MilestoneReportMWS
Martin Skarzynski
February 17, 2017
Current CPFP Fellows Analysis
The first step is to download and read in the data.
Download and read in the data
The data are available at this url: https://cpfp.nci.nih.gov/about-us/fellows.txt
Download the data
I manually added in missing entries from the current fellows website
https://cpfp.nci.nih.gov/about-us/fellows.shtml I named the new file fellows2.txt
Load filepath into memory
## You can set your working directory to final/en_US...
## and then use the filenames (wrapped in quotes)...
## but I prefer to load the path into memory...
path<-paste(getwd(),"/fellows2.txt", sep="")Read in the data
## First, I will read in all of the data, but later I will take a subsample.
## The raw binary (rb) method was the only way I could read in the full news data set.
## I skipped the embedded nuls in all, though these were only in the twitter data set.
con <- file(path, open="rb")
dat<-readLines(con, skipNul = TRUE, encoding = "ASCII")
close(con)Remove contact info
dat2<-gsub("^Phone.{1,}|^Email.*|^Contact.*", "", dat, ignore.case = TRUE)
## Remove empty lines
dat3<-dat2[which(dat2!="")]
dat4<-dat3[which(dat3!=" ")]
## dat2<-dat[-which(dat=="")] #Alternative solutionMake table of “Years of Entry”
year<- grep("^Year of entry.*", dat4, ignore.case = TRUE, value = TRUE)
year<-gsub("Year of entry ", "", year, ignore.case = TRUE)
year## [1] "2016" "2014" "2016" "2015" "2015" "2015" "2016" "2015" "2013" "2015"
## [11] "2015" "2015" "2015" "2013" "2013" "2014" "2015" "2016" "2016" "2015"
## [21] "2015" "2015" "2016" "2016" "2015" "2016" "2016" "2016" "2015" "2016"
## [31] "2015"yrtbl<-table(year)
yeardf<-as.data.frame(yrtbl)
names(yeardf) <- c("Year","Count")Generate dataframe of doctoral degrees and years the degrees were obtained
doc<- grep("^Doctoral degree.*|PhD.*", dat4, ignore.case = TRUE, value = TRUE)
doc<-gsub("Doctoral degree ", "", doc, ignore.case = TRUE)
doc<- strsplit(doc, ",")
doc<- unlist(doc)
docyear<-grep("20..", doc, ignore.case = TRUE, value = TRUE)
docyear<-gsub("\\(|\\)|[a-z]| |\\.","", docyear, ignore.case = TRUE)
doc<-grep(".*University.*|.*College.*|.*Institute.*|.*School.*|.*Academy.*", doc, ignore.case = TRUE, value = TRUE)
doc<-gsub("^ |^ |\\(.*\\)", "", doc, ignore.case = TRUE)
docFinal<-cbind(doc,docyear)
docFinal<-as.data.frame(docFinal)
names(docFinal) <- c("University","docYear")Obtain doctoral degree counts by university
doctbl<-table(doc)
docyrtbl<-table(docyear)
docdf<-as.data.frame(doctbl)
docyrdf<-as.data.frame(docyrtbl)
names(docdf) <- c("University","Count")Generate dataframe of master degrees and years the degrees were obtained
dat4## [1] "The National Cancer Institute Cancer Prevention Fellowship Program fellows are listed below in alphabetical order by last name."
## [2] "Prajakta Adsul"
## [3] "Year of entry 2016"
## [4] "Doctoral degree PhD, Public Health Studies, Saint Louis University, (2014)"
## [5] "MPH 2011, Epidemiology, Behavioral Sciences Saint Louis University"
## [6] "MBBS 2007, Medicine and Surgery, Maharashtra University of Health Sciences, Loni, India"
## [7] "Research Interests Implementation research, Global health, Health disparities, Socio-Behavioral and Health care delivery research. "
## [8] "Primary Preceptor/Branch David Chambers/Division of Cancer Control & Population Sciences/Office of the Director"
## [9] "Shelley Bluethmann"
## [10] "Year of entry 2014"
## [11] "Doctoral degree PhD, University of Texas, (2014)"
## [12] "MPH (if applicable) University of North Carolina, 2007"
## [13] "Research Interests Optimizing healthy aging in older cancer survivors, including the role of physical activity in mitigating cancer symptoms, improving co-morbidities, and enhancing quality of life."
## [14] "Primary Preceptor/Branch William Klein/Behavioral Research Program, Health Behaviors Research Branch"
## [15] "Megan Clarke"
## [16] "Year of entry 2016"
## [17] "Doctoral degree PhD, Cancer Epidemiology, Johns Hopkins University, Baltimore, MD (2016)"
## [18] "MHS, 2016, Biochemistry/Molecular Biology, Johns Hopkins University, Baltimore, MD"
## [19] "Research Interests Biomarker discovery and validation for early detection and prevention of gynecological cancers, risk prediction, translational epidemiology."
## [20] "Primary Preceptor/Branch Nicolas Wentzensen/Division of Cancer Epidemiology & Genetics/Clinical Genetics Branch"
## [21] "Diarmuid Coughlan"
## [22] "Year of Entry 2015"
## [23] "PhD, Health Economics, National University of Ireland, Galway, Ireland, (2014)"
## [24] "MPH N/A"
## [25] "Research Interests The economic burden of end-of-life cancer care stratifying by cancer type, stage of diagnosis and geographic location."
## [26] "Primary Preceptor/Branch Angela Mariotto/Division of Cancer Control & Population Sciences/Surveillance Research Program/Surveillance Informatics Branch"
## [27] "Brittny Davis"
## [28] "Year of entry 2015"
## [29] "Doctoral degree PhD, Chemistry, University of Maryland Baltimore County, (2015)"
## [30] "MPH Johns Hopkins University, 2016"
## [31] "Research Interests Modeling of national breast cancer trends, racial and geographic disparities in breast cancer, as well as risk prediction."
