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SpatLyuSpatLyu
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Merge pull request #40 from SpatLyu/dev
export surd utility
2 parents 6cbd6ee + f7e0b0c commit f10e768

3 files changed

Lines changed: 194 additions & 1 deletion

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‎R/RcppExports.R‎

Lines changed: 8 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -65,6 +65,14 @@ RcppContTE <- function(mat, target, agent, lag_p = 3L, lag_q = 3L, k = 3L, alg =
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.Call(`_infoxtr_RcppContTE`, mat, target, agent, lag_p, lag_q, k, alg, base, normalize, lag_single)
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}
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RcppDiscSURD <- function(mat, max_order = 3L, threads = 1L, base = 2.0, normalize = TRUE) {
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.Call(`_infoxtr_RcppDiscSURD`, mat, max_order, threads, base, normalize)
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}
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RcppContSURD <- function(mat, max_order = 3L, k = 3L, alg = 0L, threads = 1L, base = 2.0, normalize = TRUE) {
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.Call(`_infoxtr_RcppContSURD`, mat, max_order, k, alg, threads, base, normalize)
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}
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RcppGenLatticeLag <- function(mat, nb, lag = 1L) {
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.Call(`_infoxtr_RcppGenLatticeLag`, mat, nb, lag)
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}

‎src/InfotheoExps.cpp‎

Lines changed: 154 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -440,7 +440,7 @@ double RcppDiscTE(SEXP mat,
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bool normalize = false,
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bool lag_single = false)
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{
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infoxtr::infotheo::Matrix m = pat_r2std(mat,false);
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infoxtr::infotheo::Matrix m = pat_r2std(mat, false);
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std::vector<size_t> tg = Rcpp::as<std::vector<size_t>>(target);
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std::vector<size_t> ag = Rcpp::as<std::vector<size_t>>(agent);
@@ -513,3 +513,156 @@ double RcppContTE(const Rcpp::NumericMatrix& mat,
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static_cast<size_t>(std::abs(alg)),
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base, normalize, lag_single);
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}
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// Wrapper function to preform SURD decomposition for discrete data
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// [[Rcpp::export(rng = false)]]
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Rcpp::List RcppDiscSURD(SEXP mat,
520+
int max_order = 3,
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int threads = 1,
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double base = 2.0,
523+
bool normalize = true)
524+
{
525+
infoxtr::surd::DiscMat m = pat_r2std(mat, false);
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infoxtr::surd::SURDRes res = infoxtr::surd::surd(
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m, static_cast<size_t>(std::abs(max_order)),
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static_cast<size_t>(std::abs(threads)), base, normalize);
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const size_t k = res.size();
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Rcpp::NumericVector values(k);
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Rcpp::CharacterVector types(k);
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Rcpp::CharacterVector names(k);
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for (size_t i = 0; i < k; ++i)
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{
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values[i] = res.values[i];
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// variable name
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if (res.types[i] == 3)
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{
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// InfoLeak uses all sources
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std::string nm = "InfoLeak";
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names[i] = nm;
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types[i] = "InfoLeak";
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continue;
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}
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const auto& vars = res.var_indices[i];
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std::string nm;
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for (size_t j = 0; j < vars.size(); ++j)
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{
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if (j > 0)
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nm += "_";
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nm += "V";
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nm += std::to_string(vars[j]);
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}
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names[i] = nm;
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switch (res.types[i])
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{
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case 0:
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types[i] = "R";
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break;
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case 1:
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types[i] = "U";
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break;
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case 2:
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types[i] = "S";
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break;
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default:
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types[i] = "Unknown";
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}
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}
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// values.attr("names") = names;
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return Rcpp::List::create(
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Rcpp::Named("vars") = names,
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Rcpp::Named("types") = types,
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Rcpp::Named("values") = values
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);
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}
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// Wrapper function to preform SURD decomposition for continuous data
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// [[Rcpp::export(rng = false)]]
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Rcpp::List RcppContSURD(SEXP mat,
594+
int max_order = 3,
595+
int k = 3,
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int alg = 0,
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int threads = 1,
598+
double base = 2.0,
599+
bool normalize = true)
600+
{
601+
std::vector<std::vector<double>> m = mat_r2std(mat, false);
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infoxtr::surd::SURDRes res = infoxtr::surd::surd(
604+
m, static_cast<size_t>(std::abs(max_order)),
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static_cast<size_t>(std::abs(k)),
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static_cast<size_t>(std::abs(alg)),
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static_cast<size_t>(std::abs(threads)),
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base, normalize);
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const size_t n_vals = res.size();
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612+
Rcpp::NumericVector values(n_vals);
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Rcpp::CharacterVector types(n_vals);
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Rcpp::CharacterVector names(n_vals);
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616+
for (size_t i = 0; i < n_vals; ++i)
617+
{
618+
values[i] = res.values[i];
619+
620+
// variable name
621+
if (res.types[i] == 3)
622+
{
623+
// InfoLeak uses all sources
624+
std::string nm = "InfoLeak";
625+
names[i] = nm;
626+
types[i] = "InfoLeak";
627+
continue;
628+
}
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630+
const auto& vars = res.var_indices[i];
631+
632+
std::string nm;
633+
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for (size_t j = 0; j < vars.size(); ++j)
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{
636+
if (j > 0)
637+
nm += "_";
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nm += "V";
640+
nm += std::to_string(vars[j]);
641+
}
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names[i] = nm;
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switch (res.types[i])
646+
{
647+
case 0:
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types[i] = "R";
649+
break;
650+
case 1:
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types[i] = "U";
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break;
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case 2:
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types[i] = "S";
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break;
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default:
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types[i] = "Unknown";
658+
}
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}
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661+
// values.attr("names") = names;
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return Rcpp::List::create(
664+
Rcpp::Named("vars") = names,
665+
Rcpp::Named("types") = types,
666+
Rcpp::Named("values") = values
667+
);
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}

