Nothing
R/cancer-rates.info.R
In diseasemapping: Modelling Spatial Variation in Disease Risk for Areal Data
Defines functions
usCancer
cancerCodes = list(
site = c('All Sites'=0,'Oral Cavity and Pharynx'=20000,'Lip'=20010,'Tongue'=20020,
'Salivary Gland'=20030,'Floor of Mouth'=20040,'Gum and Other Mouth'=20050,
'Nasopharynx'=20060,'Tonsil'=20070,'Oropharynx'=20080,'Hypopharynx'=20090,
'Other Oral Cavity and Pharynx'=20100,'Digestive System'=21000,
'Esophagus'=21010,'Stomach'=21020,'Small Intestine'=21030,'Colon and Rectum'=1,
'Early Stage Colon and Rectum'=6,'Late Stage Colon and Rectum'=7,
'Colon excluding Rectum'=21040,'Cecum'=21041,'Appendix'=21042,'Ascending Colon'=21043,
'Hepatic Flexure'=21044,'Transverse Colon'=21045,'Splenic Flexure'=21046,
'Descending Colon'=21047,'Sigmoid Colon'=21048,'Large Intestine, NOS'=21049,
'Rectum and Rectosigmoid Junction'=21050,'Rectosigmoid Junction'=21051,
'Rectum'=21052,'Anus, Anal Canal, and Anorectum'=21060,
'Liver and Intrahepatic Bile Duct'=2,'Liver'=21071,'Intrahepatic Bile Duct'=21072,
'Gallbladder'=21080,'Other Biliary'=21090,'Pancreas'=21100,'Retroperitoneum'=21110,
'Peritoneum, Omentum, and Mesentery'=21120,'Other Digestive Organs'=21130,
'Respiratory System'=22000,'Nose, Nasal Cavity, and Middle Ear'=22010,
'Larynx'=22020,
'Lung and Bronchus'=22030,'Pleura'=22050,
'Trachea, Mediastinum and Other Respiratory Organs'=22060,'Bones and Joints'=23000,
'Soft Tissue including Heart'=24000,'Skin excluding Basal and Squamous'=25000,
'Melanoma of the Skin'=25010,'Other NonEpithelial Skin'=25020,'Breast'=26000,
'In Situ Breast'=3,'Early Stage Breast'=4,'Late Stage Breast'=5,
'Female Genital System'=27000,'Cervix Uteri'=27010,'Early Stage Cervix Uteri'=8,
'Late Stage Cervix Uteri'=9,'Corpus Uteri'=27020,'Uterus, NOS'=27030,
'Ovary'=27040,'Vagina'=27050,'Vulva'=27060,'Other Female Genital Organs'=27070,
'Male Genital System'=28000,'Prostate'=28010,'Testis'=28020,'Penis'=28030,
'Other Male Genital Organs'=28040,'Urinary System'=29000,'Urinary Bladder'=29010,
'Kidney and Renal pelvis'=29020,'Ureter'=29030,'Other Urinary Organs'=29040,
'Eye and Orbit'=30000,'Brain and Other Nervous System'=31000,'Brain'=31010,
'Cranial Nerves and Other Nervous System'=31040,'Endocrine System'=32000,
'Thyroid'=32010,'Other Endocrine including Thymus'=32020,'Lymphoma'=33000,
'Hodgkin Lymphoma'=33010,'Hodgkin Lymphoma Nodal'=33011,
'Hodgkin Lymphoma Extranodal'=33012,'NonHodgkin Lymphoma'=33040,
'NonHodgkin Lymphoma Nodal'=33041,'NonHodgkin Lymphoma Extranodal'=33042,
'Myeloma'=34000,'Leukemia'=35000,'Lymphocytic Leukemia'=35010,
'Acute Lymphocytic Leukemia'=35011,'Chronic Lymphocytic Leukemia'=35012,
'Other Lymphocytic Leukemia'=35013,'Myeloid and Monocytic Leukemia'=35020,
'Acute Myeloid Leukemia'=35021,'Acute Monocytic Leukemia'=35031,
