readme + data dictionary + Brazil example

.gitignore

@@ -17,3 +17,8 @@ vignettes/*.pdf
 
 # OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
 .httr-oauth
+.Rproj.user
+
+# html files
+.html
+

Brazil/BR_Data_Guide.csv

@@ -0,0 +1,8 @@
+data_field_code,data_field,full_description_en,full_description_original,report_name,unit
+BR0001,microcephaly_under_investiagion,"Reported cases of microcephaly and/or altered centreal nervous system, suggestive of congenital infection in fetuses, abortions, stillbirths or recent live births - Under Investigation","Casos notificados de Microcefalia e/ou Altera??es do SNC, sugestivos de infec??o cong?nita, em fetos, abortamentos, natimortos ou rec?m-nascidos vivos - Permanecem em investiga??o",COES_Microcephaly,cases
+BR0002,microcephaly_confirmed,"Reported cases of microcephaly and/or altered centreal nervous system, suggestive of congenital infection in fetuses, abortions, stillbirths or recent live births - Investigated and confirmed","Casos notificados de Microcefalia e/ou Altera??es do SNC, sugestivos de infec??o cong?nita, em fetos, abortamentos, natimortos ou rec?m-nascidos vivos - investigados e confirmados",COES_Microcephaly,cases
+BR0003,microcephaly_not,"Reported cases of microcephaly and/or altered centreal nervous system, suggestive of congenital infection in fetuses, abortions, stillbirths or recent live births - Discarded","Casos notificados de Microcefalia e/ou Altera??es do SNC, sugestivos de infec??o cong?nita, em fetos, abortamentos, natimortos ou rec?m-nascidos vivos - investigados e descartados",COES_Microcephaly,cases
+BR0004,municipality_microcephaly,Number of municipalities with confirmed microcephaly cases,Total de munic?pios com casos confirmados,COES_Microcephaly,municipalities
+BR0005,microcephaly_fatal_under_investiagion,Classification of suspect cases of microcephaly and/or altered central nervous system who died after birth or during pregnancy - Under investigation,Classifica??o dos casos notificados com microcefalia e/ou altera??o do SNC que evolu?ram para ?bito ap?s o parto ou durante a gesta??o - Em investiga??o,COES_Microcephaly,cases
+BR0006,microcephaly_fatal_confirmed,Classification of suspect cases of microcephaly and/or altered central nervous system who died after birth or during pregnancy - Confirmed,Classifica??o dos casos notificados com microcefalia e/ou altera??o do SNC que evolu?ram para ?bito ap?s o parto ou durante a gesta??o - Confirmado,COES_Microcephaly,cases
+BR0007,microcephaly_fatal_not,Classification of suspect cases of microcephaly and/or altered central nervous system who died after birth or during pregnancy - Discarded,Classifica??o dos casos notificados com microcefalia e/ou altera??o do SNC que evolu?ram para ?bito ap?s o parto ou durante a gesta??o - Descartado,COES_Microcephaly,cases

Brazil/BR_Places.csv

@@ -0,0 +1,28 @@
+"location","location_type","country","state_province","district_country_muncipality","city","alt_name1","alt_name2"
+"Brazil-Alagoas","state","Brazil","Alagoas",NA,NA,"Alagoas",NA
