I am running a random effects model in rjags with code:
model{
for (i in 1:N) {
mu1[i]<-(da1[1]+pow(10,(pka1[2]-ph[i]))*da1[2]+pow(10,(pka1[1]+pka1[2]-2*ph[i]))*da1[3])/(1+pow(10,(pka1[2]-ph[i]))+pow(10,(pka1[1]+pka1[2]-2*ph[i])))
mu2[i]<-(da2[1]+pow(10,(pka2[2]-ph[i]))*da2[2]+pow(10,(pka2[1]+pka2[2]-2*ph[i]))*da2[3])/(1+pow(10,(pka2[2]-ph[i]))+pow(10,(pka2[1]+pka2[2]-2*ph[i])))
}
MU[1:N,1]<-mu1
MU[1:N,2]<-mu2
for (i in 1:N) {
Y[i,1:2] ~ dmnorm(MU[i,1:2],SIGMA)
}
SIGMA ~ dwish(R,5)
for (i in 1:2) {
pka[i] ~ dunif(0,14)
}
pka<-sort(pka)
for (i in 1:2) {
pka1[i]<-dnorm(pka[i],1)T(0,14)
pka2[i]<-dnorm(pka[i],1)T(0,14)
}
for (i in 1:3) {
da1[i] ~ dunif(0,10)
da2[i] ~ dunif(0,10)
}
}
and get the error:
Error in jags.model("model2b.txt", data = data, n.chains = 4, n.adapt = 10) :
Error parsing model file:syntax error on line 25 near "T"
I have run for a less complex version of mu which has only a single pka1 and pka2 and the model runs perfectly. Any help in spotting the syntax error would be greatly appreciated!
for (i in 1:2) {
pka1[i]<-dnorm(pka[i],1)T(0,14)
pka2[i]<-dnorm(pka[i],1)T(0,14)
}
The <- should be ~
This is one of the problems, maybe there are others.
Related
I am parsing BASIC:
530 FOR I=1 TO 9:C(I,1)=0:C(I,2)=0:NEXT I
The patterns that are used in this case are:
FOR { return TOK_FOR; }
TO { return TOK_TO; }
NEXT { return TOK_NEXT; }
(many lines later...)
[A-Za-z_#][A-Za-z0-9_]*[\$%\!#]? {
yylval.s = g_string_new(yytext);
return IDENTIFIER;
}
(many lines later...)
[ \t\r\l] { /* eat non-string whitespace */ }
The problem occurs when the spaces are removed, which was common in the era of 8k RAM. So the line that is actually found in Super Star Trek is:
530 FORI=1TO9:C(I,1)=0:C(I,2)=0:NEXTI
Now I know why this is happening: "FORI" is longer than "FOR", it's a valid IDENTIFIER in my pattern, so it matches IDENTIFIER.
The original rule in MS BASIC was that variable names could be only two characters, so there was no * so the match would fail. But this version is also supporting GW BASIC and Atari BASIC, which allow variables with long names. So "FORI" is a legal variable name in my scanner, so that matches as it is the longest hit.
Now when I look at the manual, and the only similar example deliberately returns an error. It seems what I need is "match the ID, but only if it's not the same as defined %token", is there such a thing?
It's easy to recognise keywords even if they have an identifier concatenated. What's tricky is deciding in what contexts you should apply that technique.
Here's a simple pattern for recognising keywords, using trailing context:
tail [[:alnum:]]*[$%!#]?
%%
FOR/{tail} { return TOK_FOR; }
TO/{tail} { return TOK_TO; }
NEXT/{tail} { return TOK_NEXT; }
/* etc. */
[[:alpha:]]{tail} { /* Handle an ID */ }
Effectively, that just extends the keyword match without extending the matched token.
But I doubt the problem is so simple. How should FORFORTO be tokenised, for example?
I'm trying to write a Language Extension for VS Code in JavaScript and I seem to be missing something.
I have a Lexer.g4 and Parser.g4 for my language and can generate a tree using them.
My issue is that the VS Code API gives me a document and a position in that document (line #, character #). From any of the examples I've looked at for ANTLR4 I can't seem to find any functions generated that take a position in the file and give back the nodes of a tree at that position.
I want to know, for example that the cursor is placed on the name of a function.
Am I supposed to be walking the entire tree and checking the position of tokens to see if they enclose the position I'm in in the editor? Or maybe I'm not using the right tool for the job? I feel like I'm probably missing something more fundamental.
Yes, you have to walk the parse tree to find the context at a given position. This is a pretty simple task and you can see it in action in my ANLTR4 exension for vscode. There are multiple functions returning something useful for a given position. For instance this one:
/**
* Returns the parse tree which covers the given position or undefined if none could be found.
