I get the following error in caret trainControl() using the custom methods syntax documented in the package vignette (pdf) on page 46. Does anyone know if this document out of date or incorrect? It seems at odds with the caret documentation page where the "custom" parameter is not used.
> fitControl <- trainControl(custom=list(parameters=lpgrnn$grid, model=lpgrnn$fit,
prediction=lpgrnn$predict, probability=NULL,
sort=lpgrnn$sort, method="cv"),
number=10)
Error in trainControl(custom = list(parameters = lpgrnn$grid, model = lpgrnn$fit, :
unused argument (custom = list(parameters = lpgrnn$grid, model = lpgrnn$fit,
prediction = lpgrnn$predict, probability = NULL, sort = lpgrnn$sort, method = "cv",
number = 10))
The cited pdf is out of date. The caret website is the canonical source of documentation.
Related
At the moment, I am doing both:
pos = nx.spring_layout(G)
f1 = plt.figure(figsize=(18,10))
default_axes = plt.axes(frameon=True)
nx.draw_networkx(G, node_size=600, alpha=0.8, ax=default_axes, pos=pos)
edge_labels = nx.get_edge_attributes(G, "weight")
nx.draw_networkx_edge_labels(G, pos=pos, edge_labels=edge_labels)
plt.savefig('graph.jpg')
I would like to be able to select if to display, save or both (what I am doing now)
There is no built-in option for that in networkx. One option is to wrap the code in a function along these lines:
def custom(G, plot=True, save_file=False):
'''plots G by default. save_file should be a string'''
pos = nx.spring_layout(G)
f1 = plt.figure(figsize=(18,10))
default_axes = plt.axes(frameon=True)
nx.draw_networkx(G, node_size=600, alpha=0.8, ax=default_axes, pos=pos)
edge_labels = nx.get_edge_attributes(G, "weight")
nx.draw_networkx_edge_labels(G, pos=pos, edge_labels=edge_labels)
if save: plt.savefig(save) # can allow custom save name
if plot: plt.show()
return
Note that if the figure displays regardless of the option passed to the command, then the inline option might need to be disabled.
I am Trying to use add = True and I get an error message. How can I do it?
This is my code
quadratcount(schools.pp)
plot(schools.sp, col = "red")
plot(quadratcount(schools.pp), add= T)`
and this is the error message I get
Error in (function (x, y = NULL, density = NULL, angle = 45, border = NULL, : plot.new has not been called yet
Looks like you made a simple typo: In the first plot command you write plot(schools.sp, col = "red"), where you probably meant plot(schools.pp, col = "red"). For future questions please provide a reproducible example where we can run each line including library(spatstat) and the definition of schools.pp etc. If you can't share your data just either:
use the first few points of your data
use a built-in dataset
generate artificial data
I'm getting same error as this question, but with XQuery:
SaxonApiException: The context item for axis step ./CLIENT is absent
When running from the command line, all is good. So I don't think there is a syntax problem with the XQuery itself. I won't post the input file unless needed.
The XQuery is displayed with a Console.WriteLine before the error appears:
----- Start: XQUERY:
(: FLWOR = For Let Where Order-by Return :)
<MyFlightLegs>
{
for $flightLeg in //FlightLeg
where $flightLeg/DepartureAirport = 'OKC' or $flightLeg/ArrivalAirport = 'OKC'
order by $flightLeg/ArrivalDate[1] descending
return $flightLeg
}
</MyFlightLegs>
----- End : XQUERY:
Error evaluating (<MyFlightLegs {for $flightLeg in root/descendant::FlightLeg[DepartureAirport = "OKC" or ArrivalAirport = "OKC"] ... return $flightLeg}/>) on line 4 column 20
XPDY0002: The context item for axis step root/descendant::FlightLeg is absent
I think that like the other question, maybe my input XML file is not properly specified.
I took the samples/cs/ExamplesHE.cs run method of the XQuerytoStream class.
