When ever I try to run this line or any other line which uses key(following document in http://h2o-release.s3.amazonaws.com/h2o/rel-lambert/5/docs-website/Ruser/rtutorial.html)
iris.hex = h2o.uploadFile(localH2O, path = irisPath, key = "iris.hex")
I get an error in the key calling it as unused argument.
This is the first time I am using H2O and I am new to R as well. Please let me know what is the function of key and only when I run this, I get error. I could create a dataframe with the following statement. But still I would want to understand this key error
h2o.init(ip = "localhost", port = 54321, startH2O = TRUE)
irisPath = system.file("extdata", "iris.csv", package = "h2o")
iris.hex = h2o.uploadFile(path = prosPath, destination_frame = "iris.hex")
iris.data.frame<- as.data.frame(iris.hex)
summary(iris.data.frame)
H2O may be very good in various areas. but unfortunately lack of documentation and tutorial makes it's really difficult to learn...
Hoping that they watch these type of comments and improve their documentation.
At least launching one tutorial of 12GB airlines data processing can help a lot for multiple enthusiastic people who really wanted to explore H2O.
This is a very outdated version of the H2O docs and there have been some major API changes since H2O 3.0. The latest R docs can always be found at: http://h2o-release.s3.amazonaws.com/h2o/latest_stable_Rdoc.html
Our main docs landing page has a link to the latest R docs, Python docs, and a bunch of other links you may find useful. We also have a Google Group called h2ostream for posting new questions and searching through old questions. Welcome to H2O!
Related
I'm trying to use stringdb in R and i'm getting the following error when i try to plot the network:
Error in if (grepl("The document has moved", res)) { : argument is
of length zero
code:
library(STRINGdb)
#(specify organism)
string_db <- STRINGdb$new( version="10", species=9606, score_threshold=0)
filt_mapped = string_db$map(filt, "GeneID", removeUnmappedRows = TRUE)
head(filt_mapped)
(i have columns titled: GeneID, logFC, FDR, STRING_id with 156 rows)
filt_mapped_hits = filt_mapped$STRING_id
head(filt_mapped_hits)
(156 observations)
string_db$plot_network(filt_mapped_hits, add_link = FALSE)
Error in if (grepl("The document has moved", res)) { : argument is
of length zero
You are using quite few years old version of Bioconductor and by extension the STRING package.
If you update to the newest one, it will work. However the updated package only supports only the latest version STRING (currently version 11), so the underlying network may change a bit.
More detailed reason is this:
The STRING's hardware infrastructure underwent recently major changes which forced a different server setup.
Now all the old calls are forwarded to a different URL, however the cURL call, how it was implemented, does not follow our redirects which breaks the STRINGdb package functionality.
We cannot update the old bioconductor package and our server setup can’t be really changed.
That said, the fix for an old version is relatively simple.
In STRINGdb library there is script with all the methods "rstring.r".
In there you’ll find “get_png” method. In it replace this line:
urlStr = paste("http://string-db.org/version_", version, "/api/image/network", sep="" )
With this line:
urlStr = paste("http://version", version, ".string-db.org/api/image/network", sep="" )
Load the library again and it should create the PNG, as before.
I use code like below to create an AutoML object to submit an experiment for classification training
automl_settings = {
"n_cross_validations": 2,
"primary_metric": 'accuracy',
"enable_early_stopping": True,
"experiment_timeout_hours": 1.0,
"max_concurrent_iterations": 4,
"verbosity": logging.INFO,
}
automl_config = AutoMLConfig(task = 'classification',
compute_target = compute_target,
training_data = train_data,
label_column_name = label,
**automl_settings
)
ws = Workspace.from_config()
experiment = Experiment(ws, "your-experiment-name")
run = experiment.submit(automl_config, show_output=True)
I want to include my conda yml file (like below) in my experiment submission.
env = Environment.from_conda_specification(name='myenv', file_path='conda_dependencies.yml')
However, I don't see any environment parameter in AutoMLConfig class documentation (similar to what environment parameter does in ScriptRunConfig) or find any example how to do so.
I notice after the experiment is submitted, I get message like this
Running on remote.
No run_configuration provided, running on aml-compute with default configuration
Is run_configuration used for specifying environment? If so, how do I provide run_configuration in my AutoML experiment run?
Thank you.
I figured out how to fix the issues associated with the sdk 1.19.0 upgrade in the AML environment I use, thus no need for the workaround (ie. pass in a SDK 1.18.0 conda environment file to AutoML experiment run) I was thinking about. My original question no longer needs an answer, I just want to add this note in case someone else has the same question later on.