+"Brazil-Bahia","state","Brazil","Bahia",NA,NA,"Bahia",NA
+"Brazil-Ceara","state","Brazil","Ceara",NA,NA,"Cear",NA
+"Brazil-Maranhao","state","Brazil","Maranhao",NA,NA,"Maranho",NA
+"Brazil-Paraiba","state","Brazil","Paraiba",NA,NA,"Paraba",NA
+"Brazil-Pernambuco","state","Brazil","Pernambuco",NA,NA,"Pernambuco",NA
+"Brazil-Piaui","state","Brazil","Piaui",NA,NA,"Piau",NA
+"Brazil-Rio_Grande_do_Norte","state","Brazil","Rio Grande do Norte",NA,NA,"Rio Grande do Norte",NA
+"Brazil-Sergipe","state","Brazil","Sergipe",NA,NA,"Sergipe",NA
+"Brazil-Espirito_Santo","state","Brazil","Espirito Santo",NA,NA,"Esprito Santo",NA
+"Brazil-Minas_Gerais","state","Brazil","Minas Gerais",NA,NA,"Minas Gerais",NA
+"Brazil-Rio_de_Janeiro","state","Brazil","Rio de Janeiro",NA,NA,"Rio de Janeiro",NA
+"Brazil-Sao_Paulo","state","Brazil","Sao Paulo",NA,NA,"So Paulo",NA
+"Brazil-Acre","state","Brazil","Acre",NA,NA,"Acre",NA
+"Brazil-Amapa","state","Brazil","Amapa",NA,NA,"Amap",NA
+"Brazil-Amazonas","state","Brazil","Amazonas",NA,NA,"Amazonas",NA
+"Brazil-Para","state","Brazil","Para",NA,NA,"Par",NA
+"Brazil-Rondonia","state","Brazil","Rondonia",NA,NA,"Rondnia",NA
+"Brazil-Roraima","state","Brazil","Roraima",NA,NA,"Roraima",NA
+"Brazil-Tocantins","state","Brazil","Tocantins",NA,NA,"Tocantins",NA
+"Brazil-Distrito_Federal","state","Brazil","Distrito Federal",NA,NA,"Distrito Federal",NA
+"Brazil-Goias","state","Brazil","Goias",NA,NA,"Gois",NA
+"Brazil-Mato_Grosso","state","Brazil","Mato Grosso",NA,NA,"Mato Grosso",NA
+"Brazil-Mato_Grosso_do_Sul","state","Brazil","Mato Grosso do Sul",NA,NA,"Mato Grosso do Sul",NA
+"Brazil-Parana","state","Brazil","Parana",NA,NA,"Paran",NA
+"Brazil-Santa_Catarina","state","Brazil","Santa Catarina",NA,NA,"Santa Catarina",NA
+"Brazil-Rio_Grande_do_Sul","state","Brazil","Rio Grande do Sul",NA,NA,"Rio Grande do Sul",NA

Brazil/COES_Microcephaly/data/COES_Microcephaly-2016-02-13.csv

@@ -0,0 +1,140 @@
+"report_date","location","location_type","data_field","data_field_code","time_period","time_period_type","value","unit"
+"2016-02-13","Brazil-Acre","state","microcephaly_under_investiagion","BR0001",NA,NA,22,"cases"
+"2016-02-13","Brazil-Alagoas","state","microcephaly_under_investiagion","BR0001",NA,NA,90,"cases"
+"2016-02-13","Brazil-Amapa","state","microcephaly_under_investiagion","BR0001",NA,NA,NA,"cases"
+"2016-02-13","Brazil-Amazonas","state","microcephaly_under_investiagion","BR0001",NA,NA,NA,"cases"
+"2016-02-13","Brazil-Bahia","state","microcephaly_under_investiagion","BR0001",NA,NA,583,"cases"
+"2016-02-13","Brazil-Ceara","state","microcephaly_under_investiagion","BR0001",NA,NA,243,"cases"
+"2016-02-13","Brazil-Distrito_Federal","state","microcephaly_under_investiagion","BR0001",NA,NA,6,"cases"
+"2016-02-13","Brazil-Espirito_Santo","state","microcephaly_under_investiagion","BR0001",NA,NA,58,"cases"
+"2016-02-13","Brazil-Goias","state","microcephaly_under_investiagion","BR0001",NA,NA,72,"cases"
+"2016-02-13","Brazil-Maranhao","state","microcephaly_under_investiagion","BR0001",NA,NA,159,"cases"