'Chronic Myeloid Leukemia'=35022,'Other Myeloid/Monocytic Leukemia'=35023,
'Other Leukemia'=35040,'Other Acute Leukemia'=35041,
'Aleukemic, Subleukemic and NOS Leukemia'=35043,
'Mesothelioma'=36010,'Kaposi Sarcoma'=36020,'Miscellaneous'=37000),
state = c(Texas='tx', Georgia='ga', Kentucky = 'ky',
Michigan='mi', Arkansas='ar', Mississippi='ms',
Wisconsin='wi', Iowa='ia', 'New Mexico' ='nm',
Utah='ut', California='ca', Seattle='se',
Conneticut = 'ct', 'New Jersey' = 'nj'),
sex = c(M=1, F=2, both=0)
)
# minnisota
# https://apps.health.state.mn.us/mndata/cancer_query?p_auth=Wy7tICix&p_p_id=springQueryPortlet_WAR_mndataspringQueryportlet_INSTANCE_TQg4MoZMNm0w&p_p_lifecycle=1&p_p_state=normal&p_p_mode=view&p_p_col_id=column-1&p_p_col_count=2&p_p_col_pos=1&_springQueryPortlet_WAR_mndataspringQueryportlet_INSTANCE_TQg4MoZMNm0w__facesViewIdRender=%2Fpages%2Findex.xhtml
# https://apps.health.state.mn.us/mndata/cancer_query?p_auth=Wy7tICix&p_p_id=springQueryPortlet_WAR_mndataspringQueryportlet_INSTANCE_TQg4MoZMNm0w&p_p_lifecycle=1&p_p_state=normal&p_p_mode=view&p_p_col_id=column-1&p_p_col_count=2&p_p_col_pos=1&_springQueryPortlet_WAR_mndataspringQueryportlet_INSTANCE_TQg4MoZMNm0w__facesViewIdRender=%2Fpages%2Findex.xhtml
# https://apps.health.state.mn.us/mndata/cancer_query?p_auth=Wy7tICix&p_p_id=springQueryPortlet_WAR_mndataspringQueryportlet_INSTANCE_TQg4MoZMNm0w&p_p_lifecycle=1&p_p_state=normal&p_p_mode=view&p_p_col_id=column-1&p_p_col_count=2&p_p_col_pos=1&_springQueryPortlet_WAR_mndataspringQueryportlet_INSTANCE_TQg4MoZMNm0w__facesViewIdRender=%2Fpages%2Findex.xhtml
usCancer = function(
state='Kentucky',
site='Lung',
year = c(2004,2008),
sex='both'
) {
verbose = TRUE
Ssite = cancerCodes$site[grep(paste(site, collapse='|'), names(cancerCodes$site), ignore.case=TRUE)]
Ssex = cancerCodes$sex[grep(paste(sex, collapse='|'), names(cancerCodes$sex), ignore.case=TRUE)]
Sstate = cancerCodes$state[grep(paste(state, collapse='|'), names(cancerCodes$state), ignore.case=TRUE)]
if(is.matrix(year)) {
SstartYear = year[,1]
SendYear = year[,2]
} else {
SstartYear = min(year)
SendYear = max(year)
}
forUrl = expand.grid(siteCode=Ssite, sexCode=Ssex, stateCode=Sstate, startYear = SstartYear, endYear=SendYear)
for(D in c('sex','state','site')){
forUrl[,D] = names(cancerCodes[[D]])[match(forUrl[,paste(D, 'Code', sep='')], cancerCodes[[D]])]
}
allCases = data.frame()
for(D in 1:nrow(forUrl)) {
if(any(is.na(forUrl[D,]))){
warning('site, sex or state not found')
}
if(forUrl[D, 'stateCode'] %in% c('ar')) {
middleUrl = 'beta/common/v1'
depth=5
} else {
middleUrl = 'common'
depth=5
}
kUrl = paste(
'http://www.cancer-rates.info/',middleUrl, '/index.php?',
'std=us2000m&geography=1&syear=', forUrl[D, 'startYear'],
'&eyear=', forUrl[D, 'endYear'], '&site=', forUrl[D, 'siteCode'],
