I am using night-time light satellite data. I have performed a calibration method between two satellite data for the same year. for which I had converted the tiff file to dataframe. Now I need to export the data frame to tiff format. following are the codes I tried but some error is shown
library (sp)
library (raster)
library (rgdal)
writeRaster(NTL_new2, "E:\phd\data\calliberation test\rstudio\test.tif", format="GTiff", overwrite=TRUE)
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘writeRaster’ for signature ‘"data.frame", "character"’
can anyone guide me on how to go about
That is the type of message you will get when attempting to apply an S4 generic function to an object of a class for which no defined S4 method exists (or at least has been attached to the current R session).
Here's an example using the raster package (for spatial raster data), which is chock full of S4 functions.
library(raster)
## raster::rotate() is an S4 function with just one method, for "Raster" class objects
isS4(rotate)
# [1] TRUE
showMethods(rotate)
# Function: rotate (package raster)
# x="Raster"
## Lets see what happens when we pass it an object that's *not* of class "Raster"
x <- 1:10
class(x)
# [1] "integer"
rotate(x)
# Error in (function (classes, fdef, mtable) :
# unable to find an inherited method for function ‘rotate’ for signature ‘"integer"’
Related
I have been following the migrateR vignette while traying to create animal movement models.
So far I made a list of ltraj objects from the adehabitat package and have worked with that:
set.coordinates <- function(x){coordinates(x) <- c("Long","Lat"); x}
set.proj4string <- function(x){proj4string(x) <- CRS("+proj=longlat +datum=WGS84"); x}
Base_ind <- lapply(Base_ind, set.coordinates)
Base_ind <- lapply(Base_ind, set.proj4string)
make.ltraj <- function(q){as.ltraj(xy=coordinates(q), date=q$TelemDate, id=q$AID,
burst = q$AID, infolocs = q[4])}
Base_ind_tr <- lapply(Base_ind, make.ltraj)
make.nsd <- function(x){mvmtClass(x)}
Base.nsd <- lapply(Base_ind_tr, make.nsd)
After this the error appears:
Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘burst’ for signature ‘"ltraj", "missing"’
My ltraj objects look the same as in the vignette:
Type of the traject: Type II (time recorded)
Time zone: UTC *
Irregular traject. Variable time lag between two locs
Characteristics of the bursts:
id burst nb.reloc NAs date.begin date.end
1 An1 An1 1323 0 2021-05-26 11:02:26 2021-10-24 17:00:38
infolocs provided. The following variables are available:
[1] "elev"
burst exists as an attribute of the ltraj objects.
I have also gotten the error for individual animals and for all of them in a single data frame.
I have a vague idea how these sort of errors occur but am not sure how to solve it.
I'm working on Linux in R to get specific transcript sequences from the genome. I am able to import the genome, extract transcripts annotations (tx), and get transcript sequences (tx_seq). I am also able to import genomic annotations for the transcripts I'm interested in as GRanges (uorf_annotations) and convert them transcript coordinates (uorf_tx_annotations).
The libraries I have loaded are
#BiocManager::install(version="3.9")
#BiocManager::install("BSgenome.Hsapiens.UCSC.hg19")
#BiocManager::install("S4Vectors")
#BiocManager::install(c("GenomicFeatures", "Biostrings", "GenomicRanges"))
library(broom)
library(BSgenome.Hsapiens.UCSC.hg19)
library(Biostrings)
library(GenomicRanges)
library(GenomicFeatures)
library(rtracklayer)
library(tidyverse)
library(plyranges)
options(scipen=999)
The chunk of code that works is
uorf_tx_annotations <- mapToTranscripts(uorf_annotations, tx) %>%
print()
I get stuck when I try and get the transcript sequences from uorf_tx_annotations. The code I am using for this step is
uorf_transcript_seq <- extractTranscriptSeqs(genome, uorf_tx_annotations) %>%
print()
and the error I am getting is "Error in extractTranscriptSeqs(genome, uorf_tx_annotations) : failed to extract the exon ranges from 'transcripts' with exonsBy(transcripts, by="tx", ...)"
I use extractTranscriptSeqs earlier on to get tx_seq, so I'm not sure what's wrong here. I thought that everything I needed was in GRanges, but in case uorf_annotations wasn't in the GRanges I tried (inspired from documentation at https://rdrr.io/bioc/GenomicFeatures/man/extractTranscriptSeqs.html)
uorf_tx_annotations <- mapToTranscripts(uorf_annotations, tx) %>%
exonsBy(by = "tx") %>%
print()
but this just introduces a new error: "Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘exonsBy’ for signature ‘"GRanges"’"
I'm a newbie in R and need some advice with recommenderlab.
