I'm trying to read a .mat file using R.
library(R.matlab)
data <- readMat('e-060RAW.mat')
It gives me this error.
Error in readMat5(con, firstFourBytes = firstFourBytes, maxLength = maxLength) :
Reading of MAT v7.3 files is not supported. If possible, save the data in MATLAB using 'save -V6'.
How am I supposed to get this sorted out.
Is there any other way to read a .mat file using R.
From https://www.rdocumentation.org/packages/R.matlab/versions/3.6.2/topics/readMat:
MAT v7.3 files, saved using for instance save('foo.mat', '-v7.3'),
stores the data in the Hierarchical Data Format (HDF5) [6, 7], which
is a format not supported by this function/package. However, there
exist other R packages that can parse HDF5, e.g. CRAN package h5 and
Bioconductor package rhdf5.
Related
So I use SGA tools for processing my images. It gives back results in .dat files. Now in order to work on this data in R, I tried to import the .dat file using the haven package. I installed haven and then its library, but I am not able to import data still and it gives this error message.
Error: Failed to parse C:/Users/QuRana/Desktop/SGA Tools/Plate_Image_Example (1).dat: This version of the file format is not supported.
When I use this command install.packages("haven"), haven is loaded, but then when I load library using library(haven) nothing appears on my console except for this
> library(haven)
Then when I use this code:
datatrial1 <- read_dta("C:/Users/QuRana/Desktop/SGA Tools/Plate_Image_Example (1).dat")
It gives me the error mentioned above. When I try converting my .dat file to a .csv file and load my data, the imported data adds additional "t" values before the values in columns except for the first one like this:
Flags: S - Colony spill or edge interference C - Low colony circularity
# row\tcol\tsize\tcircularity\tflags
1\t1\t4355\t0.9053\t
1\t2\t4456\t0.8401\t
1\t3\t3439\t0.8219\t
1\t4\t3215\t0.8707\t
All the t's before the numeric values are not what I want. Another issue that I am facing is I cannot install the gitter package on my R version which is R 4.2.2.
You can read your tab separated file like so `read.delim("file_path", header = TRUE, sep = "\t")
I do not have any code to post, but just a question.
There are several tools I am aware of to read SDMX files in R (an SDMX is an XML file for exchanging statistical data) like for instance
https://github.com/opensdmx/rsdmx
https://github.com/amattioc/SDMX
but does anyone know a way to export some data to an SDMX format for dissemination?
Any suggestion is welcome!
This is not a ‘pure’ R solution, but the Python sdmx1 package is fully usable through reticulate, and allows to programmatically generate SDMX objects and then serialize them as SDMX-ML (XML). For example:
# Use reticulate to import the Python package
> library(reticulate)
> sdmx <- import("sdmx")
# Create an (empty) DataMessage object
> msg <- sdmx$message$DataMessage()
# Convert to XML
> xml <- sdmx$to_xml(msg, pretty_print = TRUE)
# Write to file using the built-in R method
# The Python 'bytes' object must be decoded to a string
> write(xml$decode(), file = "message.xml")
This gives output like:
<mes:GenericData xmlns:com="http://www.sdmx.org/resources/sdmxml/schemas/v2_1/common" xmlns:data="http://www.sdmx.org/resources/sdmxml/schemas/v2_1/data/structurespecific" xmlns:str="http://www.sdmx.org/resources/sdmxml/schemas/v2_1/structure" xmlns:mes="http://www.sdmx.org/resources/sdmxml/schemas/v2_1/message" xmlns:gen="http://www.sdmx.org/resources/sdmxml/schemas/v2_1/data/generic" xmlns:footer="http://www.sdmx.org/resources/sdmxml/schemas/v2_1/message/footer" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<mes:Header>
<mes:Test>false</mes:Test>
</mes:Header>
</mes:GenericData>
For more information on authoring more complex messages using sdmx1, there is a page “HOWTO Generate SDMX-ML from Python objects” in the documentation.
I try to load a .mat file using the R.matlab library. When I run:
x <- readMat("MPL.mat")
I get this error however.
Error in mat5ReadTag(this) :
Unknown data type. Not in range [1,19]: 18569
In addition: Warning message:
In readMat5Header(this, firstFourBytes = firstFourBytes) :
Unknown MAT version tag: 512. Will assume version 5.
Anybody who experienced this and has a way to deal with this?
Im familiar with this post: R.matlab/readMat : Error in readTag(this) but alternatives ways didnt work for me...
The problem is related to how is saved your "MPL.mat". If you save by default in MATLAB, it probably won't work using R.matlab in R.
When I saved my .mat object in '-v7' or '-v6' i did not have problems, but the R.matlab documentation suggest to save in '-v6' (Pag.25 in R.matlab package). For example, I saved 2 matrices (A and B) in 'MPL.mat'.
save('MPL.mat','A', 'B', '-v7')
I could read in R:
require(R.matlab)
data <- readMat("MPL.mat")
View(data$A)
View(data$B)
I have two data sets full and raw that I placed in the data/ directory of my package. However, when I load my package, they are not available. I tried looking for them using the data function, but did not see them.
data(raw, package = "pkg")
Warning message:
In data(raw, package = "pkg") : data set 'raw' not found
Do I have to export them somehow?
I noticed when I tried to open the file using load from another computer, it read in as a string. Maybe I'm not writing the data frame properly? I used:
save(df.full, file = "full.RData")
save(df.raw, file = "raw.RData")
I'm trying to import a SRTM dataset into R. I've downloaded the data in a tif file however am having trouble reading it in "R".
Ive tried using the following code:
t = readTIFF("srtm_56_06/srtm_56_06.tif", as.is=TRUE)
load('srtm_56_06/srtm_56_06.tif')
read_file<-as.matrix(raster("srtm_56_06/srtm_56_06.tif")
However I am still getting error messages:
load('srtm_56_06/srtm_56_06.tif')
# Error: bad restore file magic number (file may be corrupted) -- no data loaded
# In addition: Warning message:
# file ‘srtm_56_06.tif’ has magic number 'II*'
# Use of save versions prior to 2 is deprecated
library(raster)
t = readTIFF("srtm_56_06/srtm_56_06.tif", as.is=TRUE)
# Error: could not find function "readTIFF"
read_file<-as.matrix(raster("srtm_56_06/srtm_56_06.tif") + min(read_file)
# Error: unexpected symbol in:
# "read_file<-as.matrix(raster("srtm_56_06/srtm_56_06.tif")
# min"
Can anyone help me with the commands to import this data. I'm a novice at "R" and a little lost.
Just read it with raster, but note you depend on rgdal being installed as well to read a .tif.
library(raster)
library(rgdal)
r <- raster("srtm_56_06/srtm_56_06.tif")
If that works, try
plot(r)
r
If it's really a "TIFF" then that should be fine, if it's really a GeoTIFF then you'll have a sensible map as well. (If it's something else that GDAL can read you might get a good result anyway, remember the extension of a file is not a reliable indicator of its contents).
The SRTM clue suggests that this is a single band DEM file from the tiled global SRTM data set. If it's somehow a "multi-band image" then you could read that with brick and plot with plotRGB (but I really doubt that is the case here). Note that there is a native binary format for SRTM that raster/rgdal could read as well but either they distributed .tif as well or someone else converted it.
There are a number of misconceptions in your code:
load is for a particular file type created from R (not these .tifs)
readTIFF is not in package raster
read_file would be a sensible matrix, if you have rgdal installed (which raster must use to load a .tif), but why throw away the spatial metadata?