R/indi_c.17.R
In bigdata-icict/pcdasindi: Calculates health indicators to Brazil
Defines functions
indi_c.17
Documented in
indi_c.17
#'
#' Taxa de mortalidade específica por doenças transmissíveis - C.17
#'
#' Follows the RIPSA 2012 card \url{http://fichas.ripsa.org.br/2012/c-17}
#'
#' @param conn Connection object created with \code{\link{pcdas_connect}}.
#' @param ano numeric. Year.
#' @param agr string. Aggregation level. 'mun' for municipalities, 'uf' for "unidades federativas" or 'regsaude' for "regiões de saúde".
#' @param multi Indicator multiplier. Defaults to RIPSA recommendation.
#'
#' @return A \code{data.frame} containing the calculated indicator for the aggregation level.
#' @examples
#' c.17 <- indi_c.17(conn, ano = 2016, agr = "mun")
indi_c.17 <- function(conn, ano, agr, multi = 100000){
categorias <- c(
"A00 Colera",
"A01 Febres tifoide e paratifoide",
"A02 Outr infecc p/Salmonella",
"A03 Shiguelose",
"A04 Outr infecc intestinais bacter",
"A05 Outr intox alimentares bacter NCOP",
"A06 Amebiase",
"A07 Outr doenc intestinais p/protozoarios",
"A08 Infecc intestinais virais outr e as NE",
"A09 Diarreia e gastroenterite orig infecc presum",
"A15 Tuberc respirat c/conf bacteriol e histolog",
"A16 Tuberc vias respirat s/conf bacter histol",
"A17 Tuberc do sist nervoso",
"A18 Tuberc de outr orgaos",
"A19 Tuberc miliar",
"A21 Tularemia",
"A22 Carbunculo",
"A23 Brucelose",
"A24 Mormo e melioidose",
"A25 Febres transm p/mordedura de rato",
"A26 Erisipeloide",
"A27 Leptospirose",
"A28 Outr doenc bacter zoonoticas NCOP",
"A30 Hanseniase",
"A31 Infecc dev outr micobacterias",
"A32 Listeriose",
"A33 Tetano do recem-nascido",
"A34 Tetano obstetrico",
"A35 Outr tipos de tetano",
"A36 Difteria",
"A37 Coqueluche",
"A38 Escarlatina",
"A39 Infecc meningogocica",
"A40 Septicemia estreptococica",
"A41 Outr septicemias",
"A42 Actinomicose",
"A43 Nocardiose",
"A44 Bartonelose",
"A46 Erisipela",
"A48 Outr doenc bacter NCOP",
"A49 Infecc bacter de localiz NE",
"A50 Sifilis congen",
"A51 Sifilis precoce",
"A52 Sifilis tard",
"A53 Outr form e as NE da sifilis",
"A54 Infecc gonococica",
"A55 Linfogranuloma p/clamidia",
"A56 Outr infecc p/clamidias transm p/via sexual",
"A57 Cancro mole",
"A58 Granuloma inguinal",
"A59 Tricomoniase",
"A60 Infecc anogenitais p/virus do herpes",
"A63 Outr doenc de transm predom sexual NCOP",
"A64 Doenc sexualmente transm NE",
"A65 Sifilis nao-venerea",
"A66 Bouba",
"A67 Pinta",
"A68 Febres recorrentes",
"A69 Outr infecc p/espiroquetas",
"A70 Infecc causadas p/Clamidia psittaci",
"A71 Tracoma",
"A74 Outr doenc causadas p/Clamidias",
"A75 Tifo exantematico",
"A77 Febre maculosa",
"A79 Outr rickettsioses",
"A81 Infecc p/virus atipicos sist nervoso central",
"A82 Raiva",
"A83 Encefalite p/virus transm p/mosquitos",
"A84 Encefalite p/virus transm p/carrapatos",
"A85 Outr encefalites virais NCOP",
"A86 Encefalite viral NE",
"A87 Meningite viral",
"A88 Outr infecc virais sist nervoso central NCOP",
"A89 Infecc virais NE do sist nervoso central",
"A90 Dengue",
"A91 Febre hemorragica dev virus do dengue",
"A92 Outr febres virais transm p/mosquitos",
"A93 Outr febres p/virus transm p/artropodes NCOP",
"A94 Febre viral transm p/artropodes NE",
"A95 Febre amarela",
"A96 Febre hemorragica p/arenavirus",
"A98 Outr febres hemorragicas p/virus NCOP",
"A99 Febres hemorragicas virais NE",
"B00 Infecc p/virus do herpes",
"B01 Varicela",