*/
function parseTreeFromPosition(root: ParseTree, column: number, row: number): ParseTree | undefined {
// Does the root node actually contain the position? If not we don't need to look further.
if (root instanceof TerminalNode) {
let terminal = (root as TerminalNode);
let token = terminal.symbol;
if (token.line != row)
return undefined;
let tokenStop = token.charPositionInLine + (token.stopIndex - token.startIndex + 1);
if (token.charPositionInLine <= column && tokenStop >= column) {
return terminal;
}
return undefined;
} else {
let context = (root as ParserRuleContext);
if (!context.start || !context.stop) { // Invalid tree?
return undefined;
}
if (context.start.line > row || (context.start.line == row && column < context.start.charPositionInLine)) {
return undefined;
}
let tokenStop = context.stop.charPositionInLine + (context.stop.stopIndex - context.stop.startIndex + 1);
if (context.stop.line < row || (context.stop.line == row && tokenStop < column)) {
return undefined;
}
if (context.children) {
for (let child of context.children) {
let result = parseTreeFromPosition(child, column, row);
if (result) {
return result;
}
}
}
return context;
}
}
In this simple code:
do {
console.log('o');
} while (false);
jslint produces a warning on the last line saying Unexpected 'false'
I understand why, but I still want to mute it because in these cases that's how I want to have the control flow.
Let's look at what jslint expects in the while statement. From the source:
labeled_stmt('while', function () {
one_space();
var paren = next_token;
funct.loopage += 1;
advance('(');
step_in('control');
no_space();
edge();
this.arity = 'statement';
this.first = expected_relation(expression(0));
if (this.first.id !== 'true') {
expected_condition(this.first, 'unexpected_a');
}
no_space();
step_out(')', paren);
one_space();
this.block = block('while');
if (this.block.disrupt) {
prev_token.warn('strange_loop');
}
funct.loopage -= 1;
return this;
});
It mostly reads like English. 'while', one space, (, no space, expected expression, no space, ).
So let's look at what an expression(0) is. You can read through the source if you're really interested, but to be honest I can't really wrap my head around it either. Sorry. https://github.com/douglascrockford/JSLint/blob/master/jslint.js
As far as I can tell, though, expression(0) traverses the tree of operators and operands, and looks for values with a Right Binding Power greater than 0? And false has a binding power of 0? But variables and comparisons are okay here. I have no clue how that even works. Ask Crockford.
As for shutting up jslint, here is my suggestion:
/*jslint devel: true, continue: true */
var i = 0;
var forever = false;
do {
i = i + 1;
if (i < 5) {
continue;
}
console.log('o');
} while (forever);
This program:
type A = { a : int }
type B = { b : A }
//34567890
let r = {
b = { // line 6
a = 2 // line 7
}
}
Produces under mono/fsharpc this warning twice:
/Users/debois/git/dcr/foo.fs(7,5): warning FS0058: Possible incorrect indentation: this token is offside of context started at position (6:7). Try indenting this token further or using standard formatting conventions.
Why does this warning occur at all? The f#-spec p. 228 makes me think the token 'a' following '{' sets a new offside line, in which case there should be no problem?
Why does it occur twice?
Thanks,
Søren
Full output:
dcr > fsharpc foo.fs
F# Compiler for F# 3.0 (Open Source Edition)
Freely distributed under the Apache 2.0 Open Source License
/Users/debois/git/dcr/foo.fs(7,5): warning FS0058: Possible incorrect indentation: this token is offside of context started at position (6:7). Try indenting this token further or using standard formatting conventions.
/Users/debois/git/dcr/foo.fs(7,5): warning FS0058: Possible incorrect indentation: this token is offside of context started at position (6:7). Try indenting this token further or using standard formatting conventions.
dcr >
reformat your code as
type A = { a : int }
type B = { b : A }
//34567890
let r = { b = { a = 2 } }
or
let r =
{
b = { a = 2 }
}
i.e. the { is the left-most token.
EDIT: One off-site line starts with the { therefore you need to indent at least as much as the { the line break after is not mandatory. And the second warning is because of the same reason.
I finally worked it out. From the F# spec pp. 229–230, here are the pertinent rule about when offside contexts (lines) are introduced (rule numbering is mine):
(i) The column of the first token of a (, { or begin token.
(ii) Immediately after an = token is encountered in a record expression when the subsequent token either (a) occurs on the next line or (b) is one of try, match, if, let, for, while or use.
