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/dports/math/jags/JAGS-4.3.0/src/modules/bugs/functions/
H A Dtestbugsfun.h4 namespace jags {
41 jags::ScalarFunction *_abs;
50 jags::ScalarFunction *_cos;
51 jags::ScalarFunction *_cosh;
55 jags::LinkFunction *_exp;
65 jags::ScalarFunction *_log;
68 jags::VectorFunction *_max;
70 jags::VectorFunction *_min;
72 jags::LinkFunction *_phi;
78 jags::VectorFunction *_sd;
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H A Dtestbugsfun.cc60 using jags::checkInteger;
61 using jags::LinkFunction;
62 using jags::ScalarFunction;
63 using jags::VectorFunction;
64 using jags::Function;
77 _sin = new jags::bugs::Sin; in setUp()
78 _cos = new jags::bugs::Cos; in setUp()
79 _tan = new jags::bugs::Tan; in setUp()
94 _log = new jags::bugs::Log; in setUp()
98 _exp = new jags::bugs::Exp; in setUp()
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/dports/math/jags/JAGS-4.3.0/src/modules/bugs/distributions/
H A Dtestbugsdist.h4 namespace jags {
27 jags::RNG *_rng;
29 jags::ScalarDist *_dbern;
31 jags::RScalarDist *_dbin;
32 jags::VectorDist *_dcat;
36 jags::RScalarDist *_dexp;
37 jags::RScalarDist *_df;
46 jags::ArrayDist *_dmt;
51 jags::RScalarDist *_dnt;
56 jags::ArrayDist *_dsum;
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H A Dtestbugsdist.cc55 using jags::ScalarDist;
56 using jags::RScalarDist;
61 jags::KINDERMAN_RAMAGE); in setUp()
65 _dbin = new jags::bugs::DBin(); in setUp()
66 _dcat = new jags::bugs::DCat(); in setUp()
70 _dexp = new jags::bugs::DExp(); in setUp()
71 _df = new jags::bugs::DF(); in setUp()
80 _dmt = new jags::bugs::DMT(); in setUp()
85 _dnt = new jags::bugs::DNT(); in setUp()
86 _dpar = new jags::bugs::DPar(); in setUp()
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/dports/math/jags/JAGS-4.3.0/src/modules/base/functions/
H A Dtestbasefun.h7 namespace jags {
28 jags::ScalarFunction *_add;
29 jags::ScalarFunction *_and;
32 jags::ScalarFunction *_geq;
33 jags::ScalarFunction *_gt;
34 jags::ScalarFunction *_leq;
35 jags::ScalarFunction *_lt;
37 jags::ScalarFunction *_neg;
38 jags::ScalarFunction *_neq;
39 jags::ScalarFunction *_not;
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H A Dtestbasefun.cc23 using jags::checkInteger;
34 _add = new jags::base::Add; in setUp()
35 _and = new jags::base::And; in setUp()
36 _divide = new jags::base::Divide; in setUp()
37 _equal = new jags::base::Equal; in setUp()
41 _lt = new jags::base::LessThan; in setUp()
43 _neg = new jags::base::Neg; in setUp()
45 _not = new jags::base::Not; in setUp()
46 _or = new jags::base::Or; in setUp()
47 _pow = new jags::base::Pow; in setUp()
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/dports/math/jags/JAGS-4.3.0/src/include/function/
H A Dtestfun.h35 bool isdiscrete(jags::Function const *f, unsigned int npar,
47 bool neverscale(jags::Function const *f, unsigned int npar);
51 bool neverpow(jags::Function const *f, unsigned int npar);
61 double eval(jags::ScalarFunction const *f, const double x);
94 std::vector<double> veval(jags::VectorFunction const *f,
106 std::vector<double> veval(jags::VectorFunction const *f,
112 std::vector<double> veval(jags::VectorFunction const *f, in veval()
119 std::vector<double> veval(jags::VectorFunction const *f,
126 std::vector<double> veval(jags::VectorFunction const *f, in veval()
133 std::vector<double> veval(jags::VectorFunction const *f,
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/dports/math/jags/JAGS-4.3.0/src/terminal/
H A DMakefile.am4 libexec_PROGRAMS = jags-terminal
35 dist_bin_SCRIPTS = jags.bat
39 bin_SCRIPTS = jags script
53 jags: Makefile $(srcdir)/jags.in target
54 rm -f jags jags.tmp
55 jterm=`echo jags-terminal | sed -e '$(program_transform_name)'`; \
56 $(edit) $(srcdir)/jags.in > jags.tmp
57 chmod +x jags.tmp
58 mv jags.tmp jags
66 EXTRA_DIST = jags.in
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H A Dparser.cc148 static void setParameters(jags::ParseTree *p, jags::ParseTree *param1);
150 static void setParameters(jags::ParseTree *p, jags::ParseTree *param1, jags::ParseTree *param2);