'&race=0&sex=', forUrl[D, 'sexCode'], '&dataset=I&database=', forUrl[D, 'stateCode'],
'&datasource=inv&m_color=1&c_intrvls=0&title=Stuff&r=370,*&c=538',
sep='')
namesHere = forUrl[D, c('startYear','endYear','sex','state','site')]
myDir = file.path(tempdir(), gsub("[[:space:]]+", "_", paste(c("cfiles",as.character(namesHere)), collapse='_')))
myCommand = paste("httrack --depth=",depth, " --priority=1 -N1 -O ", myDir, " \'", kUrl, "\'", sep='')
if(verbose) cat('\ndownloading', paste(namesHere, collapse=" "))
sRes = try(system(myCommand))
if(verbose) cat(' done\n')
if(inherits(sRes, 'try-error')) {
stop("install httrack from www.httrack.com")
}
fname = system(paste("ls ", myDir, "/web/newalldetails*.html", sep=''), TRUE)
fname = grep('newalldetails[[:alnum:]]+\\.html$', fname, value=TRUE)
if(requireNamespace("XML", quietly=TRUE)) {
datHeader = XML::readHTMLTable(fname[1], isUrl=FALSE, which=2)[1,]
} else {
warning("install the XML package to use usCancer")
}
datText = scan(fname[1], what=character(), quiet=TRUE)
startTable = grep("<TABLE", datText)
startTable = startTable[length(startTable)]
endTable = grep("</TABLE", datText)
endTable = endTable[length(endTable)]
datText = datText[startTable:endTable]
startTr = grep("<TR", datText)
if(min(startTr)>1)
datText = datText[-seq(1,min(startTr)-1)]
startTr = grep("<TR", datText)
startTd = grep("<TD", datText)
earlyTr = max(which(startTr <= startTd[1]))
startTr = startTr[seq(earlyTr, length(startTr))]
datText = paste(datText, collapse='')
datText = unlist(strsplit(datText, "<TR>"))
datText = grep("^[[:space:]]?$|^<TH", datText, invert=TRUE, value=TRUE)
datSplit = strsplit(datText, "<TD")
datLen = unlist(lapply(datSplit, length))
datSplit = unlist(datSplit[which(datLen ==6)])
datSplit = gsub("</A>$", "", datSplit)
datSplit = gsub("^[[:print:]]+>", "", datSplit)
datSplit = gsub("~", "1", datSplit)
dat = as.data.frame(matrix(datSplit, ncol=6, byrow=TRUE),
stringsAsFactors=FALSE)[,-1]
colnames(dat) = as.character(unlist(datHeader))
dat = dat[grep("^$", dat$County, invert=TRUE),]
for(Dcol in grep("County", colnames(dat), invert=TRUE)) {
dat[,Dcol] = as.numeric(as.character(dat[,Dcol]))
}
cases = dat[,c('County','Cases')]
if(nrow(cases)){
cases = cbind(cases, namesHere, stateCode=forUrl[D,'stateCode'])
allCases = rbind(allCases, cases)
}
}
getRid = grep("^[[:space:]]?(Note|Data|~|The population estimates):?[[:space:]]", allCases$County)
getRidState = grep("^[[:space:]]?(STATE|\\*\\*\\*Counts|Unknown)[[:space:]]?$", allCases$County)
getRid = c(getRid, getRidState)
if(length(getRid))
allCases = allCases[-getRid,]
allCases$Cases = as.numeric(gsub("~", "1", allCases$Cases))
allCases
}
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diseasemapping documentation built on Feb. 8, 2024, 3:01 a.m.
