From 26a91565e6c683d250892e61c96c91a9315a58ce Mon Sep 17 00:00:00 2001 From: Diogo Date: Tue, 12 Sep 2017 11:15:58 -0300 Subject: [PATCH 1/2] =?UTF-8?q?Inclu=C3=ADndo=20dados=20limpos?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Incluí uma tabela com registros de algumas espécies. O arquivo é " dados_clean.csv " --- ENM/data/dados_clean.csv | 619 +++++++++++++++++++++++++++++++++++++++ ENM/data_clean.r | 79 +++++ 2 files changed, 698 insertions(+) create mode 100644 ENM/data/dados_clean.csv create mode 100644 ENM/data_clean.r diff --git a/ENM/data/dados_clean.csv b/ENM/data/dados_clean.csv new file mode 100644 index 0000000..2e82f86 --- /dev/null +++ b/ENM/data/dados_clean.csv @@ -0,0 +1,619 @@ +"sp","long","lat" +"Eugenia florida DC.",-35.019,-6.379 +"Eugenia florida DC.",-34.858,-7.775 +"Eugenia florida DC.",-34.897,-8.102 +"Eugenia florida DC.",-36.376,-10.421 +"Eugenia florida DC.",-42.073,-2.722 +"Eugenia florida DC.",-41.676,-2.92 +"Eugenia florida DC.",-39.957,-3.033 +"Eugenia florida DC.",-38.574,-3.744 +"Eugenia florida DC.",-35.002,-7.835 +"Eugenia florida DC.",-34.946,-7.999 +"Eugenia florida DC.",-34.986,-8.298 +"Eugenia florida DC.",-35.168,-8.577 +"Eugenia florida DC.",-35.175,-8.724 +"Eugenia florida DC.",-35.307,-9.08 +"Eugenia florida 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Barneby & J.W.Grimes",-48.78,-27.99 +"Abarema langsdorffii (Benth.) Barneby & J.W.Grimes",-48.96,-27.994 +"Abarema langsdorffii (Benth.) Barneby & J.W.Grimes",-48.959,-28.263 +"Abarema langsdorffii (Benth.) Barneby & J.W.Grimes",-49.232,-28.353 +"Abarema langsdorffii (Benth.) Barneby & J.W.Grimes",-49.497,-28.529 +"Abarema langsdorffii (Benth.) Barneby & J.W.Grimes",-49.59,-28.62 +"Abarema langsdorffii (Benth.) Barneby & J.W.Grimes",-49.86,-28.8 +"Abarema langsdorffii (Benth.) Barneby & J.W.Grimes",-49.983,-29.365 +"Abarema langsdorffii (Benth.) Barneby & J.W.Grimes",-42.004,-21.978 +"Abarema langsdorffii (Benth.) Barneby & J.W.Grimes",-43.893,-22.001 +"Abarema langsdorffii (Benth.) Barneby & J.W.Grimes",-42.531,-22.305 +"Abarema langsdorffii (Benth.) Barneby & J.W.Grimes",-43.413,-22.551 +"Abarema langsdorffii (Benth.) Barneby & J.W.Grimes",-43.301,-22.952 +"Abarema langsdorffii (Benth.) Barneby & J.W.Grimes",-46.479,-23.396 +"Abarema langsdorffii (Benth.) Barneby & J.W.Grimes",-46.768,-23.468 +"Abarema langsdorffii (Benth.) Barneby & J.W.Grimes",-46.729,-23.566 +"Abarema langsdorffii (Benth.) Barneby & J.W.Grimes",-45.753,-23.624 +"Abarema langsdorffii (Benth.) Barneby & J.W.Grimes",-46.888,-23.641 +"Abarema