+"2016-02-13","Brazil-Mato_Grosso","state","microcephaly_under_investiagion","BR0001",NA,NA,122,"cases"
+"2016-02-13","Brazil-Mato_Grosso_do_Sul","state","microcephaly_under_investiagion","BR0001",NA,NA,5,"cases"
+"2016-02-13","Brazil-Minas_Gerais","state","microcephaly_under_investiagion","BR0001",NA,NA,24,"cases"
+"2016-02-13","Brazil-Para","state","microcephaly_under_investiagion","BR0001",NA,NA,10,"cases"
+"2016-02-13","Brazil-Paraiba","state","microcephaly_under_investiagion","BR0001",NA,NA,423,"cases"
+"2016-02-13","Brazil-Parana","state","microcephaly_under_investiagion","BR0001",NA,NA,1,"cases"
+"2016-02-13","Brazil-Pernambuco","state","microcephaly_under_investiagion","BR0001",NA,NA,1203,"cases"
+"2016-02-13","Brazil-Piaui","state","microcephaly_under_investiagion","BR0001",NA,NA,74,"cases"
+"2016-02-13","Brazil-Rio_Grande_do_Norte","state","microcephaly_under_investiagion","BR0001",NA,NA,228,"cases"
+"2016-02-13","Brazil-Rio_Grande_do_Sul","state","microcephaly_under_investiagion","BR0001",NA,NA,0,"cases"
+"2016-02-13","Brazil-Rio_de_Janeiro","state","microcephaly_under_investiagion","BR0001",NA,NA,227,"cases"
+"2016-02-13","Brazil-Rondonia","state","microcephaly_under_investiagion","BR0001",NA,NA,1,"cases"
+"2016-02-13","Brazil-Roraima","state","microcephaly_under_investiagion","BR0001",NA,NA,8,"cases"
+"2016-02-13","Brazil-Santa_Catarina","state","microcephaly_under_investiagion","BR0001",NA,NA,0,"cases"
+"2016-02-13","Brazil-Sergipe","state","microcephaly_under_investiagion","BR0001",NA,NA,177,"cases"
+"2016-02-13","Brazil-Sao_Paulo","state","microcephaly_under_investiagion","BR0001",NA,NA,111,"cases"
+"2016-02-13","Brazil-Tocantins","state","microcephaly_under_investiagion","BR0001",NA,NA,88,"cases"
+"2016-02-13","Brazil-Acre","state","microcephaly_confirmed","BR0002",NA,NA,0,"cases"
+"2016-02-13","Brazil-Alagoas","state","microcephaly_confirmed","BR0002",NA,NA,25,"cases"
+"2016-02-13","Brazil-Amapa","state","microcephaly_confirmed","BR0002",NA,NA,NA,"cases"
+"2016-02-13","Brazil-Amazonas","state","microcephaly_confirmed","BR0002",NA,NA,NA,"cases"
+"2016-02-13","Brazil-Bahia","state","microcephaly_confirmed","BR0002",NA,NA,107,"cases"
+"2016-02-13","Brazil-Ceara","state","microcephaly_confirmed","BR0002",NA,NA,24,"cases"
+"2016-02-13","Brazil-Distrito_Federal","state","microcephaly_confirmed","BR0002",NA,NA,0,"cases"
+"2016-02-13","Brazil-Espirito_Santo","state","microcephaly_confirmed","BR0002",NA,NA,3,"cases"
+"2016-02-13","Brazil-Goias","state","microcephaly_confirmed","BR0002",NA,NA,6,"cases"
+"2016-02-13","Brazil-Maranhao","state","microcephaly_confirmed","BR0002",NA,NA,0,"cases"
+"2016-02-13","Brazil-Mato_Grosso","state","microcephaly_confirmed","BR0002",NA,NA,0,"cases"
+"2016-02-13","Brazil-Mato_Grosso_do_Sul","state","microcephaly_confirmed","BR0002",NA,NA,1,"cases"
+"2016-02-13","Brazil-Minas_Gerais","state","microcephaly_confirmed","BR0002",NA,NA,0,"cases"
+"2016-02-13","Brazil-Para","state","microcephaly_confirmed","BR0002",NA,NA,1,"cases"
+"2016-02-13","Brazil-Paraiba","state","microcephaly_confirmed","BR0002",NA,NA,56,"cases"