I still don't know why AutoML experiment run has no option to pass in a conda environment file. It would be nice if a reason is given in the AML documentation.
I really have a hard time trying to translate 1.5k responses to an open ended question from french to english. I want to use the R-Package "translateR" with the Microsoft-API. Microsoft because I got an Azure-Account due to my University without the need of spending Creditcard-Information.
Actually I am not sure if I am doing it wrong because of beeing unable to fill in the right parameter for "client id" and "client secret" or if its just outdated package which does not work with Microsoft API anymore due to migration by Microsoft or something. I researched some similar questions at stackoverflow but did not found any answer or solution already.
Here is some code to maybe replicate the problem. An exampledataset is used which is integrated in "translateR".
#install.packages("translateR")
library(translateR)
data(enron)
google.dataset.out <- translateR::translate(dataset = enron,
content.field = 'email',
microsoft.client.id = my.client.id,
microsoft.client.secret = my.client.secret,
source.lang = 'en',
target.lang = 'de')
I am constantly getting this output:
Error in function (type, msg, asError = TRUE) :
Could not resolve host: datamarket.accesscontrol.windows.net
I am quite new to using R-Language, pls be kind if I did something totaly stupid. Can anyone confirm that it is not possible to use "translateR" with microsoft API anymore? Can anyone give me advise how to deal with my data if translation is not possible with the package anymore?
The R-Package is outdated but the development version has been updated more recently. For installation the package "devtools" needs to be installed before using the following command:
###Install devtools###
install.packages("devtools")
###Install development version of translateR###
devtools::install_github("ChristopherLucas/translateR")
Within the development version the commandsyntax changed aswell.
library(translateR)
data(enron)
dataset.out <- translateR::translate(dataset = enron,
content.field = 'email',
microsoft.api.key = 'my.ms.api.key',
source.lang = 'en',
target.lang = 'de')
For more information read this:
translateR documentation update on github
I am looking into using MXNet LSTM modelling for time-series analysis for a problem i am currently working on.
As a way of understanding how to implement this, I am following the example code given by xnNet from the link: https://mxnet.incubator.apache.org/tutorials/r/MultidimLstm.html
When running this script after downloading the necessary data to my local source, i am able to execute the code fine until i get to the following section to train the model:
## train the network
system.time(model <- mx.model.buckets(symbol = symbol,
train.data = train.data,
eval.data = eval.data,
num.round = 100,
ctx = ctx,
verbose = TRUE,
metric = mx.metric.mse.seq,
initializer = initializer,
optimizer = optimizer,
batch.end.callback = NULL,
epoch.end.callback = epoch.end.callback))
When running this section, the following error occurs once gaining connection to the API.
Error in mx.nd.internal.as.array(nd) :
[14:22:53] c:\jenkins\workspace\mxnet\mxnet\src\operator\./rnn-inl.h:359:
Check failed: param_.p == 0 (0.2 vs. 0) Dropout is not supported at the moment.
Is there currently a problem internally within the XNNet R package which is unable to run this code? I can't imagine they would provide a tutorial example for the package that is not executable.
My other thought is that it is something to do with my local device execution and connection to the API. I haven't been able to find any information about this being a problem for other users though.
Any inputs or suggestions would be greatly appreciated thanks.
Looks like you're running an old version of R package. I think following instructions on this page to build a recent R-package should resolve this issue.
This is my first question to the community. I've read through the guidelines and am doing my best to ask an appropriate question and including a minimal, complete, and verifiable example. That being said, please feel free to suggest ways in which I can ask better questions going forward.
I am having trouble with the choroplethrMaps package, which I have never used in the past. I have had issues installing packages on my work computer before, but have gotten around this issue by pasting the package and its dependencies in my library directory. Part of my issues may stem from that, but I'm not sure.
Here is the code that replicates the issue on my machine.
library(choroplethrMaps)
library(choroplethrAdmin1)
library(choroplethr)
data(state.map)
df<-data.frame(region=unique(x = state.map$region),value=rnorm(n = 51,mean = 500,sd = 45))
debug(state_choropleth)
state_choropleth(df = df,title = "", legend = "", num_colors = 1)
After debugging the state_choropleth function, it looks like there is an error with the "render" portion of the code. When I execute the above code, I get the following error message.
Error in withCallingHandlers(tryCatch(evalq((function (..., call. = TRUE, :
object '.rcpp_warning_recorder' not found
Note that I am only using state_choropleth because when running the choroplethr function, I was advised to use state_choropleth instead. It seems as though choroplethr is out of date.