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Updates for JAGS 5.0.0 #80

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2 changes: 1 addition & 1 deletion DESCRIPTION
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Expand Up @@ -34,7 +34,7 @@ Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
SystemRequirements: JAGS >= 4.3.1 (https://mcmc-jags.sourceforge.io/)
SystemRequirements: JAGS >= 5.0.0 (https://mcmc-jags.sourceforge.io/)
NeedsCompilation: yes
Depends:
R (>= 4.0.0)
Expand Down
18 changes: 6 additions & 12 deletions src/Makevars.ucrt
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Expand Up @@ -7,21 +7,15 @@
###
### Note: This windows makefile requires the JAGS_ROOT variable to be set
###
### This file allows compilation with JAGS 4 (or later) without modifying RoBMA.
### This file allows compilation with JAGS 5 (or later) without modifying RoBMA.
### To force the package to compile assuming a given JAGS version is installed, use the
### JAGS_MAJOR_FORCED environmental variable. This might be necessary on windows if you have
### JAGS installed in a non-standard location.
###
######################################################################################################

## Conditionally set the JAGS_ROOT variable (if it is not already set) to a location specified by the CRAN team:
JAGS_ROOT ?= /c/progra~1/JAGS/JAGS-4.3.1

## Use the old ABI to match JAGS 4.x compilation on Windows:
#PKG_CXXFLAGS = -D_GLIBCXX_USE_CXX11_ABI=0
PKG_CXXFLAGS=
## Note: this behaviour will be changed (and RoBMA updated) before JAGS 5 is released
## If you are trying to compile this version of RoBMA against JAGS 5 you may need to remove this PKG_CXXFLAGS line
JAGS_ROOT ?= /c/progra~1/JAGS/JAGS-5.0.0

###############
### Flags
Expand Down Expand Up @@ -52,7 +46,7 @@ JAGS_FULL_VERS = $(word $(words $(JAGS_ROOT_SUB)),$(JAGS_ROOT_SUB))
JAGS_MAJOR_ASSUMED = $(strip $(word 2,$(subst .,$(space),$(subst -,$(space),$(JAGS_FULL_VERS)))))
else
# Otherwise make an assumption about JAGS_MAJOR and give a warning:
JAGS_MAJOR_ASSUMED = $(strip 4)
JAGS_MAJOR_ASSUMED = $(strip 5)
$(warning The major version of JAGS could not be determined from $(JAGS_ROOT) - assuming version $(JAGS_MAJOR_ASSUMED) (otherwise the Makevars.win file may need to be modified))
endif

Expand All @@ -62,14 +56,14 @@ endif

# Set the CPPFLAGS accordingly
# Prepending 0 to JAGS_MAJOR_VERSION prevents it being set as blank (the C++ code requires a number)
JAGS_MAJOR_ASSUMED := 4
JAGS_MAJOR_ASSUMED := 5
PKG_CPPFLAGS=-I"$(JAGS_ROOT)/include" -D JAGS_MAJOR_ASSUMED=$(JAGS_MAJOR_ASSUMED) -D JAGS_MAJOR_FORCED=0$(JAGS_MAJOR_VERSION) -DR_NO_REMAP

PKG_LIBS=-L"$(JAGS_ROOT)/${R_ARCH}/bin" -ljags-$(JAGS_MAJOR) -ljrmath-0 -llapack

###############
### Objects to be compiled
### NB: the objects in distributions/jags are only necessary for JAGS <=3, and are excluded by the sources when compiling against JAGS >= 4
### NB: the objects in distributions/jags are only necessary for JAGS <=3, and are excluded by the sources when compiling against JAGS >= 5
###############

OBJECTS = distributions/DMN.o distributions/DWMN1.o distributions/DWMN2.o distributions/DMNv.o distributions/DWMN1v.o distributions/DWMN2v.o \
Expand All @@ -92,7 +86,7 @@ OBJECTS = distributions/DMN.o distributions/DWMN1.o distributions/DWMN2.o distri
###############

# PKG_CPPFLAGS=-I"$(JAGS_ROOT)/include"
# PKG_LIBS=-L"$(JAGS_ROOT)/${R_ARCH}/bin" -ljags-4 -llapack
# PKG_LIBS=-L"$(JAGS_ROOT)/${R_ARCH}/bin" -ljags-5 -llapack
# OBJECTS = distributions/DMN.o distributions/DWMN1.o distributions/DWMN2.o distributions/DMNv.o distributions/DWMN1v.o distributions/DWMN2v.o \
# distributions/DWN1.o distributions/DWN2.o distributions/DWT1.o distributions/DWT2.o \
# distributions/DWN.o distributions/DWWN1.o distributions/DWWN2.o \
Expand Down
13 changes: 4 additions & 9 deletions src/Makevars.win
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Expand Up @@ -15,12 +15,7 @@
######################################################################################################