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Defines functions usCancer
cancerCodes = list(
site = c('All Sites'=0,'Oral Cavity and Pharynx'=20000,'Lip'=20010,'Tongue'=20020,
'Salivary Gland'=20030,'Floor of Mouth'=20040,'Gum and Other Mouth'=20050,
'Nasopharynx'=20060,'Tonsil'=20070,'Oropharynx'=20080,'Hypopharynx'=20090,
'Other Oral Cavity and Pharynx'=20100,'Digestive System'=21000,
'Esophagus'=21010,'Stomach'=21020,'Small Intestine'=21030,'Colon and Rectum'=1,
'Early Stage Colon and Rectum'=6,'Late Stage Colon and Rectum'=7,
'Colon excluding Rectum'=21040,'Cecum'=21041,'Appendix'=21042,'Ascending Colon'=21043,
'Hepatic Flexure'=21044,'Transverse Colon'=21045,'Splenic Flexure'=21046,
'Descending Colon'=21047,'Sigmoid Colon'=21048,'Large Intestine, NOS'=21049,
'Rectum and Rectosigmoid Junction'=21050,'Rectosigmoid Junction'=21051,
'Rectum'=21052,'Anus, Anal Canal, and Anorectum'=21060,
'Liver and Intrahepatic Bile Duct'=2,'Liver'=21071,'Intrahepatic Bile Duct'=21072,
'Gallbladder'=21080,'Other Biliary'=21090,'Pancreas'=21100,'Retroperitoneum'=21110,
'Peritoneum, Omentum, and Mesentery'=21120,'Other Digestive Organs'=21130,
'Respiratory System'=22000,'Nose, Nasal Cavity, and Middle Ear'=22010,
'Larynx'=22020,
'Lung and Bronchus'=22030,'Pleura'=22050,
'Trachea, Mediastinum and Other Respiratory Organs'=22060,'Bones and Joints'=23000,
'Soft Tissue including Heart'=24000,'Skin excluding Basal and Squamous'=25000,
'Melanoma of the Skin'=25010,'Other NonEpithelial Skin'=25020,'Breast'=26000,
'In Situ Breast'=3,'Early Stage Breast'=4,'Late Stage Breast'=5,
'Female Genital System'=27000,'Cervix Uteri'=27010,'Early Stage Cervix Uteri'=8,
'Late Stage Cervix Uteri'=9,'Corpus Uteri'=27020,'Uterus, NOS'=27030,
'Ovary'=27040,'Vagina'=27050,'Vulva'=27060,'Other Female Genital Organs'=27070,
'Male Genital System'=28000,'Prostate'=28010,'Testis'=28020,'Penis'=28030,
'Other Male Genital Organs'=28040,'Urinary System'=29000,'Urinary Bladder'=29010,
'Kidney and Renal pelvis'=29020,'Ureter'=29030,'Other Urinary Organs'=29040,
'Eye and Orbit'=30000,'Brain and Other Nervous System'=31000,'Brain'=31010,
'Cranial Nerves and Other Nervous System'=31040,'Endocrine System'=32000,
'Thyroid'=32010,'Other Endocrine including Thymus'=32020,'Lymphoma'=33000,
'Hodgkin Lymphoma'=33010,'Hodgkin Lymphoma Nodal'=33011,
'Hodgkin Lymphoma Extranodal'=33012,'NonHodgkin Lymphoma'=33040,
'NonHodgkin Lymphoma Nodal'=33041,'NonHodgkin Lymphoma Extranodal'=33042,
'Myeloma'=34000,'Leukemia'=35000,'Lymphocytic Leukemia'=35010,
'Acute Lymphocytic Leukemia'=35011,'Chronic Lymphocytic Leukemia'=35012,
'Other Lymphocytic Leukemia'=35013,'Myeloid and Monocytic Leukemia'=35020,
'Acute Myeloid Leukemia'=35021,'Acute Monocytic Leukemia'=35031,
