Hi Cecilia,
Alternative solution
#...
afiles <- ls(pattern= "a_")
for (ifile in 1:length(afiles))
{
fnp = mget(afiles[ifile])
#... do something with fnp
outfile <-
file.path("/Users/sisolarrosa/Documents/PhD/R_work/AF/IIC/conefor_inputs/",
paste0("distances_", afiles[ifile], ".txt"));
#...
}
cheers
Peter
> On 27 Jul 2015, at 12:50, Jim Lemon <drjimle...@gmail.com> wrote:
>
> Hi Cecilia,
> I _think_ that the error is occurring in the call to paste0. You may
> be able to get what you want like this:
>
> paste0("distances_",deparse(substitute(fnp)),".txt")
>
> Jim
>
>
> On Mon, Jul 27, 2015 at 5:06 AM, Larrosa, Cecilia
> <cecilia.larros...@imperial.ac.uk> wrote:
>> Hi,
>>
>> This is a repost from here
>> (http://r.789695.n4.nabble.com/Writing-output-of-a-looped-process-with-pdfs-tt4710348.html),
>> due to the post not being complete originally. I am running R studio on OS
>> X Yosemite 10.10.4 (Mac). I appreciate you help very much!
>>
>> The objective: I have 100 shapefiles that need to undergo the same process.
>>
>> The process: I use gDistance{rgdal} to calculate the distance between all
>> features (polygons) within each layer, and output a txt file.
>>
>> The problem: I need the name of the output txt file to contain the name of
>> the shapefile, but the shapefiles are read into R as
>> SpatialPolygonsDataFrames (spdf) and I cannot find a way to use the name of
>> the spdf objects as character in order to make it vary with each iteration.
>>
>> My questions to you: Do you know a way to solve the problem or an
>> alternative way to fulfil the objective? I have come to determine the
>> problem after searching about the error message, have I interpreted
>> correctly?
>>
>>
>> Here is a minimal dataset for replicability:
>>
>>> dput(a_1)
>> new("SpatialPolygonsDataFrame"
>> , data = structure(list(ID = 1:3, GRIDCODE = c(1L, 1L, 1L), Shape_Leng =
>> c(3349.48347556,
>> 1618.93904903, 893.268790786), Shape_Area = c(309430.38861, 90015.8325676,
>> 47507.0325775), Count = c(1L, 1L, 1L)), .Names = c("ID", "GRIDCODE",
>> "Shape_Leng", "Shape_Area", "Count"), row.names = 0:2, class = "data.frame")
>> , polygons = list(<S4 object of class structure("Polygons", package =
>> "sp")>,
>> <S4 object of class structure("Polygons", package = "sp")>,
>> <S4 object of class structure("Polygons", package = "sp")>)
>> , plotOrder = 1:3
>> , bbox = structure(c(476685.625393809, 311791.86152084, 508519.585393809,
>> 312935.41622084), .Dim = c(2L, 2L), .Dimnames = list(c("x", "y"
>> ), c("min", "max")))
>> , proj4string = new("CRS"
>> , projargs = "+proj=aea +lat_1=-5 +lat_2=-42 +lat_0=-32 +lon_0=-60 +x_0=0
>> +y_0=0 +ellps=aust_SA +units=m +no_defs"
>> )
>> )
>>> dput(a_10)
>> new("SpatialPolygonsDataFrame"
>> , data = structure(list(ID = 1:5, GRIDCODE = c(1L, 1L, 1L, 1L, 1L),
>> Shape_Leng = c(1691.7247095,
>> 2305.45647624, 1022.64650591, 1172.27848042, 94.2722341164),
>> Shape_Area = c(6.47354525991, 92111.8528756, 65.7173995386,
>> 19042.7776647, 415.253663691), Count = c(1L, 1L, 1L, 1L,
>> 1L)), .Names = c("ID", "GRIDCODE", "Shape_Leng", "Shape_Area",
>> "Count"), row.names = 0:4, class = "data.frame")
>> , polygons = list(<S4 object of class structure("Polygons", package =
>> "sp")>,
>> <S4 object of class structure("Polygons", package = "sp")>,
>> <S4 object of class structure("Polygons", package = "sp")>,
>> <S4 object of class structure("Polygons", package = "sp")>,
>> <S4 object of class structure("Polygons", package = "sp")>)
>> , plotOrder = c(2L, 4L, 5L, 3L, 1L)
>> , bbox = structure(c(825796.904693809, 815666.86152084, 831270.106493809,
>> 816562.46752084), .Dim = c(2L, 2L), .Dimnames = list(c("x", "y"
>> ), c("min", "max")))
>> , proj4string = new("CRS"
>> , projargs = "+proj=aea +lat_1=-5 +lat_2=-42 +lat_0=-32 +lon_0=-60 +x_0=0
>> +y_0=0 +ellps=aust_SA +units=m +no_defs"
>> )
>> )
>>
>>
>> Here is the code that I have been using:
>>
>> ###Load packages
>> library(rgdal)
>> library(gdistance)
>>
>> ###Read forest shape files
>> setwd("/Users/sisolarrosa/Documents/PhD/R_work/AF/IIC/R_Quest/")
>> shps<- dir(getwd(), "*.shp")
>> shps <- gsub('.{4}$', '', shps)
>> for (shp in shps) assign(shp, readOGR(".",layer=shp))
>>
>> ###Create list of spdf objects
>> fnps<- mget(ls(pattern= "a_"))
>>
>> ###For each spatial layer (object in the list), calculate distance between
>> all polygons within layer
>> for (fnp in fnps)
>> {
>> distance.matrix<- gDistance(fnp, spgeom2= NULL, byid=T);
>> row.names(distance.matrix) <- paste(1:nrow(distance.matrix), sep="”);
>> # did this because gDistance changed the IDs of the features from [1 to
>> ...] to [0 to ...], not sure why
>> colnames(distance.matrix)<- paste(1:ncol(distance.matrix), sep="”);
>> # same as above
>> dists.melt <-
>> melt(distance.matrix)[melt(upper.tri(distance.matrix))$value,]; #use only
>> lower triangle of the distances matrix
>> outfile <-
>> file.path("/Users/sisolarrosa/Documents/PhD/R_work/AF/IIC/conefor_inputs/",
>> paste0("distances_", fnp, ".txt"));
>> write.table(dists.melt, outfile,row.names=FALSE, col.names=FALSE)
>> }
>>
>> And this is the error message:
>>
>> Error in as.character.default(<S4 object of class
>> "SpatialPolygonsDataFrame">) :
>> no method for coercing this S4 class to a vector
>>
>> Thank you very much!!
>> Cecilia
>>
>>
>> [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
> ______________________________________________
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
______________________________________________
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