## Conditionally set the JAGS_ROOT variable (if it is not already set) to a location specified by the CRAN team:
JAGS_ROOT ?= /c/progra~1/JAGS/JAGS-4.3.1

## Use the old ABI to match JAGS 4.x compilation on Windows:
PKG_CXXFLAGS = -D_GLIBCXX_USE_CXX11_ABI=0
## Note: this behaviour will be changed (and RoBMA updated) before JAGS 5 is released
## If you are trying to compile this version of RoBMA against JAGS 5 you may need to remove this PKG_CXXFLAGS line
JAGS_ROOT ?= /c/progra~1/JAGS/JAGS-5.0.0

###############
### Flags
Expand Down Expand Up @@ -51,7 +46,7 @@ JAGS_FULL_VERS = $(word $(words $(JAGS_ROOT_SUB)),$(JAGS_ROOT_SUB))
JAGS_MAJOR_ASSUMED = $(strip $(word 2,$(subst .,$(space),$(subst -,$(space),$(JAGS_FULL_VERS)))))
else
# Otherwise make an assumption about JAGS_MAJOR and give a warning:
JAGS_MAJOR_ASSUMED = $(strip 4)
JAGS_MAJOR_ASSUMED = $(strip 5)
$(warning The major version of JAGS could not be determined from $(JAGS_ROOT) - assuming version $(JAGS_MAJOR_ASSUMED) (otherwise the Makevars.win file may need to be modified))
endif

Expand All @@ -72,7 +67,7 @@ PKG_LIBS=-L"$(JAGS_ROOT)/${R_ARCH}/bin" -ljags-$(JAGS_MAJOR) -ljrmath-0 -llapack
###############

OBJECTS = distributions/DMN.o distributions/DWMN1.o distributions/DWMN2.o distributions/DMNv.o distributions/DWMN1v.o distributions/DWMN2v.o \
distributions/DWN1.o distributions/DWN2.o distributions/DWT1.o distributions/DWT2.o \
distributions/DWN1.o distributions/DWN2.o distributions/DWT1.o distributions/DWT2.o \
distributions/DWN.o distributions/DWWN1.o distributions/DWWN2.o \
distributions/DWB.o \
distributions/DWNMIX.o distributions/DWWNMIX.o \
Expand All @@ -91,7 +86,7 @@ OBJECTS = distributions/DMN.o distributions/DWMN1.o distributions/DWMN2.o distri
###############

# PKG_CPPFLAGS=-I"$(JAGS_ROOT)/include"
# PKG_LIBS=-L"$(JAGS_ROOT)/${R_ARCH}/bin" -ljags-4 -ljrmath-0 -llapack
# PKG_LIBS=-L"$(JAGS_ROOT)/${R_ARCH}/bin" -ljags-5 -ljrmath-0 -llapack
# OBJECTS = distributions/DMN.o distributions/DWMN1.o distributions/DWMN2.o distributions/DMT2v.o distributions/DWMT1v.o distributions/DWMT2v.o \
# distributions/DWN1.o distributions/DWN2.o distributions/DWT1.o distributions/DWT2.o \
# distributions/DWN.o distributions/DWWN1.o distributions/DWWN2.o \
Expand Down
32 changes: 12 additions & 20 deletions src/distributions/DMN.cc
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Expand Up @@ -15,12 +15,12 @@
namespace jags {
namespace RoBMA {

std::vector<unsigned int> DMN::dim(std::vector<std::vector<unsigned int> > const &dims) const
std::vector<unsigned long> DMN::dim(std::vector<std::vector<unsigned long> > const &dims) const
{
return std::vector<unsigned int>(1,dims[0][0]);
return std::vector<unsigned long>(1,dims[0][0]);
}

bool DMN::checkParameterDim (std::vector<std::vector<unsigned int> > const &dims) const
bool DMN::checkParameterDim (std::vector<std::vector<unsigned long> > const &dims) const
{
bool sigma_OK = true; // check that sigma and mu dimension matches

Expand All @@ -29,7 +29,7 @@ namespace jags {
return sigma_OK;
}

bool DMN::checkParameterValue(std::vector<double const *> const &par, std::vector<std::vector<unsigned int> > const &dims) const
bool DMN::checkParameterValue(std::vector<double const *> const &par, std::vector<std::vector<unsigned long> > const &dims) const
{
const double *sigma = par[1];

