NORDCAN – incidences and numbers

Below components to a R-script, which will extract age-gender specific rates and proportions from Nordic databases divided by year and geography.

Link to NORDCAN website: >click here< library(XML) #Source #http://www-dep.iarc.fr/NORDCAN/DK/glossary.htm#ASR #Table mapping ICD codes and cancer types # ICD-10 Label # C00-14\C10.1 Lip, oral cavity and pharynx # C00.0-2,C00.5-9 Lip # C00.3-4,C02-04,C05.0,C06 Oral cavity # C01,C05.1-9,C09,C10.0,C10.2-9 Oropharynx # C07-08 Salivary glands # C11 Nasopharynx # C12-13 Hypopharynx # C14 Pharynx, ill-defined # C15 Oesophagus # C16 Stomach # C17 Small intestine # C18 Colon # C18-21 Colorectal # C19-21 Rectum and anus # C22 Liver # C23-24 Gallbladder # C25 Pancreas # C26,C39,C76-80, C97,D47 Unknown and ill-defined # C30-31 Nose, sinuses # C32+C10.1 Larynx # C33-34 Lung # C37,C38.0-3,C38.8,C45.1-9,C46.2-9,C47-48,C74,C75.0,C75.4-9,C88,D46 Other specified cancers # C38.4+C45.0 Pleura # C40-41 Bone # C43 Melanoma of skin # C44+C46.0 Skin, non-melanoma # C49+C46.1 Soft tissues # C50 Breast # C51-52,C57.7-9 Other female genital organs # C53 Cervix uteri # C54 Corpus uteri # C55+C58 Uterus, other # C56,C57.0-4 Ovary etc. # C60+C63 Penis etc. # C61 Prostate # C62 Testis # C64 Kidney # C65-68+D09.0-1+ D30.1-9+D41.1-9 Bladder etc. # C69 Eye # C70-72+C75.1-3+D32-33+D35.2-4,D42-43,D44.3-5 Brain, central nervous system # C73 Thyroid # C81 Hodgkin lymphoma # C82-85,C96 Non-Hodgkin lymphoma # C90 Multiple myeloma # C91-95 Leukaemia # C91.0 Acute lymphatic leukaemia # C91.1 Chronic lymphatic leukaemia # C91.2-9 Other and unspecified lymphatic leukaemia # C92.0+C93.0+C94.0+C94.2+C94.4-5 Acute myeloid leukaemia # C92.1+C93.1+C94.1 Chronic myeloid leukaemia # C92.2-9+C93.2-9+C94.3+C94.7 Other and unspecified myeloid leukaemia # C95 Leukaemia, cell unspecified # CXX.X+ D09.0-1+D30.1-9+D35.2-4+D41.1-9+D32-33+D42-43+D44.3-5+D46-47 All sites # CXX.X\(C44+C46.0)+D09.0-1+D30.1-9+D35.2-4+D41.1-9+D32-33+D42-43+D44.3-5+D46-47 All sites but non-melanoma skin cancer # CXX.X\(C44+C46.0+C50+C61)+D09.0-1+D30.1-9+D35.2-4+D41.1-9+D32-33+D42-43+D44.3-5+D46-47 All sites but non-melanoma skin, breast and prostate cancer #Coding for age specific numbers and rates (total, 5 year intervals from 0-80, 85+) #Table names #”Cancer” “Total”  “0-”     “5-”     “10-”    “15-”    “20-”    “25-”    “30-”    “35-”    “40-”    “45-”    “50-”    “55-”   “60-”    “65-”    “70-”    “75-”    “80-”    “85+”    “CR”     “ASR(W)” “ASR(E)” “ASR(N)” #Registry (Geografi – se forneden) #Sort (0 by cancer, 1 by ICD code) #Sex (0 both, 1 males, 2 females) #Type (0 incidence, 1 mortality) #Stat (0 numbers, 1 rate /100.000) #Period (years, depends on geography) #Extract cancer incidence table, national level (Denmark registry 208) incidence = “http://www-dep.iarc.fr/NORDCAN/english/Table4r.asp?registry=208&sort=0&sex=2&type=0&stat=0&period=1999&submit=Execute&#8221; incidence.table = readHTMLTable(incidence, header=T, which=2,stringsAsFactors=F) #Extract cancer mortality table, national level (Denmark registry 208) mortality= “http://www-dep.iarc.fr/NORDCAN/english/Table4r.asp?registry=208&sort=0&sex=2&type=1&stat=0&period=1999&submit=Execute&#8221; mortality.table = readHTMLTable(mortality, header=T, which=2,stringsAsFactors=F) #Extract