+"2016-02-13","Brazil-Parana","state","microcephaly_confirmed","BR0002",NA,NA,0,"cases"
+"2016-02-13","Brazil-Pernambuco","state","microcephaly_confirmed","BR0002",NA,NA,182,"cases"
+"2016-02-13","Brazil-Piaui","state","microcephaly_confirmed","BR0002",NA,NA,30,"cases"
+"2016-02-13","Brazil-Rio_Grande_do_Norte","state","microcephaly_confirmed","BR0002",NA,NA,70,"cases"
+"2016-02-13","Brazil-Rio_Grande_do_Sul","state","microcephaly_confirmed","BR0002",NA,NA,1,"cases"
+"2016-02-13","Brazil-Rio_de_Janeiro","state","microcephaly_confirmed","BR0002",NA,NA,2,"cases"
+"2016-02-13","Brazil-Rondonia","state","microcephaly_confirmed","BR0002",NA,NA,0,"cases"
+"2016-02-13","Brazil-Roraima","state","microcephaly_confirmed","BR0002",NA,NA,0,"cases"
+"2016-02-13","Brazil-Santa_Catarina","state","microcephaly_confirmed","BR0002",NA,NA,0,"cases"
+"2016-02-13","Brazil-Sergipe","state","microcephaly_confirmed","BR0002",NA,NA,0,"cases"
+"2016-02-13","Brazil-Sao_Paulo","state","microcephaly_confirmed","BR0002",NA,NA,0,"cases"
+"2016-02-13","Brazil-Tocantins","state","microcephaly_confirmed","BR0002",NA,NA,0,"cases"
+"2016-02-13","Brazil-Acre","state","microcephaly_not","BR0003",NA,NA,0,"cases"
+"2016-02-13","Brazil-Alagoas","state","microcephaly_not","BR0003",NA,NA,89,"cases"
+"2016-02-13","Brazil-Amapa","state","microcephaly_not","BR0003",NA,NA,NA,"cases"
+"2016-02-13","Brazil-Amazonas","state","microcephaly_not","BR0003",NA,NA,NA,"cases"
+"2016-02-13","Brazil-Bahia","state","microcephaly_not","BR0003",NA,NA,54,"cases"
+"2016-02-13","Brazil-Ceara","state","microcephaly_not","BR0003",NA,NA,20,"cases"
+"2016-02-13","Brazil-Distrito_Federal","state","microcephaly_not","BR0003",NA,NA,17,"cases"
+"2016-02-13","Brazil-Espirito_Santo","state","microcephaly_not","BR0003",NA,NA,3,"cases"
+"2016-02-13","Brazil-Goias","state","microcephaly_not","BR0003",NA,NA,2,"cases"
+"2016-02-13","Brazil-Maranhao","state","microcephaly_not","BR0003",NA,NA,16,"cases"
+"2016-02-13","Brazil-Mato_Grosso","state","microcephaly_not","BR0003",NA,NA,46,"cases"
+"2016-02-13","Brazil-Mato_Grosso_do_Sul","state","microcephaly_not","BR0003",NA,NA,5,"cases"
+"2016-02-13","Brazil-Minas_Gerais","state","microcephaly_not","BR0003",NA,NA,39,"cases"
+"2016-02-13","Brazil-Para","state","microcephaly_not","BR0003",NA,NA,0,"cases"
+"2016-02-13","Brazil-Paraiba","state","microcephaly_not","BR0003",NA,NA,287,"cases"
+"2016-02-13","Brazil-Parana","state","microcephaly_not","BR0003",NA,NA,9,"cases"
+"2016-02-13","Brazil-Pernambuco","state","microcephaly_not","BR0003",NA,NA,159,"cases"
+"2016-02-13","Brazil-Piaui","state","microcephaly_not","BR0003",NA,NA,12,"cases"
+"2016-02-13","Brazil-Rio_Grande_do_Norte","state","microcephaly_not","BR0003",NA,NA,20,"cases"
+"2016-02-13","Brazil-Rio_Grande_do_Sul","state","microcephaly_not","BR0003",NA,NA,0,"cases"
+"2016-02-13","Brazil-Rio_de_Janeiro","state","microcephaly_not","BR0003",NA,NA,4,"cases"
+"2016-02-13","Brazil-Rondonia","state","microcephaly_not","BR0003",NA,NA,0,"cases"