I have a "training" dataset comprised of 6 variables, and the first line looks like this:
song_id user_id title release artist_name year
3 SOAAAGQ12A8C1420C8 384e068d83822096b2ef9a35ba520d97a8f74741 Orgelblut Dolores Bohren & Der Club Of Gore 2008
I'm trying to use recommenderlab to use UBCF, and use the following code:
rec <- Recommender("train", method = "UBCF")
But get this error
Error in (function (classes, fdef, mtable) : unable to find an
inherited method for function ‘Recommender’ for signature
‘"character"’
Any idea what is wrong?
train should be your training data, not a string. Can you try this:
rec <- Recommender(train, method = "UBCF")
I also posted this question on stack gis 1. From the netcdf4 data that have sub categories, I want to be able to read "Retrieval/fs" variable. I also want to read them and convert to raster girds, but it seems that raster doesn't support netcdf4. I appreciate any suggestions.
library(ncdf4)
library(raster)
file <- "http://140906_B7101Ar_150909171225s.nc4"
names(file$var)
"latitude" ... "longitude"... "Retrieval/fs"
lat <- raster(file, varname="latitude")
lon <- raster(file, varname="longitude")
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘raster’ for signature ‘"ncdf4"’
raster does work with ncdf4 You are now showing actual code. file is a character vector. You cannot do names(file$var) with that (at least you won't get "latitude" ... "longitude"... "Retrieval/fs". So file is probably ncdf4 object (see the error message), while the raster function expects a filename (but not a url).
If you download the file and then do
library(raster)
x <- brick(filename, var="Retrieval/fs")
Things should work if the ncdf file had regular raster data.
However, it does not so you cannot directly import this as a raster. Instead you can get the lat and lon and values from the files, treat these as points and then rasterize (interpolate) these to get a regular raster.
Here is the answer to the question I asked. Since the data is not gridded, I retrieve the lon and lat information along with the variables to create a dataframe.
fs <- ncvar_get(ncfile, "Retrieval/fs")
xlon <- ncvar_get(ncfile, "longitude")
xlat <- ncvar_get(ncfile, "latitude")
d <- data.frame( as.vector(xlon),as.vector(xlat), as.vector(fs))# create a dataframe
coordinates(d) <- c("xlon","xlat")
proj4string(d) <- CRS("+proj=longlat")
spoint <- SpatialPoints(coords = d) #create a spatial point object
I am trying to convert a large number (>500) of text files into shapefiles. I can successfully convert a single .csv into a projected shapefile. And I can get lapply and 'for' loops to work when just loading, cleaning up, and exporting the text files. But the code fails when I add in steps to convert to shapefiles within the loops. Below are two ways I've tried tackling the problem and the associated error messages:
General processing/definitions-
library(rgdal)
library(sp)
crs.geo<-CRS("+proj=utm +zone=14 +ellps=GRS80 +datum=NAD83 +units=m +no_defs ") #define projection
coltype=c("character","character","character","numeric","numeric") #define data types for input .csv (x,y UTM coords are columns 4,5)
setwd("C:/.../testdata/out")
all.the.filenames <- list.files(pattern= "\\.csv") #create list of files to batch process
head(exampledata,2)
Point Location Time easting northing
1 Trackpoint 14 S 661117 3762441 12/1/2008 5:57:02 AM 661117 3762441
2 Trackpoint 14 S 661182 3762229 12/1/2008 5:58:02 AM 661182 3762229
Batch conversion with a 'for' loop
names <- substr(all.the.filenames, 1, nchar(all.the.filenames)-4) #clean up file names
for(i in names) {
filepath <- file.path("../out",paste(i,".csv",sep=""))
assign(i, read.table(filepath, colClasses=coltype, header=TRUE, sep=",", na.strings=c("NA","")))
coordinates(i) <- c(4,5) #coords in columns 4,5
proj4string(i) <- crs.geo
writeOGR(i,"C:/Users/Seth/Documents/testdata/out","*",driver="ESRI Shapefile") }
R returns this error message:
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘coordinates<-’ for signature ‘"character"’
If I end the 'for' loop after the 'assign' line, it successfully imports all .csv files as separate objects in R. The problem seems to be that function 'coordinates' is not seeing the coords as numeric, and I get the same error message no matter how explicitly I try to define them as such (e.g., coordinates(i) <- c(as.numeric("easting","northing")) Also, these lines of code work successfully when applied to a single .csv file, the problem is when I subset within a loop.
Batch conversion using lapply
files.to.process <- lapply(all.the.filenames, function(x) read.csv(x, colClasses=coltype, header=TRUE))
lapply(files.to.process, function(c) coordinates(c)<-c("easting","northing"))
[[1]]
[1] "easting" "northing"
[[2]]
[1] "easting" "northing"
[[3]]
[1] "easting" "northing"
[[4]]
[1] "easting" "northing"
[[5]]
[1] "easting" "northing"
lapply(files.to.process, function(p) proj4string(p) <- crs.geo)
which returns the error message:
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘proj4string<-’ for signature ‘"data.frame", "CRS"’
#Double-check if function 'coordinates' worked
class(files.to.process) == "SpatialPoints"
[1] FALSE
Conclusion/problem
With both approaches the problem seems to be in the 'coordinates' step to make a spatial object. What am I doing wrong in the loops? Thanks much for any help!
Seth H.
In your first attempt, the object i inside the loop is a character object. So,
coordinates(get(i))
would work better; I don't have a batch of csv files to test it on.
In the second attempt using lapply(), I'm not exactly sure what's going on, but
class(files.to.process)
should be "list", so what you want to do is
lapply(files.to.process,class)
and that will tell you if the objects are of class spatialpoints. I'm guessing they are data.frames, and you need one more step in between.