2306 (yyval.ptree) = new jags::ParseTree(jags::P_ARRAY); in yyparse()
2318 jags::ParseTree *p = new jags::ParseTree(jags::P_VAR); setName(p, (yyvsp[0].stringptr)); in yyparse()
2344 (yyval.ptree) = new jags::ParseTree(jags::P_ARRAY); in yyparse()
2356 (yyval.ptree) = new jags::ParseTree(jags::P_ARRAY); in yyparse()
2399 (yyval.ptree) = new jags::ParseTree(jags::P_VECTOR); in yyparse()
2408 (yyval.ptree) = new jags::ParseTree(jags::P_VECTOR); in yyparse()
2851 static jags::Range getRange(jags::ParseTree const *var) in getRange()
3130 void setParameters(jags::ParseTree *p, jags::ParseTree *param1) in setParameters()
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H A Dparser.yy78 static void setParameters(jags::ParseTree *p, jags::ParseTree *param1, jags::ParseTree *param2);
413 $$ = new jags::ParseTree(jags::P_VAR); setName($$, $1);
416 $$ = new jags::ParseTree(jags::P_VAR); setName($$, $1);
596 $$ = new jags::ParseTree(jags::P_ARRAY);
603 jags::ParseTree *p = new jags::ParseTree(jags::P_VAR); setName(p, $3);
621 $$ = new jags::ParseTree(jags::P_ARRAY);
628 $$ = new jags::ParseTree(jags::P_ARRAY);
657 $$ = new jags::ParseTree(jags::P_VECTOR);
661 $$ = new jags::ParseTree(jags::P_VECTOR);
777 static jags::Range getRange(jags::ParseTree const *var)
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H A DReadData.cc16 using jags::SArray;
17 using jags::ParseTree;
18 using jags::P_VAR;
19 using jags::P_VECTOR;
20 using jags::P_ARRAY;
21 using jags::P_RANGE;
/dports/math/jags/JAGS-4.3.0/src/lib/compiler/
H A Dparser.yy16 using jags::ParseTree;
54 jags::ParseTree *ptree;
55 std::vector<jags::ParseTree*> *pvec;
148 $$ = new ParseTree(jags::P_RELATIONS, yylineno);
165 $$ = new ParseTree(jags::P_FOR, yylineno);
181 $$ = new ParseTree(jags::P_DETRMREL, yylineno);
195 $$ = new ParseTree(jags::P_DETRMREL, yylineno);
209 $$ = new ParseTree(jags::P_STOCHREL, yylineno);
246 $$ = new ParseTree(jags::P_LENGTH, yylineno);
250 $$ = new ParseTree(jags::P_DIM, yylineno);
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H A Dparser.cc80 using jags::ParseTree;
213 jags::ParseTree *ptree;
214 std::vector<jags::ParseTree*> *pvec;
1530 ParseTree *p = new ParseTree(jags::P_RELATIONS, yylineno); in yyparse()
1571 (yyval.ptree) = new ParseTree(jags::P_FOR, yylineno); in yyparse()
1695 (yyval.ptree) = new ParseTree(jags::P_LENGTH, yylineno); in yyparse()
1704 (yyval.ptree) = new ParseTree(jags::P_DIM, yylineno); in yyparse()
1895 {(yyval.ptree) = new ParseTree(jags::P_RANGE, yylineno);} in yyparse()
1902 (yyval.ptree) = new ParseTree(jags::P_RANGE, yylineno); in yyparse()
2239 ParseTree *p = new ParseTree(jags::P_BOUNDS, yylineno); in Truncated()
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H A Dparser_extra.h20 int parse_bugs(std::FILE *file, std::vector<jags::ParseTree*> * &pvariables,
21 jags::ParseTree * &pdata, jags::ParseTree * &prelations,
/dports/math/jags/JAGS-4.3.0/src/modules/glm/distributions/
H A Dtestglmdist.h4 namespace jags {
29 jags::RNG *_rng;
31 jags::RScalarDist *_dscaled_gamma;
32 jags::ArrayDist *_dscaled_wishart;
33 jags::glm::DOrdered *_dordered_logit;
35 void rscalar_rpq(jags::RScalarDist const *dist,
38 void rscalar_trunclik(jags::RScalarDist const *dist,
41 void dkwtest(jags::RScalarDist const *dist,
H A Dtestglmdist.cc31 using jags::RScalarDist;
43 _rng = new jags::base::MersenneTwisterRNG(1234567, in setUp()
44 jags::KINDERMAN_RAMAGE); in setUp()
46 _dscaled_gamma = new jags::glm::DScaledGamma(); in setUp()
47 _dscaled_wishart = new jags::glm::DScaledWishart(); in setUp()
48 _dordered_logit = new jags::glm::DOrderedLogit(); in setUp()
179 if (!jags_finite(dist->d(ob, jags::PDF_FULL, par, false))) { in scalar_trunclik_cont()
202 double y0 = exp(dist->logDensity(x[0], jags::PDF_FULL, par, ll, uu)); in scalar_trunclik_cont()
204 double y = exp(dist->logDensity(x[i], jags::PDF_FULL, par, ll, uu)); in scalar_trunclik_cont()
286 vector<double const *> const &par, jags::RNG *rng) in superror()
/dports/math/ess/ess-18.10.2/doc/
H A Dhelp-jags.texi22 @code{ess-jags-chains}, @code{ess-jags-monitor}, @code{ess-jags-thin},
