I'm using the R package 'googleLanguageR' to transcribe various 30 second audio files (over 500 so want to automatize this). I've followed all the steps in the googleLanguageR tutorials, got my key, and authenticated through R.
I'm able to transcribe the test audio (.wav) that comes with the package, but whenever I apply the same function to my files (.mp3), I get NULL for both transcript and timings.
This is the code provided in tutorials:
# get the sample source file
test_audio <- system.file("woman1_wb.wav", package = "googleLanguageR")
gl_speech(test_audio)$transcript
If I use the same for my file, I get an empty element, so I've tried the following with no luck:
test_audio <- "/audio_location/filename.mp3"
gl_speech(test_audio)$transcript
Has anybody encountered a similar problem with this package or have any suspicions of why it produces NULL transcripts?
Related
I am attempting to use the streamR in R to download and analyze Twitter, under the pretense that this library can overcome the limitations from the twitteR package.
When downloading data everything seems to work fabulously, using the filterStream function (just to clarify, the function captures Twitter data, just running it will provide the json file -saved in the working directory- that needs to be used in further steps):
filterStream( file.name="tweets_test.json",
track="NFL", tweets=20, oauth=credential, timeout=10)
Capturing tweets...
Connection to Twitter stream was closed after 10 seconds with up to 21 tweets downloaded.
However, when moving on to parse the json file, I keep getting all sorts of errors:
readTweets("tweets_test.json", verbose = TRUE)
0 tweets have been parsed.
list()
Warning message:
In readLines(tweets) : incomplete final line found on 'tweets_test.json'
Or with this function from the same package:
tweet_df <- parseTweets(tweets='tweets_test.json')
Error in `$<-.data.frame`(`*tmp*`, "country_code", value = NA) :
replacement has 1 row, data has 0
In addition: Warning message:
In stream_in_int(path.expand(path)) : Parsing error on line 0
I have tried reading the json file with jsonlite and rjson with the same results.
Originally, it seemed that the error came from special characters ({, then \) within the json file that I tried to clean up following the suggestion from this post, however, not much came out of it.
I found out about the streamR package from this post, which shows the process as very straight forward and simple (which it is, except for the parsing part!).
If any of you have experience with this library and/or these parsing issues, I'd really appreciate your input. I have been searching non stop but haven't been able to locate a solution.
Thanks!
I have two hdf4 files namely file 1:"MYD04_L2.A2011001.2340.006.2014078044212.hdf" and file 2: "MYD04_L2.A2011031.mosaic.006.AOD_550_DT_DB_Combined.hdf". First one is raw data file with 72 sub-datasets and second one is the file I obtained after ordering (i.e. post-processed). For the first R code:
layer_name <- getSds("MYD04_L2.A2011001.2340.006.2014078044212.hdf",method="mrt")
layer_name$SDSnames[66:68]
[1] "AOD_550_Dark_Target_Deep_Blue_Combined"
[2] "AOD_550_Dark_Target_Deep_Blue_Combined_QA_Flag"
[3] "AOD_550_Dark_Target_Deep_Blue_Combined_Algorithm_Flag"
It works ok with method="gdal" as well. However, when I try to read file 2, a window pops up showing gdalinfo.exe has stopped working (method = "gdal"). The same kind of problem arises for mrt and it shows sdslist.exe has stopped working. I get following error message:
Error in sds[[i]] <- substr(sdsRaw[i], 1, 11) == "SDgetinfo: " :
attempt to select less than one element in integerOneIndex
Is single layer is the issue here? As the first one has 72 sub-data sets and second one has only one sub-data set (assuming because of the given file name as I couldn't read it), have R failed to read the data file? Can anyone propose any solution for reading such data files? If ncdf4 package is the solution with enabled hdf4, can anyone explain, step-by-step, how can I enable hdf4 and build ncdf4 using windows platform?
I'm trying to duplicate a text mining example on text mining Twitter data using R programming language found in
Section 10.2 of Yanchang Zhao's paper R and Data Mining: Examples and Case Studies. Zhoa includes a Twitter data sample rmdTweets.RData so the user doesn't have to get the Twitter data directly from Twitter website.
Zhoa's Twitter sample "rmdTweets.RData" is downloaded to my computer; the required R packages 'tm' and 'twitteR' have been loaded without error; and the working directory has been set to the directory containing "rmdTweets.RData", i.e. setwd("F:/R/Test tm/Twitter_Data/") .