langsdorffii (Benth.) Barneby & J.W.Grimes",-46.625,-23.656 +"Abarema langsdorffii (Benth.) Barneby & J.W.Grimes",-46.491,-23.767 +"Abarema langsdorffii (Benth.) Barneby & J.W.Grimes",-46.971,-23.772 +"Abarema langsdorffii (Benth.) Barneby & J.W.Grimes",-48.683,-24.533 +"Abarema langsdorffii (Benth.) Barneby & J.W.Grimes",-50.13,-27 +"Abarema langsdorffii (Benth.) Barneby & J.W.Grimes",-49.14,-27.27 +"Abarema langsdorffii (Benth.) Barneby & J.W.Grimes",-49.41,-27.27 +"Abarema langsdorffii (Benth.) Barneby & J.W.Grimes",-49.41,-27.36 +"Abarema langsdorffii (Benth.) Barneby & J.W.Grimes",-49.05,-27.54 +"Abarema langsdorffii (Benth.) Barneby & J.W.Grimes",-49.23,-27.9 +"Abarema langsdorffii (Benth.) 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Barneby & J.W.Grimes",-50.606,-21.133 +"Abarema langsdorffii (Benth.) Barneby & J.W.Grimes",-51.826,-23.279 +"Abarema langsdorffii (Benth.) Barneby & J.W.Grimes",-53.368,-23.691 +"Abarema langsdorffii (Benth.) Barneby & J.W.Grimes",-47.11,-22.822 +"Abarema langsdorffii (Benth.) Barneby & J.W.Grimes",-46.704,-22.935 +"Abarema langsdorffii (Benth.) Barneby & J.W.Grimes",-51.254,-23.45 +"Ouratea semiserrata (Mart. & Nees) Engl.",-40.027,-16.364 +"Ouratea semiserrata (Mart. & Nees) Engl.",-42.482,-20.701 +"Ouratea semiserrata (Mart. & Nees) Engl.",-42.431,-19.511 +"Ouratea semiserrata (Mart. & Nees) Engl.",-42.865,-19.627 +"Ouratea semiserrata (Mart. & Nees) Engl.",-42.618,-19.684 +"Ouratea semiserrata (Mart. & Nees) Engl.",-41.823,-19.721 +"Ouratea semiserrata (Mart. & Nees) Engl.",-42.484,-19.748 +"Ouratea semiserrata (Mart. & Nees) Engl.",-41.708,-19.804 +"Ouratea semiserrata (Mart. & Nees) Engl.",-42.929,-20.428 +"Ouratea semiserrata (Mart. & Nees) Engl.",-43.02,-20.502 +"Ouratea semiserrata (Mart. & Nees) Engl.",-41.778,-17.614 +"Ouratea semiserrata (Mart. & Nees) Engl.",-42.529,-17.879 +"Ouratea semiserrata (Mart. & Nees) Engl.",-41.466,-18.073 +"Ouratea semiserrata (Mart. & Nees) Engl.",-43.083,-18.38 +"Ouratea semiserrata (Mart. & Nees) Engl.",-42.755,-18.546 +"Ouratea semiserrata (Mart. & Nees) Engl.",-41.552,-19.301 +"Ouratea semiserrata (Mart. & Nees) Engl.",-43.117,-19.847 +"Ouratea semiserrata (Mart. & Nees) Engl.",-43.363,-19.902 +"Ouratea semiserrata (Mart. & Nees) Engl.",-43.386,-20.369 +"Ouratea semiserrata (Mart. & Nees) Engl.",-44.616,-20.437 +"Ouratea semiserrata (Mart. & Nees) Engl.",-43.372,-20.629 +"Ouratea semiserrata (Mart. & Nees) Engl.",-42.873,-20.778 +"Ouratea semiserrata (Mart. & Nees) Engl.",-42.105,-15.389 +"Ouratea semiserrata (Mart. & Nees) Engl.",-41.578,-15.394 +"Ouratea semiserrata (Mart. & Nees) Engl.",-41.221,-16.639 +"Ouratea semiserrata (Mart. & Nees) Engl.",-43.191,-17.507 +"Ouratea semiserrata (Mart. & Nees) Engl.",-40.73,-14.846 +"Ouratea semiserrata (Mart. & Nees) Engl.",-41.201,-15.178 +"Ouratea semiserrata (Mart. & Nees) Engl.",-40.52,-15.78 +"Ouratea semiserrata (Mart. & Nees) Engl.",-41.301,-15.954 +"Ouratea semiserrata (Mart. & Nees) Engl.",-40.844,-16.058 +"Ouratea semiserrata (Mart. & Nees) Engl.",-41.064,-16.127 +"Ouratea semiserrata (Mart. & Nees) Engl.",-42.235,-16.748 +"Ouratea semiserrata (Mart. & Nees) Engl.",-42.703,-17.034 +"Ouratea semiserrata (Mart. & Nees) Engl.",-43.671,-19.813 +"Ouratea semiserrata (Mart. & Nees) Engl.",-43.669,-20.072 +"Ouratea semiserrata (Mart. & Nees) Engl.",-43.477,-20.121 +"Ouratea semiserrata (Mart. & Nees) Engl.",-43.548,-20.291 +"Ouratea semiserrata (Mart. & Nees) Engl.",-43.724,-20.497 +"Ouratea semiserrata (Mart. & Nees) Engl.",-43.501,-20.434 +"Ouratea semiserrata (Mart. & Nees) Engl.",-43.533,-19.215 +"Ouratea semiserrata (Mart. & Nees) Engl.",-43.512,-20.18 +"Ouratea semiserrata (Mart. & Nees) Engl.",-43.531,-18.983 +"Ouratea semiserrata (Mart. & Nees) Engl.",-43.972,-19.877 +"Ouratea semiserrata (Mart. & Nees) Engl.",-44.242,-19.948 +"Ouratea semiserrata (Mart. & Nees) Engl.",-41.309,-12.923 +"Ouratea semiserrata (Mart. & Nees) Engl.",-41.798,-13.32 +"Ouratea semiserrata (Mart. & Nees) Engl.",-41.267,-13.39 +"Ouratea semiserrata (Mart. & Nees) Engl.",-41.963,-13.511 +"Ouratea semiserrata (Mart. & Nees) Engl.",-47.249,-24.521 +"Ouratea semiserrata (Mart. & Nees) Engl.",-46.973,-23.23 +"Ouratea semiserrata (Mart. & Nees) Engl.",-46.479,-23.396 +"Ouratea semiserrata (Mart. & Nees) Engl.",-46.729,-23.566 +"Ouratea semiserrata (Mart. & Nees) Engl.",-46.52,-23.18 +"Ouratea semiserrata (Mart. & Nees) Engl.",-43.885,-21.708 +"Ouratea semiserrata (Mart. & Nees) Engl.",-43.89,-21.969 +"Ouratea semiserrata (Mart. & Nees) Engl.",-44.738,-22.135 +"Ouratea semiserrata (Mart. & Nees) Engl.",-44.82,-22.361 +"Ouratea semiserrata (Mart. & Nees) Engl.",-45.901,-22.747 +"Ouratea semiserrata (Mart. & Nees) Engl.",-44.82,-22.377 +"Ouratea semiserrata (Mart. & Nees) Engl.",-42.882,-21.964 +"Ouratea semiserrata (Mart. & Nees) Engl.",-44.651,-22.407 +"Ouratea semiserrata (Mart. & Nees) Engl.",-44.876,-22.428 +"Ouratea semiserrata (Mart. & Nees) Engl.",-42.07,-20.893 +"Ouratea semiserrata (Mart. & Nees) Engl.",-42.429,-21.08 +"Ouratea semiserrata (Mart. & Nees) Engl.",-42.615,-21.245 +"Ouratea semiserrata (Mart. & Nees) Engl.",-43.105,-21.273 +"Ouratea semiserrata (Mart. & Nees) Engl.",-43.252,-21.551 +"Ouratea semiserrata (Mart. & Nees) Engl.",-43.318,-21.748 +"Ouratea semiserrata (Mart. & Nees) Engl.",-45.622,-22.766 +"Ouratea semiserrata (Mart. & Nees) Engl.",-49.719,-24.111 +"Ouratea semiserrata (Mart. & Nees) Engl.",-50.033,-25.221 +"Ouratea semiserrata (Mart. & Nees) Engl.",-47.415,-20.416 +"Ouratea semiserrata (Mart. & Nees) Engl.",-44.916,-20.845 +"Ouratea semiserrata (Mart. & Nees) Engl.",-45.473,-21.155 +"Ouratea semiserrata (Mart. & Nees) Engl.",-44.904,-21.158 +"Ouratea semiserrata (Mart. & Nees) Engl.",-45.121,-21.193 +"Ouratea semiserrata (Mart. & Nees) Engl.",-44.789,-21.225 +"Ouratea semiserrata (Mart. & Nees) Engl.",-44.971,-21.229 +"Ouratea semiserrata (Mart. & Nees) Engl.",-44.609,-21.353 +"Ouratea semiserrata (Mart. & Nees) Engl.",-46.28,-21.371 +"Ouratea semiserrata (Mart. & Nees) Engl.",-45.398,-21.617 +"Ouratea semiserrata (Mart. & Nees) Engl.",-43.703,-21.191 +"Ouratea semiserrata (Mart. & Nees) Engl.",-44.986,-21.331 +"Ouratea semiserrata (Mart. & Nees) Engl.",-44.945,-21.686 +"Ouratea semiserrata (Mart. & Nees) Engl.",-45.323,-21.934 +"Ouratea semiserrata (Mart. & Nees) Engl.",-46.567,-22.048 +"Ouratea semiserrata (Mart. & Nees) Engl.",-46.348,-22.081 +"Ouratea semiserrata (Mart. & Nees) Engl.",-46.556,-21.773 +"Ouratea semiserrata (Mart. & Nees) Engl.",-44.143,-21.067 +"Leandra carassana (DC.) Cogn.",-39.331,-15.165 +"Leandra carassana (DC.) Cogn.",-39.575,-15.382 +"Leandra carassana (DC.) Cogn.",-40.729,-20.016 +"Leandra carassana (DC.) Cogn.",-41.174,-20.303 +"Leandra carassana (DC.) Cogn.",-41.468,-20.379 +"Leandra carassana (DC.) Cogn.",-41.74,-20.493 +"Leandra carassana (DC.) Cogn.",-42.482,-20.701 +"Leandra carassana (DC.) Cogn.",-41.844,-20.441 +"Leandra carassana (DC.) Cogn.",-43.501,-20.434 +"Leandra carassana (DC.) Cogn.",-43.512,-20.18 +"Leandra carassana (DC.) Cogn.",-43.458,-20.079 +"Leandra carassana (DC.) Cogn.",-41.798,-13.32 +"Leandra carassana (DC.) Cogn.",-43.614,-18.265 +"Leandra carassana (DC.) Cogn.",-41.963,-13.511 +"Leandra carassana (DC.) Cogn.",-50.038,-27.092 +"Leandra carassana (DC.) Cogn.",-49.77,-27.27 +"Leandra carassana (DC.) Cogn.",-42.531,-22.305 +"Leandra carassana (DC.) Cogn.",-43.413,-22.551 +"Leandra carassana (DC.) Cogn.",-45.753,-23.624 +"Leandra carassana (DC.) Cogn.",-46.325,-23.769 +"Leandra carassana (DC.) Cogn.",-48.935,-24.69 +"Leandra carassana (DC.) Cogn.",-48.901,-25.333 +"Leandra carassana (DC.) Cogn.",-49.141,-26.187 +"Leandra carassana (DC.) Cogn.",-49.947,-26.549 +"Leandra carassana (DC.) Cogn.",-50.04,-26.73 +"Leandra carassana (DC.) Cogn.",-50.13,-27 +"Leandra carassana (DC.) Cogn.",-49.23,-27.09 +"Leandra carassana (DC.) Cogn.",-49.68,-27.18 +"Leandra carassana (DC.) Cogn.",-50.13,-27.18 +"Leandra carassana (DC.) Cogn.",-49.41,-27.27 +"Leandra carassana (DC.) Cogn.",-49.771,-27.45 +"Leandra carassana (DC.) Cogn.",-49.05,-27.54 +"Leandra carassana (DC.) Cogn.",-49.23,-27.9 +"Leandra carassana (DC.) Cogn.",-48.87,-28.08 +"Leandra carassana (DC.) Cogn.",-49.522,-28.462 +"Leandra carassana (DC.) Cogn.",-44.54,-22.217 +"Leandra carassana (DC.) Cogn.",-44.623,-22.428 +"Leandra carassana (DC.) Cogn.",-42.95,-22.454 +"Leandra carassana (DC.) Cogn.",-44.393,-22.825 +"Leandra carassana (DC.) Cogn.",-49.41,-26.55 +"Leandra carassana (DC.) Cogn.",-49.538,-26.896 +"Leandra carassana (DC.) Cogn.",-49.15,-27.628 +"Leandra carassana (DC.) Cogn.",-43.89,-21.969 +"Leandra carassana (DC.) Cogn.",-48.97,-25.523 +"Leandra carassana (DC.) Cogn.",-48.859,-25.609 +"Leandra carassana (DC.) Cogn.",-48.691,-25.627 +"Leandra carassana (DC.) Cogn.",-49.05,-26.1 +"Leandra carassana (DC.) Cogn.",-50.223,-26.817 +"Leandra carassana (DC.) Cogn.",-49.771,-27.54 +"Leandra carassana (DC.) Cogn.",-48.819,-27.822 +"Leandra carassana (DC.) Cogn.",-49.496,-28.172 +"Leandra carassana (DC.) Cogn.",-42.882,-21.964 +"Leandra carassana (DC.) Cogn.",-45.944,-22.723 +"Leandra carassana (DC.) Cogn.",-46.031,-22.88 +"Leandra carassana (DC.) Cogn.",-49.588,-28.432 +"Leandra carassana (DC.) Cogn.",-44.651,-22.407 +"Leandra carassana (DC.) Cogn.",-44.876,-22.428 +"Leandra carassana (DC.) Cogn.",-43.913,-21.741 +"Leandra carassana (DC.) Cogn.",-44.603,-22.336 +"Leandra carassana (DC.) Cogn.",-46.104,-22.785 +"Leandra carassana (DC.) Cogn.",-44.772,-22.127 +"Leandra carassana (DC.) Cogn.",-45.622,-22.766 +"Leandra carassana (DC.) Cogn.",-49.305,-25.418 +"Leandra carassana (DC.) Cogn.",-49.818,-28.55 +"Leandra carassana (DC.) Cogn.",-50.201,-29.313 +"Leandra carassana (DC.) Cogn.",-50.392,-29.421 +"Leandra carassana (DC.) Cogn.",-52.194,-24.562 +"Leandra carassana (DC.) Cogn.",-52.997,-24.987 +"Leandra carassana (DC.) Cogn.",-50.018,-25.6 +"Leandra carassana (DC.) Cogn.",-50.251,-25.651 +"Leandra carassana (DC.) Cogn.",-49.715,-25.816 +"Leandra carassana (DC.) Cogn.",-51.519,-26.096 +"Leandra carassana (DC.) Cogn.",-52.678,-26.193 +"Leandra carassana (DC.) Cogn.",-52.217,-26.317 +"Leandra carassana (DC.) Cogn.",-51.837,-24.771 +"Leandra carassana (DC.) Cogn.",-51.285,-25.075 +"Leandra carassana (DC.) Cogn.",-50.674,-28.928 +"Leandra carassana (DC.) Cogn.",-44.986,-21.331 +"Leandra carassana (DC.) Cogn.",-44.945,-21.686 +"Leandra carassana (DC.) Cogn.",-46.253,-21.922 +"Leandra carassana (DC.) Cogn.",-45.323,-21.934 +"Leandra carassana (DC.) Cogn.",-46.556,-21.773 diff --git a/ENM/data_clean.r b/ENM/data_clean.r new file mode 100644 index 0000000..001a583 --- /dev/null +++ b/ENM/data_clean.r @@ -0,0 +1,79 @@ + +library(raster) +source("https://raw.githubusercontent.com/diogosbr/modelagem/master/clean.R") +abio=raster::stack(list.files("./env", pattern = '.gri',full.names = T)) + + + +pts=read.table("./data/FLORA_occs_final.csv", h=T, sep=",") +pts + + +#sp1 +eug=pts[pts$sp==levels(pts$sp)[654],] +dim(eug) + +raster::plot(abio[[1]]) +points(eug[,3:4]) + +eug.c=clean(eug[,3:4], abio[[1]]) +eug.c$sp=eug$sp[1] + +#sp2 +sp2=pts[pts$sp==levels(pts$sp)[5],] +dim(sp2) + +raster::plot(abio[[1]]) +points(sp2[,3:4]) + +sp2.c=clean(sp2[,3:4], abio[[1]]) +sp2.c$sp=sp2$sp[1] + +#sp3 +#Não +sp3=pts[pts$sp==levels(pts$sp)[2046],] +dim(sp3) + +raster::plot(abio[[1]]) +points(sp3[,3:4]) + +sp3.c=clean(sp3[,3:4], abio[[1]]) +sp3.c$sp=sp3$sp[1] + +#sp4 +sp4=pts[pts$sp==levels(pts$sp)[1431],] +dim(sp4) + +raster::plot(abio[[1]]) +points(sp4[,3:4]) + +sp4.c=clean(sp4[,3:4], abio[[1]]) +sp4.c$sp=sp4$sp[1] + +#sp5 +sp5=pts[pts$sp==levels(pts$sp)[969],] +dim(sp5) + +raster::plot(abio[[1]]) +points(sp5[,3:4]) + +sp5.c=clean(sp5[,3:4], abio[[1]]) +sp5.c$sp=sp5$sp[1] + + +#concatenando + +dados=rbind(eug.c,sp2.c,sp4.c,sp5.c) +dados=dados[,c(3,1,2)] + +dim(dados) + +write.table(dados,"./data/dados_clean.csv", sep=",", row.names = F) + + + + + + + + From 2b12405495af554af933c1895b30fd84bf3197ec Mon Sep 17 00:00:00 2001 From: Guilherme Gall Date: Wed, 13 Sep 2017 13:22:29 -0300 Subject: [PATCH 2/2] Muda nome da coluna "long" para "lon" em dados_clean.csv MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit A troca foi feita pela mesma razão citada em Model-R/Front-end#8: as funções de modelagem aceitam um data frame com colunas nomeadas "lon" e "lat". Se usarmos esse formato já no arquivo de ocorrências, não precisamos fazer pós-processamento disso depois da leitura. --- ENM/data/dados_clean.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ENM/data/dados_clean.csv b/ENM/data/dados_clean.csv index 2e82f86..358c596 100644 --- a/ENM/data/dados_clean.csv +++ b/ENM/data/dados_clean.csv @@ -1,4 +1,4 @@ -"sp","long","lat" +"sp","lon","lat" "Eugenia florida DC.",-35.019,-6.379 "Eugenia florida DC.",-34.858,-7.775 "Eugenia florida DC.",-34.897,-8.102