## [32] "Primary Preceptor/Branch William Anderson/Division of Cancer Epidemiology and Genetics/Biostatistics Branch"
## [33] "Maryam Doroudi"
## [34] "Year of Entry 2015"
## [35] "PhD, Molecular Biology, Georgia Institute of Technology, (2013)"
## [36] "MPH Johns Hopkins University, 2015"
## [37] "Research Interests Evaluate clinical and economic outcomes related to cancer screening and cancer treatment; Evaluating medical overuse; De-implementation Research."
## [38] "Primary Preceptor/Branch Paul Pinsky/Division of Cancer Prevention/Early Detection Research Group</p>"
## [39] "Danielle Durham"
## [40] "Year of entry 2016"
## [41] "Doctoral degree PhD, Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC (2015)"
## [42] "MHS, 2008, Community Health Education, The University of North Carolina at Greensboro, Greensboro, NC"
## [43] "Research Interests Breast Cancer Epidemiology, Screening, Health Disparities, Health Services Research, Outcomes."
## [44] "Primary Preceptor/Branch Pamela Marcus/Division of Cancer Control & Population Sciences (DCCPS)/Epidemiology and Genomics Research Program"
## [45] "Erin Ellis"
## [46] "Year of Entry 2015"
## [47] "PhD, Community Health and Health Behavior, University at Buffalo, (2014) "
## [48] "MPH Johns Hopkins University, 2015"
## [49] "Research Interests The role of affect and emotion in health decision making; dual process models of cognition; risk perceptions as they relate to cancer screening and other behavioral risk factors."
## [50] "Primary Preceptor/Branch Rebecca Ferrer/Behavioral Research Program/Basic Biobehavioral and Psychological Sciences Branch"
## [51] "Felisa Gonzales"
## [52] "Year of entry 2013"
## [53] "Doctoral degree PhD, Applied Social Psychology, George Washington University, (2013)"
## [54] "MPH (if applicable) University of California <U+0096> Berkeley, 2014 "
## [55] "Research Interests Disparities in cancer screening, treatment, and survival; health services research; health policy."
## [56] "Primary Preceptor/Branch Steve Taplin/Healthcare Delivery Research Program, Health Systems and Interventions Research Branch"
## [57] "Melinda Krakow"
## [58] "Year of entry 2015"
## [59] "Doctoral degree PhD, Health Communication, University of Utah, (2015)"
## [60] "MPH Johns Hopkins University, 2016"
## [61] "Research Interests Public health communication; narrative persuasion and media effects in the contexts of cancer prevention and screening; communication in healthcare systems; media coverage of cancer/science journalism."
## [62] "Primary Preceptor/Branch Brad Hesse/Division of Cancer Control & Population Sciences/Health Communication and Informatics Research Branch"
## [63] "Tamara Litwin"
## [64] "Year of entry 2015"
## [65] "Doctoral degree PhD, Biological Studies, University of Cambridge (United Kingdom), (2014)"
## [66] "MPH Johns Hopkins University, 2016"
## [67] "Research Interests Biomarker discovery and translation for prevention and early detection of gynecologic cancers, clinical trial design and implementation."
## [68] "Primary Preceptor/Branch Nicolas Wentzensen/Division of Cancer Epidemiology and Genetics/Clinical Genetics Branch"
## [69] "Claire Meaney"
## [70] "Year of Entry 2015"
## [71] "PhD, Biomedical Engineering, University of Limerick, (2013)"
## [72] "MPH University College Dublin, 2015"
## [73] "Research Interests The identification of biomarkers and molecular mechanisms associated with increased cancer risk and survival; the characterization of tumor microenvironment and its role in cancer progression; the development of 3D, tissue-mimetic models for cell behavior analysis."
## [74] "Primary Preceptor/Branch Brid Ryan/Center for Cancer Research/Human Carcinogenes Implementation Science"
## [75] "Jennifer Moss"
## [76] "Year of Entry 2015"
## [77] "PhD, Health Behavior, University of North Carolina, (2015)"
## [78] "MSPH University of North Carolina, 2012 (MPH)s"
## [79] "Research Interests Geographic disparities in cancer prevention behaviors, especially for HPV vaccination."
## [80] "Primary Preceptor/Branch Kathy Cronin/Division of Cancer Control & Population Sciences/Surveillance Research Program"
## [81] "Maeve Mullooly"
## [82] "Year of entry 2013"
## [83] "Doctoral degree PhD, Translational Medicine <U+0096> Tumor Biology, University College Dublin, (2013)"
## [84] "MPH (if applicable) University College Dublin, 2014"
## [85] "Research Interests The molecular epidemiology of risk factors for breast cancer, especially mammographic breast density, and molecular mechanisms that drive its association with increased cancer risk."
## [86] "Primary Preceptor/Branch Gretchen Gierach/Hormonal and Reproductive Epidemiology Branch"
## [87] "Primary Preceptor/Branch Gretchen Gierach/Division of Cancer Epidemiology and Genetics/Metabolic Epidemiology Branch"
## [88] "Shakira Nelson"
## [89] "Year of entry 2013"
## [90] "Doctoral degree PhD, Immunology and Infectious Disease, Penn State University, (2013)"
## [91] "MPH (if applicable) Johns Hopkins University, 2014 "
## [92] "Research Interests The associations between nutrition, genetics, and metabolomics with prostate and other cancer development; and understanding the underlying impact of health disparities."
## [93] "Primary Preceptor/Branch Demetrius Albanes/Nutritional Epidemiology Branch"
## [94] "Minal Patel"
## [95] "Year of entry 2014"
## [96] "Doctoral degree PhD, Community Health Sciences, University of California <U+0097> Los Angeles, (2014)"
## [97] "MPH (if applicable) San Diego State University, 2005"
## [98] "Research Interests The impact of social, built, and policy environments on cancer-related behaviors; tobacco use, physical activity, and nutrition behaviors related to cancer; multilevel factors involving neighborhood contextual and lifestyle factors; cancer health disparities; and adolescent/young adult cancer prevention."