23 @code{ess-jags-burnin} and @code{ess-jags-update}; they appear in the
28 The @code{ess-jags-chains} variable is the number of chains that
30 The @code{ess-jags-monitor} variable is a list of variables
36 The @code{ess-jags-thin} variable is the thinning parameter.
38 The @code{ess-jags-burnin} variable is the number of initial samples
42 @code{ess-jags-burnin} and @code{ess-jags-update} are multiplied by
43 @code{ess-jags-thin} since JAGS does not do it automatically.
48 @file{.jmd} file, there is only one variable, @code{ess-jags-command},
54 The @code{ess-jags-command} variable allows you to specify a different
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/dports/math/jags/JAGS-4.3.0/src/modules/mix/distributions/
H A Dtestmixdist.h4 namespace jags {
27 jags::RNG *_rng;
29 jags::RScalarDist *_dbetabin;
30 jags::VectorDist *_dnormmix;
32 void rscalar_rpq(jags::RScalarDist const *dist,
35 void dkwtest(jags::RScalarDist const *dist,
H A Dtestmixdist.cc25 using jags::ScalarDist;
26 using jags::RScalarDist;
27 using jags::PDF_FULL;
31 _rng = new jags::base::MersenneTwisterRNG(1234567, in setUp()
32 jags::KINDERMAN_RAMAGE); in setUp()
34 _dbetabin = new jags::mix::DBetaBin(); in setUp()
35 _dnormmix = new jags::mix::DNormMix(); in setUp()
200 vector<double const *> const &par, jags::RNG *rng) in superror()
/dports/math/jags/JAGS-4.3.0/src/modules/glm/samplers/
H A DOrderedLogit.cc19 static double llogit(double left, jags::RNG *rng, double mu) in llogit()
27 static double rlogit(double right, jags::RNG *rng, double mu) in rlogit()
35 static double ilogit(double left, double right, jags::RNG *rng, double mu) in ilogit()
44 namespace jags { namespace
H A DBinaryLogit.cc19 static double llogit(double left, jags::RNG *rng, double mu) in llogit()
27 static double rlogit(double right, jags::RNG *rng, double mu) in rlogit()
35 namespace jags { namespace
H A DScaledWishart.cc53 jags::RNG *rng) in sampleWishart()
62 jags::throwLogicError("invalid length in DWish::randomSample"); in sampleWishart()
76 jags::throwRuntimeError("Failed to get Cholesky decomposition of R"); in sampleWishart()
80 jags::throwRuntimeError("Failed to invert Cholesky decomposition of R"); in sampleWishart()
119 namespace jags { namespace
/dports/math/jags/JAGS-4.3.0/etc/
H A DMakefile.am1 EXTRA_DIST = jags.pc.in
4 pkgconfig_DATA = jags.pc
/dports/math/jags/JAGS-4.3.0/win/
H A Djags.nsi74 …WriteRegStr ${INSTDIR_REG_ROOT} "${INSTDIR_REG_KEY}" "URLInfoAbout" "http://mcmc-jags.sourceforge.…
98 File inst32\libexec\jags-terminal.exe
116 Push $INSTDIR\i386\bin\jags.bat #file to replace in
119 …AccessControl::GrantOnFile "$INSTDIR\i386\bin\jags.bat" "BUILTIN\USERS" "GenericRead + GenericExec…
127 …ateShortCut "$SMPROGRAMS\$SM_FOLDER\${JAGS_VISIBLE_NAME} (32-bit).lnk" "$INSTDIR\i386\bin\jags.bat"
129 … CreateShortCut "$SMPROGRAMS\$SM_FOLDER\${JAGS_VISIBLE_NAME}.lnk" "$INSTDIR\i386\bin\jags.bat"
145 File inst64\libexec\jags-terminal.exe
163 Push $INSTDIR\x64\bin\jags.bat #file to replace in
166 …AccessControl::GrantOnFile "$INSTDIR\x64\bin\jags.bat" "BUILTIN\USERS" "GenericRead + GenericExecu…
172 …CreateShortCut "$SMPROGRAMS\$SM_FOLDER\${JAGS_VISIBLE_NAME} (64-bit).lnk" "$INSTDIR\x64\bin\jags.b…
/dports/math/jags/JAGS-4.3.0/src/lib/graph/
H A DParentError.cc47 jags::SimpleRange range(dim); in printArray()
48 jags::RangeIterator r(range); in printArray()
65 namespace jags { namespace

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