‎src/RcppExports.cpp‎

Lines changed: 32 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -253,6 +253,36 @@ BEGIN_RCPP
253253
return rcpp_result_gen;
254254
END_RCPP
255255
}
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// RcppDiscSURD
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Rcpp::List RcppDiscSURD(SEXP mat, int max_order, int threads, double base, bool normalize);
258+
RcppExport SEXP _infoxtr_RcppDiscSURD(SEXP matSEXP, SEXP max_orderSEXP, SEXP threadsSEXP, SEXP baseSEXP, SEXP normalizeSEXP) {
259+
BEGIN_RCPP
260+
Rcpp::RObject rcpp_result_gen;
261+
Rcpp::traits::input_parameter< SEXP >::type mat(matSEXP);
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Rcpp::traits::input_parameter< int >::type max_order(max_orderSEXP);
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Rcpp::traits::input_parameter< int >::type threads(threadsSEXP);
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Rcpp::traits::input_parameter< double >::type base(baseSEXP);
265+
Rcpp::traits::input_parameter< bool >::type normalize(normalizeSEXP);
266+
rcpp_result_gen = Rcpp::wrap(RcppDiscSURD(mat, max_order, threads, base, normalize));
267+
return rcpp_result_gen;
268+
END_RCPP
269+
}
270+
// RcppContSURD
271+
Rcpp::List RcppContSURD(SEXP mat, int max_order, int k, int alg, int threads, double base, bool normalize);
272+
RcppExport SEXP _infoxtr_RcppContSURD(SEXP matSEXP, SEXP max_orderSEXP, SEXP kSEXP, SEXP algSEXP, SEXP threadsSEXP, SEXP baseSEXP, SEXP normalizeSEXP) {
273+
BEGIN_RCPP
274+
Rcpp::RObject rcpp_result_gen;
275+
Rcpp::traits::input_parameter< SEXP >::type mat(matSEXP);
276+
Rcpp::traits::input_parameter< int >::type max_order(max_orderSEXP);
277+
Rcpp::traits::input_parameter< int >::type k(kSEXP);
278+
Rcpp::traits::input_parameter< int >::type alg(algSEXP);
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Rcpp::traits::input_parameter< int >::type threads(threadsSEXP);
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Rcpp::traits::input_parameter< double >::type base(baseSEXP);
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Rcpp::traits::input_parameter< bool >::type normalize(normalizeSEXP);
282+
rcpp_result_gen = Rcpp::wrap(RcppContSURD(mat, max_order, k, alg, threads, base, normalize));
283+
return rcpp_result_gen;
284+
END_RCPP
285+
}
256286
// RcppGenLatticeLag
257287
Rcpp::NumericMatrix RcppGenLatticeLag(const Rcpp::NumericMatrix& mat, const Rcpp::List& nb, int lag);
258288
RcppExport SEXP _infoxtr_RcppGenLatticeLag(SEXP matSEXP, SEXP nbSEXP, SEXP lagSEXP) {
@@ -362,6 +392,8 @@ static const R_CallMethodDef CallEntries[] = {
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{"_infoxtr_RcppContCMI", (DL_FUNC) &_infoxtr_RcppContCMI, 8},
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{"_infoxtr_RcppDiscTE", (DL_FUNC) &_infoxtr_RcppDiscTE, 9},
364394
{"_infoxtr_RcppContTE", (DL_FUNC) &_infoxtr_RcppContTE, 10},
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{"_infoxtr_RcppDiscSURD", (DL_FUNC) &_infoxtr_RcppDiscSURD, 5},
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{"_infoxtr_RcppContSURD", (DL_FUNC) &_infoxtr_RcppContSURD, 7},
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{"_infoxtr_RcppGenLatticeLag", (DL_FUNC) &_infoxtr_RcppGenLatticeLag, 3},
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{"_infoxtr_RcppGenGridLag", (DL_FUNC) &_infoxtr_RcppGenGridLag, 3},
367399
{"_infoxtr_RcppGenTSLag", (DL_FUNC) &_infoxtr_RcppGenTSLag, 2},

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