## [99] "Primary Preceptor/Branch Linda Nebeling/Behavioral Research Program, Health Behaviors Research Branch <U+0096> Tobacco Control "
## [100] "Research Branch"
## [101] "Carly Paterson"
## [102] "Year of entry 2015"
## [103] "Doctoral degree PhD, Nursing, University of South Florida, (2015)"
## [104] "MPH Dartmouth College, 2016"
## [105] "Research Interests Cancer survivorship, symptom management, palliative care, personalized medicine."
## [106] "Primary Preceptor/Branch Ann O'Mara/Division of Cancer Prevention/Community Oncology and Prevention Trials Research Group"
## [107] "Dudith Pierre-Victor"
## [108] "Year of Entry 2016"
## [109] "Doctoral Degree PhD, Public Health, Florida International University, Miami, FL (2016)"
## [110] "MPH 2011, Epidemiology, Florida International University, Miami, FL"
## [111] "Research Interests Coordination of cancer care; integration of primary care providers in cancer treatment planning; bidirectional communication between primary care providers and medical oncologists; patients<U+0092> experience and satisfaction with cancer care; enrollment of minority patients in oncology trials; and cancer disparities."
## [112] "Primary Preceptor/Branch Worta McCaskill-Stevens/Division of Cancer Prevention/Community Oncology and Prevention Trials Research Group"
## [113] "Kristen Pluchino"
## [114] "Year of entry 2016"
## [115] "Doctoral degree PhD, Oxford University, (2015)"
## [116] "MPH Harvard University (2017)"
## [117] "MS Johns Hopkins University"
## [118] "Research Interests Molecular targets; multidrug resistance; translational research; biomarker development; regulatory review."
## [119] "Katherine Rendle"
## [120] "Year of Entry 2015"
## [121] "PhD, Social Work, Anthropology, University of Michigan, (2014)"
## [122] "MPH University of California Berkeley, 2015"
## [123] "Research Interests Healthcare delivery and outcomes; cancer prevention and screening; patient-reported outcomes research; medical decision-making; social determinants of health; clinical epidemiology; medical anthropology."
## [124] "Primary Preceptor/Branch Sarah Kobrin/Healthcare Delivery Research Program/Health Systems and Interventions Research Branch"
## [125] "Megan Roberts"
## [126] "Year of Entry 2015"
## [127] "PhD, Health Policy and Management, University of North Carolina, (2015)"
## [128] "MPH N/A"
## [129] "Research Interests Health disparities, especially those related to access to precision medicine."
## [130] "Primary Preceptor/Branch William Klein/Division of Cancer Control & Population Sciences/Behavioral Research Program/Office of the Associate Director"
## [131] "Cendrine Robinson"
## [132] "Year of entry 2015"
## [133] "Doctoral degree PhD, Medical and Clinical Psychology, Uniformed Services University of the Health Sciences, (2015)"
## [134] "MPH Harvard University (2016)"
## [135] "Research Interests Using mobile health technology to deliver behavioral health interventions and smoking cessation among youth and ethnic minorities."
## [136] "Primary Preceptor/Branch Eric Augustson/Division of Cancer Control & Population Sciences/Behavioral Research Program/Tobacco Control Research Branch"
## [137] "Elizabeth Sarma"
## [138] "Year of entry 2016"
## [139] "Doctoral degree PhD, Psychology, Stony Brook University (2016)"
## [140] "MPH Harvard University (2017)"
## [141] "MA Stony Brook University"
## [142] "Research Interests Cancer prevention; health behavior; cancer screening; multiple health behavior change."
## [143] "Elizabeth Siembida"
## [144] "Year of entry 2016"
## [145] "Doctoral degree PhD, Human Development and Family Studies, University of Connecticut (2016)"
## [146] "MPH Johns Hopkins University, 2017"
## [147] "MA University of Connecticut"
## [148] "Research Interests Translational research in adolescent and young adult oncology."
## [149] "Michelle Silver"
## [150] "Year of Entry 2015"
## [151] "PhD, Epidemiology, Johns Hopkins University, (2015)"
## [152] "MPH Johns Hopkins University, 2009 (ScM)"
## [153] "Research Interests HPV, cervical cancer screening, prevention, translational epidemiology, and health services research."
## [154] "Primary Preceptor/Branch Mark Schiffman/Division of Cancer Epidemiology and Genetics/Clinical Genetics Branch"
## [155] "Susan Spillane"
## [156] "Year of entry 2016"
## [157] "Doctoral degree PhD, Cancer Pharmacoepidemiology, Trinity College, Dublin. (2015)"
## [158] "MPH London School of Hygiene & Tropical Medicine, 2017"
## [159] "MPh Royal College of Surgeons, Dublin, Ireland"
## [160] "Research Interests Cancer pharmacoepidemiology; biostatistics; chemoprevention outcomes; pharmacoeconomics; health economics; health policy."