"B02 Herpes zoster",
"B05 Sarampo",
"B06 Rubeola",
"B07 Verrugas orig viral",
"B08 Outr inf virais lesoes pele membr muc NCOP",
"B09 Inf viral NE caract p/lesoes pele membr muco",
"B15 Hepatite aguda A",
"B16 Hepatite aguda B",
"B17 Outr hepatites virais agudas",
"B18 Hepatite viral cronica",
"B19 Hepatite viral NE",
"B20 Doenc p/HIV result doenc infecc e parasit",
"B21 Doenc p/HIV result em neopl malig",
"B22 Doenc p/HIV result em outr doenc espec",
"B23 Doenc p/HIV result em outr doenc",
"B24 Doenc p/HIV NE",
"B25 Doenc p/citomegalovirus",
"B26 Caxumba",
"B27 Mononucleose infecc",
"B30 Conjuntivite viral",
"B33 Outr doenc p/virus NCOP",
"B34 Doenc p/virus de localiz NE",
"B35 Dermatofitose",
"B36 Outr micoses superf",
"B37 Candidiase",
"B38 Coccidioidomicose",
"B39 Histoplasmose",
"B40 Blastomicose",
"B41 Paracoccidioidomicose",
"B42 Esporotricose",
"B43 Cromomicose e abscesso feomicotico",
"B44 Aspergilose",
"B45 Criptococose",
"B46 Zigomicose",
"B47 Micetoma",
"B48 Outr micoses NCOP",
"B49 Micose NE",
"B50 Malaria p/Plasmodium falciparum",
"B51 Malaria p/Plasmodium vivax",
"B52 Malaria p/Plasmodium malariae",
"B53 Outr form malaria conf p/exames parasitolog",
"B54 Malaria NE",
"B55 Leishmaniose",
"B56 Tripanossomiase africana",
"B57 Doenc de Chagas",
"B58 Toxoplasmose",
"B59 Pneumocistose",
"B60 Outr doenc dev protozoarios NCOP",
"B64 Doenc NE dev protozoarios",
"B65 Esquistossomose",
"B66 Outr infestacoes p/trematodeos",
"B67 Equinococose",
"B68 Infestacao p/Taenia",
"B69 Cisticercose",
"B71 Outr infestacoes p/cestoides",
"B72 Dracontiase",
"B73 Oncocercose",
"B74 Filariose",
"B75 Triquinose",
"B76 Ancilostomiase",
"B77 Ascaridiase",
"B78 Estrongiloidiase",
"B79 Tricuriase",
"B80 Oxiuriase",
"B81 Outr helmintiases intestinais NCOP",
"B82 Parasitose intestinal NE",
"B83 Outr helmintiases",
"B85 Pediculose e ftiriase",
"B86 Escabiose",
"B87 Miiase",
"B88 Outr infestacoes",
"B89 Doenc parasit NE",
"B90 Sequelas de tuberc",
"B91 Sequelas de poliomielite",
"B92 Sequelas de hanseniase",
"B94 Sequelas de outr doenc infecc e parasit e NE",
"B95 Estr/estafilococo causa doenc class outr cap",
"B96 Outr agent bacter causa doenc class outr cap",
"B97 Virus como doenc class outr cap",
"B99 Doenc infecc outr e as NE",
"G00 Meningite bacter NCOP",
"G03 Meningite dev outr causas e a causas NE",
"J00 Nasofaringite aguda",
"J01 Sinusite aguda",
"J02 Faringite aguda",
"J03 Amigdalite aguda",
"J04 Laringite e traqueite agudas",
"J05 Laringite obstrutiva aguda e epiglotite",
"J06 Infecc agudas vias aereas super loc mult NE",
"J09 Influenza dev virus gripe aviária",
"J10 Influenza dev outro virus influenza ident",
"J11 Influenza dev virus nao identificado",
"J12 Pneumonia viral NCOP",
"J13 Pneumonia dev Streptococcus pneumoniae",
"J14 Pneumonia dev Haemophilus infuenzae",
"J15 Pneumonia bacter NCOP",
"J16 Pneumonia dev out microorg infecc espec NCOP",
"J18 Pneumonia p/microorg NE",
"J20 Bronquite aguda",
"J21 Bronquiolite aguda",
"J22 Infecc agudas NE das vias aereas infer"
)
join_names <- join_names(agr = agr)
sim <- get_sim_categorias(conn = conn, ano = ano, agr = agr, causabas_categorias = categorias)
pop <- get_pop(conn = conn, ano = ano, agr = agr)
df <- dplyr::left_join(sim, pop, by = join_names) %>%
mutate(indi_c.17 = sim/pop*multi) %>%
select(1, 4)
return(df)
}
bigdata-icict/pcdasindi documentation built on March 11, 2020, 5:15 p.m.