When running this command from Zhoa's paper
df <- do.call("rbind", lapply(rdmTweets, as.data.frame))
I get the error:
Error in lapply(rdmTweets, as.data.frame) : object 'rdmTweets' not found
Can you help me with this error?
Also, I'm new to R and am having trouble finding help on the do.call function written in 'beginner' language, so I can understand "rbind" and lapply
You need to load the data file in first.
load("rmdTweets.RData")
I am clustering time series in R using package KmL. I have read both manual and paper how to use this package, but Im not very clear how to export the results (data frame, where each trajectories are assign to some clusters e.g.
trajectory (i), time1, time2, time3, clustername)
I have read several answers here Output from 'choice' in R's kml
but if I do the same (run choice(myCld, typeGraph= "bmp")) my R says:
~ Choice : menu ~ 'Arrow' : change partition 'Space' : select/unselect a partition ... etc. e : change the display (both)
~ 'Return' when its done ~
And only thing that is saved to my library is myCld.Rdata and it runs for very long time without any more results. (my dataset: N trajectories, with time= 1:53) I want to have csv. files as manual suggest (objectName-Cx-y-Clusters.csv)
I am also not very clear WHERE should I PRESS on "Return" or "Arrow"? There is no option to press on anything in my Rstudio workplace.
I am really a beginner with R so any help would be appreciated. Thanks!
I am not sure that kml is compatible with Rstudio. The older version of Rstudio did not handle instruction like getGraphicsEvent that was used by choice.
I've searched the web for this without much luck. More or less you always get to the example from the VariantAnnotation Package. And since this example works fine on my computer I have no idea why the VCF I created does not.
The problem: I want to determine the number and location of SNPs in selected genes. I have a large VCF file (over 5GB) that has info on all SNPs on all chromosomes for several mice strains. Obviously my computer freezes if I try to do anything on the whole genome scale, so I first determined genomic locations of genes of interest on chromosome 1. I then used the VariantAnnotation Package to get only the data relating to my genes of interest out of the VCF file:
library(VariantAnnotation)
param<-ScanVcfParam(
info=c("AC1","AF1","DP","DP4","INDEL","MDV","MQ","MSD","PV0","PV1","PV2","PV3","PV4","QD"),
geno=c("DP","GL","GQ","GT","PL","SP","FI"),
samples=strain,
fixed="FILTER",
which=gnrng
)
The code above is taken out of a function I wrote which takes strain as an argument. gnrng refers to a GRanges object containing genomic locations of my genes of interest.
vcf<-readVcf(file, "mm10",param)
This works fine and I get my vcf (dim: 21783 1) but when I try to save it won't work
file.vcf<-tempfile()
writeVcf(vcf, file.vcf)
Error in .pasteCollapse(ALT, ",") : 'x' must be a CharacterList
I even tried in parallel, doing the example from the package first and then substituting for my VCF file:
#This is the example:
out1.vcf<-tempfile()
in1<-readVcf(fl,"hg19")
writeVcf(in1,out1.vcf)
This works just fine, but if I only substitute in1 for my vcf I get the same error.
I hope I made myself clear... And any help will be greatly appreciated!! Thanks in advance!
Thanks for reporting this bug. The problem is fixed in version 1.9.47 (devel branch). The fix will be available in the release branch after April 14.
The problem was that you selectively imported 'FILTER' from the 'fixed' field but not 'ALT'. writeVcf() was throwing an error because there was no ALT value to write out. If you don't have access to the version with the fix, a work around would be to import the ALT field.
ScanVcfParam(fixed = c("ALT", "FILTER"))
You can see what values were imorted with the fixed() accessor:
fixed(vcf)
Please report and bugs or problems on the Bioconductor mailing list Martin referenced. More Bioc users will see the question and you'll get help more quickly.
Valerie
Here's a reproducible example
library(VariantAnnotation)
fl <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation")
param <- ScanVcfParam(fixed="FILTER")
writeVcf(readVcf(fl, "hg19", param=param), tempfile())
## Error in .pasteCollapse(ALT, ",") : 'x' must be a CharacterList
The problem seems to be that writeVcf expects the object to have an 'ALT' field, so
param <- ScanVcfParam(fixed="ALT")
writeVcf(readVcf(fl, "hg19", param=param), tempfile())
succeeds.