## [161] "Calvin Tribby"
## [162] "Year of entry 2016"
## [163] "Doctoral degree PhD, Geography, Ohio State University, (2016)"
## [164] "MPH Columbia University, 2017"
## [165] "MS University of New Mexico in Albuquerque"
## [166] "Research Interests Active transportation; built environment; geographic information science; livability."
## [167] "Sabrina Tsang"
## [168] "Year of entry 2016"
## [169] "Doctoral degree PhD, Cell and Molecular Biology, University of Pennsylvania (2016)"
## [170] "MPH Harvard University (2017)"
## [171] "MS Biology, Massachusetts Institute of Technology"
## [172] "Research Interests Tumor viruses; virology; DNA damage response; oncogenesis; vaccines; clinical trials."
## [173] "Christopher Wheldon"
## [174] "Year of Entry 2015"
## [175] "PhD, Public Health, University of South Florida, (2015)"
## [176] "MPH University of South Florida, 2007 (MSPH)"
## [177] "Research Interests My research projects focus on providing a bettering understanding of disparities experienced by minority and underserved populations across the cancer control continuum with the ultimate goal of identifying modifiable factors (e.g., health behaviors, organizational norms, and policies) that could help decrease these disparities. "
## [178] "Primary Preceptor/Branch Richard Moser/Division of Cancer Control & Population Sciences/Behavioral Research Program/Science of Research and Technology Branch"
## [179] "Erik Willis"
## [180] "Year of entry 2016"
## [181] "Doctoral degree PhD, Exercise Physiology, University of Kansas (2016)"
## [182] "MPH Yale University, 2017"
## [183] "MS Health and Physical Activity, University of Pittsburgh"
## [184] "Research Interests Population and individual level physical activity; nutrition; health."
## [185] "Kara Wiseman"
## [186] "Year of Entry 2015"
## [187] "PhD, Epidemiology, Virginia Commonwealth University, (2015)"
## [188] "MPH Virginia Commonwealth University, 2011"
## [189] "Research Interests Behavioral intervention research, including study development, implementation and evaluation."
## [190] "Primary Preceptor/Branch Erik Augustson/Division of Cancer Control & Population Sciences/Behavioral Research Program/Tobacco Control Research Branch"mph<-grep("^MPH |^MHS|^MSPH", dat4, ignore.case = FALSE, value = TRUE)
mph<-gsub("MPH |MHS, |^MSPH", "", mph, ignore.case = TRUE)
mphyear<- gsub("[^0-9]", "", mph)
mph<- strsplit(mph, ",")
mph<- unlist(mph)
mph<-gsub("/", "", mph, ignore.case = TRUE)
mph<-gsub("[^a-z A-Z]", "", mph, ignore.case = TRUE)
mph<-grep(".*University.*|.*College.*|.*Institute.*|.*School.*|.*Academy.*|NA", mph, ignore.case = TRUE, value = TRUE)
mph<-gsub("if applicable|Behavioral Sciences","", mph, ignore.case = TRUE)
mph<-gsub("^ +", "", mph)
mphyear## [1] "2011" "2007" "2016" "" "2016" "2015" "2008" "2015" "2014" "2016"
## [11] "2016" "2015" "2012" "2014" "2014" "2005" "2016" "2011" "2017" "2015"
## [21] "" "2016" "2017" "2017" "2009" "2017" "2017" "2017" "2007" "2017"
## [31] "2011"?getstr## No documentation for 'getstr' in specified packages and libraries:
## you could try '??getstr'mph## [1] "Saint Louis University"
## [2] "University of North Carolina"
## [3] "Johns Hopkins University"
## [4] "NA"
## [5] "Johns Hopkins University"
## [6] "Johns Hopkins University"
## [7] "The University of North Carolina at Greensboro"
## [8] "Johns Hopkins University"
## [9] "University of California Berkeley"
## [10] "Johns Hopkins University"
## [11] "Johns Hopkins University"
## [12] "University College Dublin"
## [13] "University of North Carolina"
## [14] "University College Dublin"
## [15] "Johns Hopkins University"
## [16] "San Diego State University"
## [17] "Dartmouth College"
## [18] "Florida International University"
## [19] "Harvard University "
## [20] "University of California Berkeley"
## [21] "NA"
## [22] "Harvard University "
## [23] "Harvard University "
## [24] "Johns Hopkins University"
## [25] "Johns Hopkins University"
## [26] "London School of Hygiene Tropical Medicine"
## [27] "Columbia University"
## [28] "Harvard University "
## [29] "University of South Florida"
## [30] "Yale University"
## [31] "Virginia Commonwealth University"str## function (object, ...)
## UseMethod("str")
## <bytecode: 0x00000000065bd998>
## <environment: namespace:utils>mphyear## [1] "2011" "2007" "2016" "" "2016" "2015" "2008" "2015" "2014" "2016"
## [11] "2016" "2015" "2012" "2014" "2014" "2005" "2016" "2011" "2017" "2015"
## [21] "" "2016" "2017" "2017" "2009" "2017" "2017" "2017" "2007" "2017"
## [31] "2011"mphFinal<-cbind(mph,mphyear)
mphFinal<-as.data.frame(mphFinal)
names(mphFinal) <- c("University","mphYear")Subset MPH degrees that Fellows obtained as postdocs
include<- ifelse(docyear < mphyear,1,ifelse(docyear > mphyear,0,NA))
include<-as.data.frame(include)
docmphFinal<-cbind(docFinal,mphFinal)
mphFinal2<-cbind(mphFinal,include)
#for (i in 1:ncol(dat)){dat[,i]=as.vector(dat[,i])}).