+"2016-02-13","Brazil-Roraima","state","microcephaly_not","BR0003",NA,NA,0,"cases"
+"2016-02-13","Brazil-Santa_Catarina","state","microcephaly_not","BR0003",NA,NA,1,"cases"
+"2016-02-13","Brazil-Sergipe","state","microcephaly_not","BR0003",NA,NA,8,"cases"
+"2016-02-13","Brazil-Sao_Paulo","state","microcephaly_not","BR0003",NA,NA,29,"cases"
+"2016-02-13","Brazil-Tocantins","state","microcephaly_not","BR0003",NA,NA,17,"cases"
+"2016-02-13","Brazil-Alagoas","state","municipality_microcephaly","BR0004",NA,NA,14,"municipalities"
+"2016-02-13","Brazil-Bahia","state","municipality_microcephaly","BR0004",NA,NA,26,"municipalities"
+"2016-02-13","Brazil-Ceara","state","municipality_microcephaly","BR0004",NA,NA,15,"municipalities"
+"2016-02-13","Brazil-Espirito_Santo","state","municipality_microcephaly","BR0004",NA,NA,3,"municipalities"
+"2016-02-13","Brazil-Goias","state","municipality_microcephaly","BR0004",NA,NA,5,"municipalities"
+"2016-02-13","Brazil-Mato_Grosso_do_Sul","state","municipality_microcephaly","BR0004",NA,NA,1,"municipalities"
+"2016-02-13","Brazil-Para","state","municipality_microcephaly","BR0004",NA,NA,1,"municipalities"
+"2016-02-13","Brazil-Paraiba","state","municipality_microcephaly","BR0004",NA,NA,27,"municipalities"
+"2016-02-13","Brazil-Pernambuco","state","municipality_microcephaly","BR0004",NA,NA,65,"municipalities"
+"2016-02-13","Brazil-Piaui","state","municipality_microcephaly","BR0004",NA,NA,9,"municipalities"
+"2016-02-13","Brazil-Rio_Grande_do_Norte","state","municipality_microcephaly","BR0004",NA,NA,34,"municipalities"
+"2016-02-13","Brazil-Rio_Grande_do_Sul","state","municipality_microcephaly","BR0004",NA,NA,1,"municipalities"
+"2016-02-13","Brazil-Rio_de_Janeiro","state","municipality_microcephaly","BR0004",NA,NA,2,"municipalities"
+"2016-02-13","Brazil-Acre","state","microcephaly_fatal_under_investiagion","BR0005",NA,NA,1,"cases"
+"2016-02-13","Brazil-Alagoas","state","microcephaly_fatal_under_investiagion","BR0005",NA,NA,2,"cases"
+"2016-02-13","Brazil-Bahia","state","microcephaly_fatal_under_investiagion","BR0005",NA,NA,18,"cases"
+"2016-02-13","Brazil-Ceara","state","microcephaly_fatal_under_investiagion","BR0005",NA,NA,3,"cases"
+"2016-02-13","Brazil-Goias","state","microcephaly_fatal_under_investiagion","BR0005",NA,NA,1,"cases"
+"2016-02-13","Brazil-Maranhao","state","microcephaly_fatal_under_investiagion","BR0005",NA,NA,1,"cases"
+"2016-02-13","Brazil-Mato_Grosso","state","microcephaly_fatal_under_investiagion","BR0005",NA,NA,3,"cases"
+"2016-02-13","Brazil-Minas_Gerais","state","microcephaly_fatal_under_investiagion","BR0005",NA,NA,0,"cases"
+"2016-02-13","Brazil-Paraiba","state","microcephaly_fatal_under_investiagion","BR0005",NA,NA,10,"cases"
+"2016-02-13","Brazil-Parana","state","microcephaly_fatal_under_investiagion","BR0005",NA,NA,0,"cases"
+"2016-02-13","Brazil-Pernambuco","state","microcephaly_fatal_under_investiagion","BR0005",NA,NA,16,"cases"
+"2016-02-13","Brazil-Piaui","state","microcephaly_fatal_under_investiagion","BR0005",NA,NA,0,"cases"