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Defines functions indi_c.17
Documented in indi_c.17
#'
#' Taxa de mortalidade específica por doenças transmissíveis - C.17
#'
#' Follows the RIPSA 2012 card \url{http://fichas.ripsa.org.br/2012/c-17}
#'
#' @param conn Connection object created with \code{\link{pcdas_connect}}.
#' @param ano numeric. Year.
#' @param agr string. Aggregation level. 'mun' for municipalities, 'uf' for "unidades federativas" or 'regsaude' for "regiões de saúde".
#' @param multi Indicator multiplier. Defaults to RIPSA recommendation.
#'
#' @return A \code{data.frame} containing the calculated indicator for the aggregation level.
#' @examples
#' c.17 <- indi_c.17(conn, ano = 2016, agr = "mun")
indi_c.17 <- function(conn, ano, agr, multi = 100000){
categorias <- c(
"A00 Colera",
"A01 Febres tifoide e paratifoide",
"A02 Outr infecc p/Salmonella",
"A03 Shiguelose",
"A04 Outr infecc intestinais bacter",
"A05 Outr intox alimentares bacter NCOP",
"A06 Amebiase",
"A07 Outr doenc intestinais p/protozoarios",
"A08 Infecc intestinais virais outr e as NE",
"A09 Diarreia e gastroenterite orig infecc presum",
"A15 Tuberc respirat c/conf bacteriol e histolog",
"A16 Tuberc vias respirat s/conf bacter histol",
"A17 Tuberc do sist nervoso",
"A18 Tuberc de outr orgaos",
"A19 Tuberc miliar",
"A21 Tularemia",
"A22 Carbunculo",
"A23 Brucelose",
"A24 Mormo e melioidose",
"A25 Febres transm p/mordedura de rato",
"A26 Erisipeloide",
"A27 Leptospirose",
"A28 Outr doenc bacter zoonoticas NCOP",
"A30 Hanseniase",
"A31 Infecc dev outr micobacterias",
"A32 Listeriose",
"A33 Tetano do recem-nascido",
"A34 Tetano obstetrico",
"A35 Outr tipos de tetano",
"A36 Difteria",
"A37 Coqueluche",
"A38 Escarlatina",
"A39 Infecc meningogocica",
"A40 Septicemia estreptococica",
"A41 Outr septicemias",
"A42 Actinomicose",
"A43 Nocardiose",
"A44 Bartonelose",
"A46 Erisipela",
"A48 Outr doenc bacter NCOP",
"A49 Infecc bacter de localiz NE",
"A50 Sifilis congen",
"A51 Sifilis precoce",
"A52 Sifilis tard",
"A53 Outr form e as NE da sifilis",
"A54 Infecc gonococica",
"A55 Linfogranuloma p/clamidia",
"A56 Outr infecc p/clamidias transm p/via sexual",
"A57 Cancro mole",
"A58 Granuloma inguinal",
"A59 Tricomoniase",
"A60 Infecc anogenitais p/virus do herpes",
"A63 Outr doenc de transm predom sexual NCOP",
"A64 Doenc sexualmente transm NE",
"A65 Sifilis nao-venerea",
"A66 Bouba",
"A67 Pinta",
"A68 Febres recorrentes",
"A69 Outr infecc p/espiroquetas",
"A70 Infecc causadas p/Clamidia psittaci",
"A71 Tracoma",
"A74 Outr doenc causadas p/Clamidias",
"A75 Tifo exantematico",
"A77 Febre maculosa",
"A79 Outr rickettsioses",
"A81 Infecc p/virus atipicos sist nervoso central",
"A82 Raiva",
"A83 Encefalite p/virus transm p/mosquitos",
"A84 Encefalite p/virus transm p/carrapatos",
"A85 Outr encefalites virais NCOP",
"A86 Encefalite viral NE",
"A87 Meningite viral",
"A88 Outr infecc virais sist nervoso central NCOP",
"A89 Infecc virais NE do sist nervoso central",
"A90 Dengue",
"A91 Febre hemorragica dev virus do dengue",
"A92 Outr febres virais transm p/mosquitos",
"A93 Outr febres p/virus transm p/artropodes NCOP",
"A94 Febre viral transm p/artropodes NE",
"A95 Febre amarela",
"A96 Febre hemorragica p/arenavirus",
"A98 Outr febres hemorragicas p/virus NCOP",
"A99 Febres hemorragicas virais NE",
"B00 Infecc p/virus do herpes",
"B01 Varicela",