mphFinal2<-mphFinal2[which(mphFinal2$include=="1"),]
mphFinal3<- mphFinal2[,-3]Obtain counts of master degree by university
mphtbl<-table(mph)
mphdf<-as.data.frame(mphtbl)
names(mphdf) <- c("University","Count")
mphdf<-mphdf[which(mphdf$University!="NA"),]Obtain counts of master degree by university
mphtbl<-table(as.vector(mphFinal3[,1]))
mphdfFinal<-as.data.frame(mphtbl)
names(mphdfFinal) <- c("University","Count")Order data by count
yeardf<-yeardf[order(yeardf$Year,decreasing = TRUE),]
mphdf<-mphdf[order(mphdf$Count,decreasing = TRUE),]
mphdfFinal<-mphdfFinal[order(mphdfFinal$Count,decreasing = TRUE),]
docdf<-docdf[order(docdf$Count,decreasing = TRUE),]
names(mphFinal3) <- c("University","Year")
mphFinal3<-mphFinal3[order(mphFinal3$Year, mphFinal3$University,decreasing = FALSE),]Plot the mph data subset as pie charts
pack<-"plotly"
newPack <- pack[!(pack %in% installed.packages()[,"Package"])]
if(length(newPack)) install.packages(newPack)
library(plotly)## Loading required package: ggplot2##
## Attaching package: 'plotly'## The following object is masked from 'package:ggplot2':
##
## last_plot## The following object is masked from 'package:stats':
##
## filter## The following object is masked from 'package:graphics':
##
## layoutpmph <- plot_ly(mphdfFinal, labels = ~University, values = ~Count, type = 'pie') %>%
layout(title = 'MPH programs completed by 1st year Cancer Prevention Fellows',
xaxis = list(showgrid = FALSE, zeroline = FALSE, showticklabels = FALSE),
yaxis = list(showgrid = FALSE, zeroline = FALSE, showticklabels = FALSE))
pmphhtmlwidgets::saveWidget(as.widget(pmph), "mphPie.html")Present remaining data as tables
yeardf## Year Count
## 4 2016 11
## 3 2015 15
## 2 2014 2
## 1 2013 3docdf## University Count
## 4 Johns Hopkins University 2
## 23 University of North Carolina 2
## 25 University of South Florida 2
## 1 Florida International University 1
## 2 George Washington University 1
## 3 Georgia Institute of Technology 1
## 5 National University of Ireland 1
## 6 Ohio State University 1
## 7 Oxford University 1
## 8 Penn State University 1
## 9 Saint Louis University 1
## 10 Stony Brook University 1
## 11 The University of North Carolina at Chapel Hill 1
## 12 Trinity College 1
## 13 Uniformed Services University of the Health Sciences 1
## 14 University at Buffalo 1
## 15 University College Dublin 1
## 16 University of California <U+0097> Los Angeles 1
## 17 University of Cambridge 1
## 18 University of Connecticut 1
## 19 University of Kansas 1
## 20 University of Limerick 1
## 21 University of Maryland Baltimore County 1
## 22 University of Michigan 1
## 24 University of Pennsylvania 1
## 26 University of Texas 1
## 27 University of Utah 1
## 28 Virginia Commonwealth University 1Obtain Research Interest data
pack<-c("tm","wordcloud")
newPack <- pack[!(pack %in% installed.packages()[,"Package"])]
if(length(newPack)) install.packages(newPack)
library(tm)## Loading required package: NLP##
## Attaching package: 'NLP'## The following object is masked from 'package:ggplot2':
##
## annotatelibrary(wordcloud)## Loading required package: RColorBrewerdat4## [1] "The National Cancer Institute Cancer Prevention Fellowship Program fellows are listed below in alphabetical order by last name."
## [2] "Prajakta Adsul"
## [3] "Year of entry 2016"
## [4] "Doctoral degree PhD, Public Health Studies, Saint Louis University, (2014)"
## [5] "MPH 2011, Epidemiology, Behavioral Sciences Saint Louis University"
## [6] "MBBS 2007, Medicine and Surgery, Maharashtra University of Health Sciences, Loni, India"
## [7] "Research Interests Implementation research, Global health, Health disparities, Socio-Behavioral and Health care delivery research. "
## [8] "Primary Preceptor/Branch David Chambers/Division of Cancer Control & Population Sciences/Office of the Director"
## [9] "Shelley Bluethmann"
## [10] "Year of entry 2014"
## [11] "Doctoral degree PhD, University of Texas, (2014)"
## [12] "MPH (if applicable) University of North Carolina, 2007"
## [13] "Research Interests Optimizing healthy aging in older cancer survivors, including the role of physical activity in mitigating cancer symptoms, improving co-morbidities, and enhancing quality of life."
## [14] "Primary Preceptor/Branch William Klein/Behavioral Research Program, Health Behaviors Research Branch"
## [15] "Megan Clarke"
## [16] "Year of entry 2016"
## [17] "Doctoral degree PhD, Cancer Epidemiology, Johns Hopkins University, Baltimore, MD (2016)"
## [18] "MHS, 2016, Biochemistry/Molecular Biology, Johns Hopkins University, Baltimore, MD"
## [19] "Research Interests Biomarker discovery and validation for early detection and prevention of gynecological cancers, risk prediction, translational epidemiology."
## [20] "Primary Preceptor/Branch Nicolas Wentzensen/Division of Cancer Epidemiology & Genetics/Clinical Genetics Branch"
## [21] "Diarmuid Coughlan"
## [22] "Year of Entry 2015"
## [23] "PhD, Health Economics, National University of Ireland, Galway, Ireland, (2014)"
## [24] "MPH N/A"
## [25] "Research Interests The economic burden of end-of-life cancer care stratifying by cancer type, stage of diagnosis and geographic location."
## [26] "Primary Preceptor/Branch Angela Mariotto/Division of Cancer Control & Population Sciences/Surveillance Research Program/Surveillance Informatics Branch"
## [27] "Brittny Davis"
## [28] "Year of entry 2015"
## [29] "Doctoral degree PhD, Chemistry, University of Maryland Baltimore County, (2015)"
## [30] "MPH Johns Hopkins University, 2016"
## [31] "Research Interests Modeling of national breast cancer trends, racial and geographic disparities in breast cancer, as well as risk prediction."
## [32] "Primary Preceptor/Branch William Anderson/Division of Cancer Epidemiology and Genetics/Biostatistics Branch"
## [33] "Maryam Doroudi"
## [34] "Year of Entry 2015"
## [35] "PhD, Molecular Biology, Georgia Institute of Technology, (2013)"
## [36] "MPH Johns Hopkins University, 2015"
## [37] "Research Interests Evaluate clinical and economic outcomes related to cancer screening and cancer treatment; Evaluating medical overuse; De-implementation Research."