Expand All @@ -49,8 +49,8 @@ namespace jags {

DMN::DMN():ArrayDist("dmnorm", 2) {}

double DMN::logDensity(double const *x, unsigned int length, PDFType type, std::vector<double const *> const &par,
std::vector<std::vector<unsigned int> > const &dims, double const *lower, double const *upper) const
double DMN::logDensity(double const *x, PDFType type, std::vector<double const *> const &par,
std::vector<std::vector<unsigned long> > const &dims) const
{
// reassign the addresses to pointers
const double *mu = par[0];
Expand All @@ -64,33 +64,25 @@ namespace jags {
return log_lik;
}

void DMN::randomSample(double *x, unsigned int length, std::vector<double const *> const &par,
std::vector<std::vector<unsigned int> > const &dims,
double const *lower, double const *upper,
void DMN::randomSample(double *x, std::vector<double const *> const &par,
std::vector<std::vector<unsigned long> > const &dims,
RNG *rng) const
{
// not implemented
}

void DMN::support(double *lower, double *upper, unsigned int length,
void DMN::support(double *lower, double *upper,
std::vector<double const *> const &par,
std::vector<std::vector<unsigned int> > const &dims) const
std::vector<std::vector<unsigned long> > const &dims) const
{
unsigned long length = product(dim(dims));
// no idea whether this is correct
for (unsigned int i = 0; i < length; ++i) {
for (unsigned long i = 0; i < length; ++i) {
lower[i] = JAGS_NEGINF;
upper[i] = JAGS_POSINF;
}
}

void DMN::typicalValue(double *x, unsigned int length,
std::vector<double const *> const &par,
std::vector<std::vector<unsigned int> > const &dims,
double const *lower, double const *upper) const
{
// not implemented
}

bool DMN::isSupportFixed(std::vector<bool> const &fixmask) const
{
return true;
Expand Down
27 changes: 11 additions & 16 deletions src/distributions/DMN.h
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Expand Up @@ -9,26 +9,21 @@ class DMN : public ArrayDist {
public:
DMN();

double logDensity(double const *x, unsigned int length, PDFType type,
double logDensity(double const *x, PDFType type,
std::vector<double const *> const &parameters,
std::vector<std::vector<unsigned int> > const &dims,
double const *lower, double const *upper) const;
void randomSample(double *x, unsigned int length,
std::vector<std::vector<unsigned long> > const &dims) const override;
void randomSample(double *x,
std::vector<double const *> const &parameters,
std::vector<std::vector<unsigned int> > const &dims,
double const *lower, double const *upper, RNG *rng) const;
void typicalValue(double *x, unsigned int length,
std::vector<double const *> const &parameters,
std::vector<std::vector<unsigned int> > const &dims,
double const *lower, double const *upper) const;
bool checkParameterDim(std::vector<std::vector<unsigned int> > const &dims) const;
std::vector<std::vector<unsigned long> > const &dims,
RNG *rng) const override;
bool checkParameterDim(std::vector<std::vector<unsigned long> > const &dims) const;
bool checkParameterValue(std::vector<double const *> const &parameters,
std::vector<std::vector<unsigned int> > const &dims) const;
std::vector<unsigned int> dim(std::vector<std::vector<unsigned int> > const &dims) const;
void support(double *lower, double *upper, unsigned int length,
std::vector<std::vector<unsigned long> > const &dims) const override;
std::vector<unsigned long> dim(std::vector<std::vector<unsigned long> > const &dims) const override;
void support(double *lower, double *upper,
std::vector<double const *> const &parameters,
std::vector<std::vector<unsigned int> > const &dims) const;
bool isSupportFixed(std::vector<bool> const &fixmask) const;
std::vector<std::vector<unsigned long> > const &dims) const override;
bool isSupportFixed(std::vector<bool> const &fixmask) const override;
};

}}
Expand Down
40 changes: 16 additions & 24 deletions src/distributions/DMNv.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -15,13 +15,13 @@
namespace jags {
namespace RoBMA {

std::vector<unsigned int> DMNv::dim(std::vector<std::vector<unsigned int> > const &dims) const
std::vector<unsigned long> DMNv::dim(std::vector<std::vector<unsigned long> > const &dims) const
{
return std::vector<unsigned int>(1,dims[0][0]);
return std::vector<unsigned long>(1,dims[0][0]);
}


bool DMNv::checkParameterDim (std::vector<std::vector<unsigned int> > const &dims) const
bool DMNv::checkParameterDim (std::vector<std::vector<unsigned long> > const &dims) const
{
bool se2_OK = true; // check that standard errors squared and mu dimension matches
bool tau2_OK = true; // check that tau squared is a single double
Expand All @@ -35,7 +35,7 @@ namespace jags {
}


bool DMNv::checkParameterValue(std::vector<double const *> const &par, std::vector<std::vector<unsigned int> > const &dims) const
bool DMNv::checkParameterValue(std::vector<double const *> const &par, std::vector<std::vector<unsigned long> > const &dims) const
{
const double *tau2 = par[2];
const double *rho = par[3];
Expand All @@ -52,8 +52,8 @@ namespace jags {