'Chronic Myeloid Leukemia'=35022,'Other Myeloid/Monocytic Leukemia'=35023,
'Other Leukemia'=35040,'Other Acute Leukemia'=35041,
'Aleukemic, Subleukemic and NOS Leukemia'=35043,
'Mesothelioma'=36010,'Kaposi Sarcoma'=36020,'Miscellaneous'=37000),
state = c(Texas='tx', Georgia='ga', Kentucky = 'ky',
Michigan='mi', Arkansas='ar', Mississippi='ms',
Wisconsin='wi', Iowa='ia', 'New Mexico' ='nm',
Utah='ut', California='ca', Seattle='se',
Conneticut = 'ct', 'New Jersey' = 'nj'),
sex = c(M=1, F=2, both=0)
)
# minnisota
# https://apps.health.state.mn.us/mndata/cancer_query?p_auth=Wy7tICix&p_p_id=springQueryPortlet_WAR_mndataspringQueryportlet_INSTANCE_TQg4MoZMNm0w&p_p_lifecycle=1&p_p_state=normal&p_p_mode=view&p_p_col_id=column-1&p_p_col_count=2&p_p_col_pos=1&_springQueryPortlet_WAR_mndataspringQueryportlet_INSTANCE_TQg4MoZMNm0w__facesViewIdRender=%2Fpages%2Findex.xhtml
# https://apps.health.state.mn.us/mndata/cancer_query?p_auth=Wy7tICix&p_p_id=springQueryPortlet_WAR_mndataspringQueryportlet_INSTANCE_TQg4MoZMNm0w&p_p_lifecycle=1&p_p_state=normal&p_p_mode=view&p_p_col_id=column-1&p_p_col_count=2&p_p_col_pos=1&_springQueryPortlet_WAR_mndataspringQueryportlet_INSTANCE_TQg4MoZMNm0w__facesViewIdRender=%2Fpages%2Findex.xhtml
# https://apps.health.state.mn.us/mndata/cancer_query?p_auth=Wy7tICix&p_p_id=springQueryPortlet_WAR_mndataspringQueryportlet_INSTANCE_TQg4MoZMNm0w&p_p_lifecycle=1&p_p_state=normal&p_p_mode=view&p_p_col_id=column-1&p_p_col_count=2&p_p_col_pos=1&_springQueryPortlet_WAR_mndataspringQueryportlet_INSTANCE_TQg4MoZMNm0w__facesViewIdRender=%2Fpages%2Findex.xhtml
usCancer = function(
state='Kentucky',
site='Lung',
year = c(2004,2008),
sex='both'
) {
verbose = TRUE
Ssite = cancerCodes$site[grep(paste(site, collapse='|'), names(cancerCodes$site), ignore.case=TRUE)]
Ssex = cancerCodes$sex[grep(paste(sex, collapse='|'), names(cancerCodes$sex), ignore.case=TRUE)]
Sstate = cancerCodes$state[grep(paste(state, collapse='|'), names(cancerCodes$state), ignore.case=TRUE)]
if(is.matrix(year)) {
SstartYear = year[,1]
SendYear = year[,2]
} else {
SstartYear = min(year)
SendYear = max(year)
}
forUrl = expand.grid(siteCode=Ssite, sexCode=Ssex, stateCode=Sstate, startYear = SstartYear, endYear=SendYear)
for(D in c('sex','state','site')){
forUrl[,D] = names(cancerCodes[[D]])[match(forUrl[,paste(D, 'Code', sep='')], cancerCodes[[D]])]
}
allCases = data.frame()
for(D in 1:nrow(forUrl)) {
if(any(is.na(forUrl[D,]))){
warning('site, sex or state not found')
}
if(forUrl[D, 'stateCode'] %in% c('ar')) {
middleUrl = 'beta/common/v1'
depth=5
} else {
middleUrl = 'common'
depth=5
}
kUrl = paste(
'http://www.cancer-rates.info/',middleUrl, '/index.php?',
'std=us2000m&geography=1&syear=', forUrl[D, 'startYear'],