Code there for easy reference is:
public class XQueryToStream : Example
{
public override string testName
{
get { return "XQueryToStream"; }
}
public override void run(Uri samplesDir)
{
Processor processor = new Processor();
XQueryCompiler compiler = processor.NewXQueryCompiler();
compiler.BaseUri = samplesDir.ToString();
compiler.DeclareNamespace("saxon", "http://saxon.sf.net/");
XQueryExecutable exp = compiler.Compile("<saxon:example>{static-base-uri()}</saxon:example>");
XQueryEvaluator eval = exp.Load();
Serializer qout = processor.NewSerializer();
qout.SetOutputProperty(Serializer.METHOD, "xml");
qout.SetOutputProperty(Serializer.INDENT, "yes");
qout.SetOutputStream(new FileStream("testoutput.xml", FileMode.Create, FileAccess.Write));
Console.WriteLine("Output written to testoutput.xml");
eval.Run(qout);
}
}
I changed to pass the Xquery file name, the xml file name, and the output file name, and tried to make a static method out of it. (Had success doing the same with the XSLT processor.)
static void DemoXQuery(string xmlInputFilename, string xqueryInputFilename, string outFilename)
{
// Create a Processor instance.
Processor processor = new Processor();
// Load the source document
DocumentBuilder loader = processor.NewDocumentBuilder();
loader.BaseUri = new Uri(xmlInputFilename);
XdmNode indoc = loader.Build(loader.BaseUri);
XQueryCompiler compiler = processor.NewXQueryCompiler();
//BaseUri is inconsistent with Transform= Processor?
//compiler.BaseUri = new Uri(xqueryInputFilename);
//compiler.DeclareNamespace("saxon", "http://saxon.sf.net/");
string xqueryFileContents = File.ReadAllText(xqueryInputFilename);
Console.WriteLine("----- Start: XQUERY:");
Console.WriteLine(xqueryFileContents);
Console.WriteLine("----- End : XQUERY:");
XQueryExecutable exp = compiler.Compile(xqueryFileContents);
XQueryEvaluator eval = exp.Load();
Serializer qout = processor.NewSerializer();
qout.SetOutputProperty(Serializer.METHOD, "xml");
qout.SetOutputProperty(Serializer.INDENT, "yes");
qout.SetOutputStream(new FileStream(outFilename,
FileMode.Create, FileAccess.Write));
eval.Run(qout);
}
Also two questions regarding "BaseURI".
1. Should it be a directory name, or can it be same as the Xquery file name?
2. I get this compile error: "Cannot implicity convert to "System.Uri" to "String".
compiler.BaseUri = new Uri(xqueryInputFilename);
It's exactly the same thing I did for XSLT which worked. But it looks like BaseUri is a string for XQuery, but a real Uri object for XSLT? Any reason for the difference?
You seem to be asking a whole series of separate questions, which are hard to disentangle.
Your C# code appears to be compiling the query
<saxon:example>{static-base-uri()}</saxon:example>
which bears no relationship to the XQuery code you supplied that involves MyFlightLegs.
The MyFlightLegs query uses //FlightLeg and is clearly designed to run against a source document containing a FlightLeg element, but your C# code makes no attempt to supply such a document. You need to add an eval.ContextItem = value statement.
Your second C# fragment creates an input document in the line
XdmNode indoc = loader.Build(loader.BaseUri);
but it doesn't supply it to the query evaluator.
A base URI can be either a directory or a file; resolving relative.xml against file:///my/dir/ gives exactly the same result as resolving it against file:///my/dir/query.xq. By convention, though, the static base URI of the query is the URI of the resource (eg file) containing the source query text.
Yes, there's a lot of inconsistency in the use of strings versus URI objects in the API design. (There's also inconsistency about the spelling of BaseURI versus BaseUri.) Sorry about that; you're just going to have to live with it.
Bottom line solution based on Michael Kay's response; I added this line of code after doing the exp.Load():
eval.ContextItem = indoc;
The indoc object created earlier is what relates to the XML input file to be processed by the XQuery.
I am writing a csv reader to generate Genbank files to capture annotations with sequence.
First I used a Bio.SeqRecord and got correctly formatted output but the SeqRecord class lacks fields that I need.
Blockquote
FEATURES Location/Qualifiers
HCDR1 27..35
HCDR2 50..66
HCDR3 99..109
I switched to Bio.GenBank.Record and have the needed fields except now the annotation formatting is wrong. It can't have the extra "type:" "location:" and "qualifiers:" text and the information should all be on one line.