Now recall the problem:
//34567890
let r = {
b = { // line 6
a = 2 // line 7
}
}
The b on line 6 follows a { and so pushes an offside-line on column 3 by (i). Then, the { on line 6 follows a record expression = and so pushes a new offside line on column 7 by (ii). The a on line 7 column 5 violates that offside line.
The tricky bit is that the { on line 5 makes the next token define an offside-line, whereas the { on line 6 is itself an offside line (because it follows a record-expression equal sign).
Spec says:
Other structured constructs also introduce offside lines at the following places:
The column of the first token of a (, { or begin token.
Why do you decide that offside line should be introduced by the token after the { when spec says that it should be the { itself?
NOTE: I agree that phrase "first token of ...token " sounds confusing. More likely it should be "first character of ...token" as this is applicable to begin\end case (offside line is introduced by the column of 'b' character)
begin
begin
end // possible incorrect indentation: this token is offside of the context started at (2,2)
end
Having two warnings for the same position looks like a bug.
I'm trying to implement a parser by directly reading a treeWalker and implementing the commands needed for the compiler on the fly. So if I have a command like:
statement
:
^('WRITE' expression)
{
//Here is the command that is created by my Tree Parser
ch.emitRO("OUT",0,0,0,"write out the value of ac");
//and then I handle it in my other classes
}
;
I want it to write OUT 0,0,0; to a file. That's my grammar.
I have a problem though with the loop section in my grammar it is:
'WHILE'^ expression 'DO' stat_seq 'ENDDO'
and in the tree parser:
doWhileStatement
:
^('WHILE' expression 'DO' stat_seq 'ENDDO')
;
What I want to do is directly parse the code from the while loop into the commands I need. I came up with this solution but it doesn't work:
doWhileStatement
:
^('WHILE' e=expression head='DO'
{
int loopHead =((CommonTree) head).getTokenStartIndex();
}
stat_seq
{
if ($e.result==1) {
input.seek(loopHead);
doWhileStatement();
}
}
'ENDDO')
;
for the record here are some of the other commands I've written:
(ignore the code written in brackets, it's for the generation of the commands in a text file.)
stat_seq
:
(statement)+
;
statement
:
^(':=' ID e=expression) { variables.put($ID.text,e); }
| ^('WRITE' expression)
{
ch.emitRM("LDC",ac,$expression.result,0,"pass the expression value to the ac reg");
ch.emitRO("OUT",ac,0,0,"write out the value of ac");
}
| ^('READ' ID)
{
ch.emitRO("IN",ac,0,0,"read value");
}
| ^('IF' expression 'THEN'
{
ch.emitRM("LDC",ac1,$expression.result,0,"pass the expression result to the ac reg");
int savedLoc1 = ch.emitSkip(1);
}
sseq1=stat_seq
'ELSE'
{
int savedLoc2 = ch.emitSkip(1);
ch.emitBackup(savedLoc1);
ch.emitRM("JEQ",ac1,savedLoc2+1,0,"skip as many places as needed depending on the expression");
ch.emitRestore();
}
sseq2=stat_seq
{
int savedLoc3 = ch.emitSkip(0);
ch.emitBackup(savedLoc2);
ch.emitRM("LDC",PC_REG,savedLoc3,0,"skip for the else command");
ch.emitRestore();
}
'ENDIF')
| doWhileStatement
;
Any help would be appreciated, thank you
I found it for everyone who has the same problem I did it like this and it's working:
^('WHILE'
{int c = input.index();}
expression
{int s=input.index();}
.* )// .* is a sequence of statements
{
int next = input.index(); // index of node following WHILE
input.seek(c);
match(input, Token.DOWN, null);
pushFollow(FOLLOW_expression_in_statement339);
int condition = expression();
state._fsp--;
//there is a problem here
//expression() seemed to be reading from the grammar file and I couldn't
//get it to read from the tree walker rule somehow
//It printed something like no viable alt at input 'DOWN'
//I googled it and found this mistake
// So I copied the code from the normal while statement
// And pasted it here and it works like a charm
// Normally there should only be int condition = expression()
while ( condition == 1 ) {
input.seek(s);
stat_seq();//stat_seq is a sequence of statements: (statement ';')+
input.seek(c);
match(input, Token.DOWN, null); //Copied value from EvaluatorWalker.java
//cause couldn't find another way to do it
pushFollow(FOLLOW_expression_in_statement339);
condition = expression();
state._fsp--;
System.out.println("condition:"+condition + " i:"+ variables.get("i"));
}
input.seek(next);
}
I wrote the problem at the comments of my code. If anyone can help me out and answer this for me how to do it I would be grateful. It's so weird that there is nearly no feedback on a correct way to implement loops within a tree grammar on the fly.
Regards,
Alex