n" " 2008-06-15\n" 
$ Clinical Details:  : chr " Ongoing antral gastritis despite treatment with PPI,Reflux sx.,High dyshagia OGD - fundic gastritis.,Chronic "| __truncated__ " Quadrantic biopsies were taken at.,OGD - only 3cm sliding hiatus.\n7 specimen. Nature of specimen: Nature of"| __truncated__ 
$ Macroscopic description:: chr " 3 specimens collected the largest measuring 3 x 2 x 1 mm and the smallest 2 x 1 x 5 mm\n" " 4 specimens collected the largest measuring 4 x 4 x 4 mm and the smallest 5 x 3 x 1 mm\n" 
$ Histology:    : chr " Two biopsies consist of small bowel mucosa and are within normal histological limits.\n" " modified giemsa stain.,These are biopsies of gastric mucosa ,There is no evidence of coeliac disease.,The nuc"| __truncated__ 
$ Diagnosis:    : chr " Distal transverse colon polyp excision:- tubular adenoma, low grade dysplasia.,Ileo-caecal valve, biopsies:.,"| __truncated__ " Rectum, polyp biopsy: - Tubular adenoma with mild dysplasia,- Raised intra-epithelial lymphocytes ,Duodenum, "| __truncated__ 
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