## [38] "Primary Preceptor/Branch Paul Pinsky/Division of Cancer Prevention/Early Detection Research Group</p>"
## [39] "Danielle Durham"
## [40] "Year of entry 2016"
## [41] "Doctoral degree PhD, Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC (2015)"
## [42] "MHS, 2008, Community Health Education, The University of North Carolina at Greensboro, Greensboro, NC"
## [43] "Research Interests Breast Cancer Epidemiology, Screening, Health Disparities, Health Services Research, Outcomes."
## [44] "Primary Preceptor/Branch Pamela Marcus/Division of Cancer Control & Population Sciences (DCCPS)/Epidemiology and Genomics Research Program"
## [45] "Erin Ellis"
## [46] "Year of Entry 2015"
## [47] "PhD, Community Health and Health Behavior, University at Buffalo, (2014) "
## [48] "MPH Johns Hopkins University, 2015"
## [49] "Research Interests The role of affect and emotion in health decision making; dual process models of cognition; risk perceptions as they relate to cancer screening and other behavioral risk factors."
## [50] "Primary Preceptor/Branch Rebecca Ferrer/Behavioral Research Program/Basic Biobehavioral and Psychological Sciences Branch"
## [51] "Felisa Gonzales"
## [52] "Year of entry 2013"
## [53] "Doctoral degree PhD, Applied Social Psychology, George Washington University, (2013)"
## [54] "MPH (if applicable) University of California <U+0096> Berkeley, 2014 "
## [55] "Research Interests Disparities in cancer screening, treatment, and survival; health services research; health policy."
## [56] "Primary Preceptor/Branch Steve Taplin/Healthcare Delivery Research Program, Health Systems and Interventions Research Branch"
## [57] "Melinda Krakow"
## [58] "Year of entry 2015"
## [59] "Doctoral degree PhD, Health Communication, University of Utah, (2015)"
## [60] "MPH Johns Hopkins University, 2016"
## [61] "Research Interests Public health communication; narrative persuasion and media effects in the contexts of cancer prevention and screening; communication in healthcare systems; media coverage of cancer/science journalism."
## [62] "Primary Preceptor/Branch Brad Hesse/Division of Cancer Control & Population Sciences/Health Communication and Informatics Research Branch"
## [63] "Tamara Litwin"
## [64] "Year of entry 2015"
## [65] "Doctoral degree PhD, Biological Studies, University of Cambridge (United Kingdom), (2014)"
## [66] "MPH Johns Hopkins University, 2016"
## [67] "Research Interests Biomarker discovery and translation for prevention and early detection of gynecologic cancers, clinical trial design and implementation."
## [68] "Primary Preceptor/Branch Nicolas Wentzensen/Division of Cancer Epidemiology and Genetics/Clinical Genetics Branch"
## [69] "Claire Meaney"
## [70] "Year of Entry 2015"
## [71] "PhD, Biomedical Engineering, University of Limerick, (2013)"
## [72] "MPH University College Dublin, 2015"
## [73] "Research Interests The identification of biomarkers and molecular mechanisms associated with increased cancer risk and survival; the characterization of tumor microenvironment and its role in cancer progression; the development of 3D, tissue-mimetic models for cell behavior analysis."
## [74] "Primary Preceptor/Branch Brid Ryan/Center for Cancer Research/Human Carcinogenes Implementation Science"
## [75] "Jennifer Moss"
## [76] "Year of Entry 2015"
## [77] "PhD, Health Behavior, University of North Carolina, (2015)"
## [78] "MSPH University of North Carolina, 2012 (MPH)s"
## [79] "Research Interests Geographic disparities in cancer prevention behaviors, especially for HPV vaccination."
## [80] "Primary Preceptor/Branch Kathy Cronin/Division of Cancer Control & Population Sciences/Surveillance Research Program"
## [81] "Maeve Mullooly"
## [82] "Year of entry 2013"
## [83] "Doctoral degree PhD, Translational Medicine <U+0096> Tumor Biology, University College Dublin, (2013)"
## [84] "MPH (if applicable) University College Dublin, 2014"
## [85] "Research Interests The molecular epidemiology of risk factors for breast cancer, especially mammographic breast density, and molecular mechanisms that drive its association with increased cancer risk."
## [86] "Primary Preceptor/Branch Gretchen Gierach/Hormonal and Reproductive Epidemiology Branch"
## [87] "Primary Preceptor/Branch Gretchen Gierach/Division of Cancer Epidemiology and Genetics/Metabolic Epidemiology Branch"
## [88] "Shakira Nelson"
## [89] "Year of entry 2013"
## [90] "Doctoral degree PhD, Immunology and Infectious Disease, Penn State University, (2013)"
## [91] "MPH (if applicable) Johns Hopkins University, 2014 "
## [92] "Research Interests The associations between nutrition, genetics, and metabolomics with prostate and other cancer development; and understanding the underlying impact of health disparities."
## [93] "Primary Preceptor/Branch Demetrius Albanes/Nutritional Epidemiology Branch"
## [94] "Minal Patel"
## [95] "Year of entry 2014"
## [96] "Doctoral degree PhD, Community Health Sciences, University of California <U+0097> Los Angeles, (2014)"
## [97] "MPH (if applicable) San Diego State University, 2005"
## [98] "Research Interests The impact of social, built, and policy environments on cancer-related behaviors; tobacco use, physical activity, and nutrition behaviors related to cancer; multilevel factors involving neighborhood contextual and lifestyle factors; cancer health disparities; and adolescent/young adult cancer prevention."