DMNv::DMNv():ArrayDist("dmnorm_v", 5) {}

double DMNv::logDensity(double const *x, unsigned int length, PDFType type, std::vector<double const *> const &par,
std::vector<std::vector<unsigned int> > const &dims, double const *lower, double const *upper) const
double DMNv::logDensity(double const *x, PDFType type, std::vector<double const *> const &par,
std::vector<std::vector<unsigned long> > const &dims) const
{
// reassign the addresses to pointers
const double *mu = par[0];
Expand Down Expand Up @@ -96,31 +96,23 @@ namespace jags {
return log_lik;
}

void DMNv::randomSample(double *x, unsigned int length, std::vector<double const *> const &par,
std::vector<std::vector<unsigned int> > const &dims,
double const *lower, double const *upper,
void DMNv::randomSample(double *x, std::vector<double const *> const &par,
std::vector<std::vector<unsigned long> > const &dims,
RNG *rng) const
{
// not implemented
}

void DMNv::support(double *lower, double *upper, unsigned int length,
void DMNv::support(double *lower, double *upper,
std::vector<double const *> const &par,
std::vector<std::vector<unsigned int> > const &dims) const
std::vector<std::vector<unsigned long> > const &dims) const
{
// no idea whether this is correct
for (unsigned int i = 0; i < length; ++i) {
lower[i] = JAGS_NEGINF;
upper[i] = JAGS_POSINF;
}
}

void DMNv::typicalValue(double *x, unsigned int length,
std::vector<double const *> const &par,
std::vector<std::vector<unsigned int> > const &dims,
double const *lower, double const *upper) const
{
// not implemented
unsigned long length = product(dim(dims));
// no idea whether this is correct
for (unsigned long i = 0; i < length; ++i) {
lower[i] = JAGS_NEGINF;
upper[i] = JAGS_POSINF;
}
}

bool DMNv::isSupportFixed(std::vector<bool> const &fixmask) const
Expand Down
26 changes: 10 additions & 16 deletions src/distributions/DMNv.h
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Expand Up @@ -9,26 +9,20 @@ class DMNv : public ArrayDist {
public:
DMNv();

double logDensity(double const *x, unsigned int length, PDFType type,
double logDensity(double const *x, PDFType type,
std::vector<double const *> const &parameters,
std::vector<std::vector<unsigned int> > const &dims,
double const *lower, double const *upper) const;
void randomSample(double *x, unsigned int length,
std::vector<std::vector<unsigned long> > const &dims) const override;
void randomSample(double *x,
std::vector<double const *> const &parameters,
std::vector<std::vector<unsigned int> > const &dims,
double const *lower, double const *upper, RNG *rng) const;
void typicalValue(double *x, unsigned int length,
std::vector<double const *> const &parameters,
std::vector<std::vector<unsigned int> > const &dims,
double const *lower, double const *upper) const;
bool checkParameterDim(std::vector<std::vector<unsigned int> > const &dims) const;
std::vector<std::vector<unsigned long> > const &dims, RNG *rng) const override;
bool checkParameterDim(std::vector<std::vector<unsigned long> > const &dims) const override;
bool checkParameterValue(std::vector<double const *> const &parameters,
std::vector<std::vector<unsigned int> > const &dims) const;
std::vector<unsigned int> dim(std::vector<std::vector<unsigned int> > const &dims) const;
void support(double *lower, double *upper, unsigned int length,
std::vector<std::vector<unsigned long> > const &dims) const override;
std::vector<unsigned long> dim(std::vector<std::vector<unsigned long> > const &dims) const override;
void support(double *lower, double *upper,
std::vector<double const *> const &parameters,
std::vector<std::vector<unsigned int> > const &dims) const;
bool isSupportFixed(std::vector<bool> const &fixmask) const;
std::vector<std::vector<unsigned long> > const &dims) const override;
bool isSupportFixed(std::vector<bool> const &fixmask) const override;
};

}}
Expand Down
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