'&eyear=', forUrl[D, 'endYear'], '&site=', forUrl[D, 'siteCode'],
'&race=0&sex=', forUrl[D, 'sexCode'], '&dataset=I&database=', forUrl[D, 'stateCode'],
'&datasource=inv&m_color=1&c_intrvls=0&title=Stuff&r=370,*&c=538',
sep='')
namesHere = forUrl[D, c('startYear','endYear','sex','state','site')]
myDir = file.path(tempdir(), gsub("[[:space:]]+", "_", paste(c("cfiles",as.character(namesHere)), collapse='_')))
myCommand = paste("httrack --depth=",depth, " --priority=1 -N1 -O ", myDir, " \'", kUrl, "\'", sep='')
if(verbose) cat('\ndownloading', paste(namesHere, collapse=" "))
sRes = try(system(myCommand))
if(verbose) cat(' done\n')
if(inherits(sRes, 'try-error')) {
stop("install httrack from www.httrack.com")
}
fname = system(paste("ls ", myDir, "/web/newalldetails*.html", sep=''), TRUE)
fname = grep('newalldetails[[:alnum:]]+\\.html$', fname, value=TRUE)
if(requireNamespace("XML", quietly=TRUE)) {
datHeader = XML::readHTMLTable(fname[1], isUrl=FALSE, which=2)[1,]
} else {
warning("install the XML package to use usCancer")
}
datText = scan(fname[1], what=character(), quiet=TRUE)
startTable = grep("<TABLE", datText)
startTable = startTable[length(startTable)]
endTable = grep("</TABLE", datText)
endTable = endTable[length(endTable)]
datText = datText[startTable:endTable]
startTr = grep("<TR", datText)
if(min(startTr)>1)
datText = datText[-seq(1,min(startTr)-1)]
startTr = grep("<TR", datText)
startTd = grep("<TD", datText)
earlyTr = max(which(startTr <= startTd[1]))
startTr = startTr[seq(earlyTr, length(startTr))]
datText = paste(datText, collapse='')
datText = unlist(strsplit(datText, "<TR>"))
datText = grep("^[[:space:]]?$|^<TH", datText, invert=TRUE, value=TRUE)
datSplit = strsplit(datText, "<TD")
datLen = unlist(lapply(datSplit, length))
datSplit = unlist(datSplit[which(datLen ==6)])
datSplit = gsub("</A>$", "", datSplit)
datSplit = gsub("^[[:print:]]+>", "", datSplit)
datSplit = gsub("~", "1", datSplit)
dat = as.data.frame(matrix(datSplit, ncol=6, byrow=TRUE),
stringsAsFactors=FALSE)[,-1]
colnames(dat) = as.character(unlist(datHeader))
dat = dat[grep("^$", dat$County, invert=TRUE),]
for(Dcol in grep("County", colnames(dat), invert=TRUE)) {
dat[,Dcol] = as.numeric(as.character(dat[,Dcol]))
}
cases = dat[,c('County','Cases')]
if(nrow(cases)){
cases = cbind(cases, namesHere, stateCode=forUrl[D,'stateCode'])
allCases = rbind(allCases, cases)
}
}
getRid = grep("^[[:space:]]?(Note|Data|~|The population estimates):?[[:space:]]", allCases$County)
getRidState = grep("^[[:space:]]?(STATE|\\*\\*\\*Counts|Unknown)[[:space:]]?$", allCases$County)
getRid = c(getRid, getRidState)
if(length(getRid))
allCases = allCases[-getRid,]
allCases$Cases = as.numeric(gsub("~", "1", allCases$Cases))
allCases
}
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