## [99] "Primary Preceptor/Branch Linda Nebeling/Behavioral Research Program, Health Behaviors Research Branch <U+0096> Tobacco Control "
## [100] "Research Branch"
## [101] "Carly Paterson"
## [102] "Year of entry 2015"
## [103] "Doctoral degree PhD, Nursing, University of South Florida, (2015)"
## [104] "MPH Dartmouth College, 2016"
## [105] "Research Interests Cancer survivorship, symptom management, palliative care, personalized medicine."
## [106] "Primary Preceptor/Branch Ann O'Mara/Division of Cancer Prevention/Community Oncology and Prevention Trials Research Group"
## [107] "Dudith Pierre-Victor"
## [108] "Year of Entry 2016"
## [109] "Doctoral Degree PhD, Public Health, Florida International University, Miami, FL (2016)"
## [110] "MPH 2011, Epidemiology, Florida International University, Miami, FL"
## [111] "Research Interests Coordination of cancer care; integration of primary care providers in cancer treatment planning; bidirectional communication between primary care providers and medical oncologists; patients<U+0092> experience and satisfaction with cancer care; enrollment of minority patients in oncology trials; and cancer disparities."
## [112] "Primary Preceptor/Branch Worta McCaskill-Stevens/Division of Cancer Prevention/Community Oncology and Prevention Trials Research Group"
## [113] "Kristen Pluchino"
## [114] "Year of entry 2016"
## [115] "Doctoral degree PhD, Oxford University, (2015)"
## [116] "MPH Harvard University (2017)"
## [117] "MS Johns Hopkins University"
## [118] "Research Interests Molecular targets; multidrug resistance; translational research; biomarker development; regulatory review."
## [119] "Katherine Rendle"
## [120] "Year of Entry 2015"
## [121] "PhD, Social Work, Anthropology, University of Michigan, (2014)"
## [122] "MPH University of California Berkeley, 2015"
## [123] "Research Interests Healthcare delivery and outcomes; cancer prevention and screening; patient-reported outcomes research; medical decision-making; social determinants of health; clinical epidemiology; medical anthropology."
## [124] "Primary Preceptor/Branch Sarah Kobrin/Healthcare Delivery Research Program/Health Systems and Interventions Research Branch"
## [125] "Megan Roberts"
## [126] "Year of Entry 2015"
## [127] "PhD, Health Policy and Management, University of North Carolina, (2015)"
## [128] "MPH N/A"
## [129] "Research Interests Health disparities, especially those related to access to precision medicine."
## [130] "Primary Preceptor/Branch William Klein/Division of Cancer Control & Population Sciences/Behavioral Research Program/Office of the Associate Director"
## [131] "Cendrine Robinson"
## [132] "Year of entry 2015"
## [133] "Doctoral degree PhD, Medical and Clinical Psychology, Uniformed Services University of the Health Sciences, (2015)"
## [134] "MPH Harvard University (2016)"
## [135] "Research Interests Using mobile health technology to deliver behavioral health interventions and smoking cessation among youth and ethnic minorities."
## [136] "Primary Preceptor/Branch Eric Augustson/Division of Cancer Control & Population Sciences/Behavioral Research Program/Tobacco Control Research Branch"
## [137] "Elizabeth Sarma"
## [138] "Year of entry 2016"
## [139] "Doctoral degree PhD, Psychology, Stony Brook University (2016)"
## [140] "MPH Harvard University (2017)"
## [141] "MA Stony Brook University"
## [142] "Research Interests Cancer prevention; health behavior; cancer screening; multiple health behavior change."
## [143] "Elizabeth Siembida"
## [144] "Year of entry 2016"
## [145] "Doctoral degree PhD, Human Development and Family Studies, University of Connecticut (2016)"
## [146] "MPH Johns Hopkins University, 2017"
## [147] "MA University of Connecticut"
## [148] "Research Interests Translational research in adolescent and young adult oncology."
## [149] "Michelle Silver"
## [150] "Year of Entry 2015"
## [151] "PhD, Epidemiology, Johns Hopkins University, (2015)"
## [152] "MPH Johns Hopkins University, 2009 (ScM)"
## [153] "Research Interests HPV, cervical cancer screening, prevention, translational epidemiology, and health services research."
## [154] "Primary Preceptor/Branch Mark Schiffman/Division of Cancer Epidemiology and Genetics/Clinical Genetics Branch"
## [155] "Susan Spillane"
## [156] "Year of entry 2016"
## [157] "Doctoral degree PhD, Cancer Pharmacoepidemiology, Trinity College, Dublin. (2015)"
## [158] "MPH London School of Hygiene & Tropical Medicine, 2017"
## [159] "MPh Royal College of Surgeons, Dublin, Ireland"
## [160] "Research Interests Cancer pharmacoepidemiology; biostatistics; chemoprevention outcomes; pharmacoeconomics; health economics; health policy."
## [161] "Calvin Tribby"
## [162] "Year of entry 2016"
## [163] "Doctoral degree PhD, Geography, Ohio State University, (2016)"
## [164] "MPH Columbia University, 2017"
## [165] "MS University of New Mexico in Albuquerque"
## [166] "Research Interests Active transportation; built environment; geographic information science; livability."
## [167] "Sabrina Tsang"
## [168] "Year of entry 2016"
## [169] "Doctoral degree PhD, Cell and Molecular Biology, University of Pennsylvania (2016)"
## [170] "MPH Harvard University (2017)"
## [171] "MS Biology, Massachusetts Institute of Technology"
## [172] "Research Interests Tumor viruses; virology; DNA damage response; oncogenesis; vaccines; clinical trials."
## [173] "Christopher Wheldon"
## [174] "Year of Entry 2015"
## [175] "PhD, Public Health, University of South Florida, (2015)"
## [176] "MPH University of South Florida, 2007 (MSPH)"
## [177] "Research Interests My research projects focus on providing a bettering understanding of disparities experienced by minority and underserved populations across the cancer control continuum with the ultimate goal of identifying modifiable factors (e.g., health behaviors, organizational norms, and policies) that could help decrease these disparities. "
## [178] "Primary Preceptor/Branch Richard Moser/Division of Cancer Control & Population Sciences/Behavioral Research Program/Science of Research and Technology Branch"
## [179] "Erik Willis"
## [180] "Year of entry 2016"
## [181] "Doctoral degree PhD, Exercise Physiology, University of Kansas (2016)"
## [182] "MPH Yale University, 2017"
## [183] "MS Health and Physical Activity, University of Pittsburgh"
## [184] "Research Interests Population and individual level physical activity; nutrition; health."
## [185] "Kara Wiseman"
## [186] "Year of Entry 2015"
## [187] "PhD, Epidemiology, Virginia Commonwealth University, (2015)"
## [188] "MPH Virginia Commonwealth University, 2011"
## [189] "Research Interests Behavioral intervention research, including study development, implementation and evaluation."