"B02 Herpes zoster",
"B05 Sarampo",
"B06 Rubeola",
"B07 Verrugas orig viral",
"B08 Outr inf virais lesoes pele membr muc NCOP",
"B09 Inf viral NE caract p/lesoes pele membr muco",
"B15 Hepatite aguda A",
"B16 Hepatite aguda B",
"B17 Outr hepatites virais agudas",
"B18 Hepatite viral cronica",
"B19 Hepatite viral NE",
"B20 Doenc p/HIV result doenc infecc e parasit",
"B21 Doenc p/HIV result em neopl malig",
"B22 Doenc p/HIV result em outr doenc espec",
"B23 Doenc p/HIV result em outr doenc",
"B24 Doenc p/HIV NE",
"B25 Doenc p/citomegalovirus",
"B26 Caxumba",
"B27 Mononucleose infecc",
"B30 Conjuntivite viral",
"B33 Outr doenc p/virus NCOP",
"B34 Doenc p/virus de localiz NE",
"B35 Dermatofitose",
"B36 Outr micoses superf",
"B37 Candidiase",
"B38 Coccidioidomicose",
"B39 Histoplasmose",
"B40 Blastomicose",
"B41 Paracoccidioidomicose",
"B42 Esporotricose",
"B43 Cromomicose e abscesso feomicotico",
"B44 Aspergilose",
"B45 Criptococose",
"B46 Zigomicose",
"B47 Micetoma",
"B48 Outr micoses NCOP",
"B49 Micose NE",
"B50 Malaria p/Plasmodium falciparum",
"B51 Malaria p/Plasmodium vivax",
"B52 Malaria p/Plasmodium malariae",
"B53 Outr form malaria conf p/exames parasitolog",
"B54 Malaria NE",
"B55 Leishmaniose",
"B56 Tripanossomiase africana",
"B57 Doenc de Chagas",
"B58 Toxoplasmose",
"B59 Pneumocistose",
"B60 Outr doenc dev protozoarios NCOP",
"B64 Doenc NE dev protozoarios",
"B65 Esquistossomose",
"B66 Outr infestacoes p/trematodeos",
"B67 Equinococose",
"B68 Infestacao p/Taenia",
"B69 Cisticercose",
"B71 Outr infestacoes p/cestoides",
"B72 Dracontiase",
"B73 Oncocercose",
"B74 Filariose",
"B75 Triquinose",
"B76 Ancilostomiase",
"B77 Ascaridiase",
"B78 Estrongiloidiase",
"B79 Tricuriase",
"B80 Oxiuriase",
"B81 Outr helmintiases intestinais NCOP",
"B82 Parasitose intestinal NE",
"B83 Outr helmintiases",
"B85 Pediculose e ftiriase",
"B86 Escabiose",
"B87 Miiase",
"B88 Outr infestacoes",
"B89 Doenc parasit NE",
"B90 Sequelas de tuberc",
"B91 Sequelas de poliomielite",
"B92 Sequelas de hanseniase",
"B94 Sequelas de outr doenc infecc e parasit e NE",
"B95 Estr/estafilococo causa doenc class outr cap",
"B96 Outr agent bacter causa doenc class outr cap",
"B97 Virus como doenc class outr cap",
"B99 Doenc infecc outr e as NE",
"G00 Meningite bacter NCOP",
"G03 Meningite dev outr causas e a causas NE",
"J00 Nasofaringite aguda",
"J01 Sinusite aguda",
"J02 Faringite aguda",
"J03 Amigdalite aguda",
"J04 Laringite e traqueite agudas",
"J05 Laringite obstrutiva aguda e epiglotite",
"J06 Infecc agudas vias aereas super loc mult NE",
"J09 Influenza dev virus gripe aviária",
"J10 Influenza dev outro virus influenza ident",
"J11 Influenza dev virus nao identificado",
"J12 Pneumonia viral NCOP",
"J13 Pneumonia dev Streptococcus pneumoniae",
"J14 Pneumonia dev Haemophilus infuenzae",
"J15 Pneumonia bacter NCOP",
"J16 Pneumonia dev out microorg infecc espec NCOP",
"J18 Pneumonia p/microorg NE",
"J20 Bronquite aguda",
"J21 Bronquiolite aguda",
"J22 Infecc agudas NE das vias aereas infer"
)
join_names <- join_names(agr = agr)
sim <- get_sim_categorias(conn = conn, ano = ano, agr = agr, causabas_categorias = categorias)
pop <- get_pop(conn = conn, ano = ano, agr = agr)
df <- dplyr::left_join(sim, pop, by = join_names) %>%
mutate(indi_c.17 = sim/pop*multi) %>%
select(1, 4)
return(df)
}
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