+"2016-02-13","Brazil-Rio_Grande_do_Norte","state","microcephaly_fatal_under_investiagion","BR0005",NA,NA,6,"cases"
+"2016-02-13","Brazil-Sergipe","state","microcephaly_fatal_under_investiagion","BR0005",NA,NA,7,"cases"
+"2016-02-13","Brazil-Sao_Paulo","state","microcephaly_fatal_under_investiagion","BR0005",NA,NA,2,"cases"
+"2016-02-13","Brazil-Acre","state","microcephaly_fatal_confirmed","BR0006",NA,NA,0,"cases"
+"2016-02-13","Brazil-Alagoas","state","microcephaly_fatal_confirmed","BR0006",NA,NA,2,"cases"
+"2016-02-13","Brazil-Bahia","state","microcephaly_fatal_confirmed","BR0006",NA,NA,0,"cases"
+"2016-02-13","Brazil-Ceara","state","microcephaly_fatal_confirmed","BR0006",NA,NA,9,"cases"
+"2016-02-13","Brazil-Goias","state","microcephaly_fatal_confirmed","BR0006",NA,NA,0,"cases"
+"2016-02-13","Brazil-Maranhao","state","microcephaly_fatal_confirmed","BR0006",NA,NA,0,"cases"
+"2016-02-13","Brazil-Mato_Grosso","state","microcephaly_fatal_confirmed","BR0006",NA,NA,0,"cases"
+"2016-02-13","Brazil-Minas_Gerais","state","microcephaly_fatal_confirmed","BR0006",NA,NA,0,"cases"
+"2016-02-13","Brazil-Paraiba","state","microcephaly_fatal_confirmed","BR0006",NA,NA,3,"cases"
+"2016-02-13","Brazil-Parana","state","microcephaly_fatal_confirmed","BR0006",NA,NA,0,"cases"
+"2016-02-13","Brazil-Pernambuco","state","microcephaly_fatal_confirmed","BR0006",NA,NA,0,"cases"
+"2016-02-13","Brazil-Piaui","state","microcephaly_fatal_confirmed","BR0006",NA,NA,3,"cases"
+"2016-02-13","Brazil-Rio_Grande_do_Norte","state","microcephaly_fatal_confirmed","BR0006",NA,NA,10,"cases"
+"2016-02-13","Brazil-Sergipe","state","microcephaly_fatal_confirmed","BR0006",NA,NA,0,"cases"
+"2016-02-13","Brazil-Sao_Paulo","state","microcephaly_fatal_confirmed","BR0006",NA,NA,0,"cases"
+"2016-02-13","Brazil-Acre","state","microcephaly_fatal_not","BR0007",NA,NA,0,"cases"
+"2016-02-13","Brazil-Alagoas","state","microcephaly_fatal_not","BR0007",NA,NA,0,"cases"
+"2016-02-13","Brazil-Bahia","state","microcephaly_fatal_not","BR0007",NA,NA,0,"cases"
+"2016-02-13","Brazil-Ceara","state","microcephaly_fatal_not","BR0007",NA,NA,0,"cases"
+"2016-02-13","Brazil-Goias","state","microcephaly_fatal_not","BR0007",NA,NA,1,"cases"
+"2016-02-13","Brazil-Maranhao","state","microcephaly_fatal_not","BR0007",NA,NA,0,"cases"
+"2016-02-13","Brazil-Mato_Grosso","state","microcephaly_fatal_not","BR0007",NA,NA,0,"cases"
+"2016-02-13","Brazil-Minas_Gerais","state","microcephaly_fatal_not","BR0007",NA,NA,2,"cases"
+"2016-02-13","Brazil-Paraiba","state","microcephaly_fatal_not","BR0007",NA,NA,1,"cases"
+"2016-02-13","Brazil-Parana","state","microcephaly_fatal_not","BR0007",NA,NA,2,"cases"
+"2016-02-13","Brazil-Pernambuco","state","microcephaly_fatal_not","BR0007",NA,NA,0,"cases"
+"2016-02-13","Brazil-Piaui","state","microcephaly_fatal_not","BR0007",NA,NA,3,"cases"
+"2016-02-13","Brazil-Rio_Grande_do_Norte","state","microcephaly_fatal_not","BR0007",NA,NA,0,"cases"
+"2016-02-13","Brazil-Sergipe","state","microcephaly_fatal_not","BR0007",NA,NA,0,"cases"
+"2016-02-13","Brazil-Sao_Paulo","state","microcephaly_fatal_not","BR0007",NA,NA,2,"cases"