Blockquote
FEATURES Location/Qualifiers
type: HCDR1
location: [26:35]
qualifiers:
type: HCDR2
location: [49:66]
qualifiers:
type: HCDR3
location: [98:109]
qualifiers:
The code for pulling annotations is the same for both versions. Only the class changed.
# Read csv entries and create a container with the data
container = Record()
container.locus = row['Sample']
container.size = len(row['Seq'])
container.residue_type="PROTEIN"
container.data_file_division="PRI"
container.date = (datetime.date.today().strftime("%d-%b-%Y")) # today's date
container.definition = row['FullCloneName']
container.accession = [row['Vgene'],row['HCDR3']]
container.version = getpass.getuser()
container.keywords = [row['ProjectName']]
container.source = "test"
container.organism = "Homo Sapiens"
container.sequence = row['Seq']
annotations = []
CDRS = ["HCDR1", "HCDR2", "HCDR3"]
for CDR in CDRS:
start = row['Seq'].find(row[CDR])
end = start + len(row[CDR])
feature = SeqFeature(FeatureLocation(start=start, end=end), type=CDR)
container.features.append(feature)
I have looked at the source code for Bio.Genbank.Record but can't figure out why the SeqFeature class has different formatting output compared to Bio.SeqRecord.
Is there an elegant fix or do I write a separate tool to reformat the annotations in the Genbank file?
After reading the source code again, I discovered Bio.Genbank.Record has its own Features method that takes key and location as strings. These are formatted correctly in the output Genbank file.
CDRS = ["HCDR1", "HCDR2", "HCDR3"]
for CDR in CDRS:
start = row['Seq'].find(row[CDR])
end = start + len(row[CDR])
feature = Feature()
feature.key = "{}".format(CDR)
feature.location = "{}..{}".format(start, end)
container.features.append(feature)
assign wfwe = wb_acc & (adr_i == 2'b10) & ack_o & we_i;
For the above assign statement which is in verilog, i getting error while implememting it in z3
My code:
BitVecExpr[] wfwe = new BitVecExpr[1];
BitVecExpr[] wb_acc = new BitVecExpr[1];
BitVecExpr[] adr_i = new BitVecExpr[1];
BitVecExpr[] ack_o = new BitVecExpr[1];
BitVecExpr[] we_i = new BitVecExpr[1];
wfwe[0] = ctx.mkBVConst("wfwe",1);
wb_acc[0] = ctx.mkBVConst("wb_acc",1);
adr_i[0] = ctx.mkBVConst("adr_i",2);
ack_o[0] = ctx.mkBVConst("ack_o",1);
we_i[0] = ctx.mkBVConst("we_i",1);
Solver s = ctx.mkSolver();
s.add(ctx.mkBVAND(wb_acc[0],ctx.mkEq(adr_i[0],ctx.mkNumeral("2",2)),ack_o[0],we_i[0]));
I am getting error in above add statement:
error: method mkBVAND in class Context cannot be applied to given types;
required: BitVecExpr,BitVecExpr
found: BitVecExpr,BoolExpr
Which is true. Can anyone suggest me workaround. Am i implementing it incorrectly please let me know.
This error is reported because the second argument of mkBVAND is a Boolean expression (ctx.mkEq ...). Note that Booleans and BitVectors of size 1 are not the same thing, and they will not be converted automatically. The easiest way to convert between them is an if-then-else the selects the right values.
These are the problems with this example:
1) ctx.mkNumeral("2",2) is incorrect. I guess the intention was to create a bv-numeral of 2 bits with value 2; the easiest way to achieve that is ctx.mkBV(2, 2)
2) The 2nd argument of mkBVAND needs to be converted from Bool to BitVector, e.g., like so:
BoolExpr c = ctx.mkEq(adr_i[0], ctx.mkBV(2, 2));
BitVecExpr e = (BitVecExpr) ctx.mkITE(c, ctx.mkBV(1, 1), ctx.mkBV(0, 1));
e being the result.
3) ctx.mkBVAND takes exactly 2 arguments, no more and no less. Thus, the BVAND expression needs to be rewritten, e.g., like so:
ctx.mkBVAND(ctx.mkBVAND(wb_acc[0], e), ctx.mkBVAND(ack_o[0], we_i[0])))
4) The result needs to be converted to a Boolean expression again, e.g.
ctx.mkEq(q, ctx.mkBV(1, 1))
where q is the result of the BVAND.