## [190] "Primary Preceptor/Branch Erik Augustson/Division of Cancer Control & Population Sciences/Behavioral Research Program/Tobacco Control Research Branch"RI <- grep("^Research Interests ", dat4, ignore.case = TRUE, value = TRUE)
RI<-gsub("Research Interests ", "", RI, ignore.case = TRUE)Clean Research Interest data
RI<- removePunctuation(RI)
RI<- stripWhitespace(RI)
RI <- removeWords(RI, stopwords("english"))
RI <- removeWords(RI, "the")
RI<- tolower(RI)Tokenization
Here I put together lists of unigrams, bigrams and trigrams.
Download ngram_tokenizer and tokenize
## I was not able to install RWeka package, because of a java version problem.
## Instead of trying to figure it out, I used the ngram_tokenizer snippet
## created by Maciej Szymkiewicz, aka zero323 on Github.
if (!file.exists("ngram_tokenizer.R")) {
download.file("https://raw.githubusercontent.com/zero323/r-snippets/master/R/ngram_tokenizer.R",
destfile = paste(getwd(),"/ngram_tokenizer.R", sep=""))
}
source("ngram_Tokenizer.R")
unigram_tokenizer <- ngram_tokenizer(1)
uniList <- unigram_tokenizer(RI)
freqNames <- as.vector(names(table(unlist(uniList))))
freqCount <- as.numeric(table(unlist(uniList)))
dfUni <- data.frame(Word = freqNames,
Count = freqCount)
attach(dfUni)
dfUniSort<-dfUni[order(-Count),]
detach(dfUni)
bigram_tokenizer <- ngram_tokenizer(2)
biList <- bigram_tokenizer(RI)
freqNames <- as.vector(names(table(unlist(biList))))
freqCount <- as.numeric(table(unlist(biList)))
dfBi <- data.frame(Word = freqNames,
Count = freqCount)
attach(dfBi)
dfBiSort<-dfBi[order(-Count),]
detach(dfBi)
trigram_tokenizer <- ngram_tokenizer(3)
triList <- trigram_tokenizer(RI)
freqNames <- as.vector(names(table(unlist(triList))))
freqCount <- as.numeric(table(unlist(triList)))
dfTri <- data.frame(Word = freqNames,
Count = freqCount)
attach(dfTri)
dfTriSort<-dfTri[order(-Count),]
detach(dfTri)
quadgram_tokenizer <- ngram_tokenizer(4)
quadList <- quadgram_tokenizer(RI)
freqNames <- as.vector(names(table(unlist(quadList))))
freqCount <- as.numeric(table(unlist(quadList)))
dfQuad <- data.frame(Word = freqNames,
Count = freqCount)
attach(dfQuad)
dfQuadSort<-dfQuad[order(-Count),]
detach(dfQuad)
wordbank<-rbind(dfUniSort, dfBiSort, dfTriSort, dfQuadSort)
wordbank<-wordbank[order(wordbank$Count,decreasing = TRUE),]
head(wordbank, n=40)## Word Count
## 28 cancer 32
## 94 health 22
## 63 disparities 11
## 182 research 11
## 168 prevention 8
## 190 screening 8
## 32 care 7
## 186 risk 7
## 206 the 6
## 25 breast 5
## 78 epidemiology 5
## 86 factors 5
## 150 outcomes 5
## 491 cancer prevention 5
## 521 cancer screening 5
## 1701 health disparities 5
## 19 behaviors 4
## 39 clinical 4
## 60 development 4
## 89 geographic 4
## 123 medical 4
## 134 molecular 4
## 210 translational 4
## 3510 breast cancer 4
## 5 activity 3
## 17 behavior 3
## 18 behavioral 3
## 22 biomarker 3
## 41 communication 3
## 79 especially 3
## 102 implementation 3
## 143 nutrition 3
## 160 physical 3
## 163 policy 3
## 181 related 3
## 187 role 3
## 191 services 3
## 212 treatment 3
## 4010 cancer care 3
## 1751 health services 3Create a wordcloud
require(RColorBrewer)
set.seed(20170304)
colors <- brewer.pal(8, "Dark2")
pal <- colorRampPalette(colors)
wc1<-wordcloud(words = dfUniSort$Word, freq = dfUniSort$Count, min.freq = 1,
max.words=40, random.order=FALSE, rot.per=0.35, ordered.colors = FALSE,
colors=pal(40))
text(x=0.5, y=0, "Research Interest Word Cloud")
png("RIwordcloud.png", width=3, height=3, units="in", res=300)
wordcloud(words = dfUniSort$Word, freq = dfUniSort$Count, min.freq = 1,
max.words=40, random.order=FALSE, rot.per=0.35, ordered.colors = FALSE,
colors=pal(40))
dev.off()## png
## 2Unused code
Preceptor and Branch info
PP <- grep(“Primary Preceptor”, dat4, ignore.case = TRUE, value = TRUE) PP<-gsub(“Primary Preceptor/Branch”, “”, PP, ignore.case = TRUE)
RI PP
```