cancer prevalence (National level, age-intervals) #Cancer encoding (danish):  #Akut lymfatisk leukæmi, 420 #Akut myeloid leukæmi, 450 #Alle kræftformer, 510 #Alle kræftformer undtagen anden hud, 520 #Alle kræftformer undtagen anden hud, bryst og prostata, 530 #Anden hud (ikke modermærke), 320 #Anden og uspecificeret lymfatisk leukæmi, 440 #Anden og uspecificeret myeloid leukæmi, 470 #Andre specificerede, 490 #Bindevæv, 370 #Blære og andre urinveje, 300 #Bryst, 200 #Bugspytkirtel, 150 #Endetarm og anus, 120 #Galdeblære og galdeveje, 140 #Hjerne og centralnervesystem, 340 #Hodgkins lymfom, 390 #Hypopharynx, 60 #Knogle, 360 #Kronisk lymfatisk leukæmi, 430 #Kronisk myeloid leukæmi, 460 #Leukæmi, 410 #Leukæmi, uspecificerede celler, 480 #Lever, 130 #Livmoder, 222 #Livmoder uden specifikation 232 #Livmoderhals, 212 #Lunge (inkl. luftrør), 180 #Lungehinde, 190 #Læbe, 10 #Læbe, mundhule og svælg, 540 #Mave, 90 #Modermærkekræft, 310 #Mundhule, 20 #Myelomatose, 400 #Nasopharynx, 50 #Non- Hodgkin lymfom, 380 #Nyre, 290 #Næse og bihuler, 160 #Oropharynx, 40 #Penis og andre mandlige kønsorganer, 281 #Pharynx, dårligt defineret, 70 #Prostata, 261 #Skjoldbruskkirtel, 350 #Spiserør, 80 #Spytkirtel, 30 #Strube, 170 #Testikel, 271 #Tyk- og endetarm, 550 #Tyktarm, 110 #Tyndtarm, 100 #Ukendte og dårligt definerede, 500 #Æggestok, æggeleder mv., 242 #Øje, 330 #Øvrige kvindelige kønsorganer, 252 # prevalence=”http://www-dep.iarc.fr/NORDCAN/english/table11.asp?cancer=510&sex=1&registry=208&sYear=1963&eYear=2014&stat=2&age_from=1&age_to=18&submit=Execute&#8221; #Cancer (number coded, sYear as incidence/mortality, eYear (2014 limit as of 11/6-2017)), stat (0, 2 raw number /proportion per 100.000, 3 raw number /proportion W, 4 raw number /proportion E, 5 raw number/proportion N) prevalence.table=readHTMLTable(prevalence, header=T, which=2, stringsAsFactors=F,skip.rows = 1) names(prevalence.table) #Cancer survival (Nation level, year intervals) survival=”http://www-dep.iarc.fr/NORDCAN/english/table23.asp?registry=208&sex=1&time=1&sort=0&submit=Execute&#8221; survival.table=readHTMLTable(survival, header=T, which=2, stringsAsFactors=F,skip.rows = 1) names(survival.table)                          “1975-1979 (number)”,”1975-1979 (CI)”,”1980-1984 (number)”,”1980-1984 (CI)”,                          “1985-1989 (number)”,”1985-1989 (CI)”,”1990-1994 (number)”,”1990-1994 (CI)”,                          “1995-1999 (number)”,”1995-1999 (CI)”,”2000-2004 (number)”,”2000-2004 (CI)”,                          “2005-2009 (number)”,”2005-2009 (CI)”,”2010-2014 (number)”,”2010-2014 (CI)”) #Population numbers per gender (National level/region level, five year age intervals and total) pop=”http://www-dep.iarc.fr/NORDCAN/English/graph5.asp?registry=208&period=2014&grid=1&submit=Execute&#8221; pop.table=readHTMLTable(pop, header=T, which=2, stringsAsFactors=F,skip.rows = 1) #National data Denmark (registry 208) #Regional information Denmark (registry 2080 til 2084) #Scandinavia (Norden registry 0, years 1960 ->) #Faroe Islands (registry 234, years 1960 ->) #Greenland (registry 304, years 1968 ->) #Iceland (registry 352, years 1955 ->) #Sweden (registry 752, years 1960 ->) #Norway (registry 578, years 1953 ->) #Finland (registry 246, years 1953 ->)