swap argument order

R/RcppExports.R

@@ -9,15 +9,15 @@ RcppFNN <- function(target, rt, eps, lib, pred, E, tau = 1L, style = 0L, dist_me
     .Call(`_pc_RcppFNN`, target, rt, eps, lib, pred, E, tau, style, dist_metric, k, threads, parallel_level, nb, nrows, na_comp)
 }
 
-RcppPC <- function(target, source, lib, pred, E, tau, style = 0L, num_neighbors = 4L, zero_tolerance = 0L, dist_metric = "euclidean", relative = TRUE, weighted = TRUE, threads = 1L, h = 0L, nb = NULL, nrows = NULL, na_comp = TRUE) {
-    .Call(`_pc_RcppPC`, target, source, lib, pred, E, tau, style, num_neighbors, zero_tolerance, dist_metric, relative, weighted, threads, h, nb, nrows, na_comp)
+RcppPC <- function(source, target, lib, pred, E, tau, style = 0L, num_neighbors = 4L, zero_tolerance = 0L, dist_metric = "euclidean", relative = TRUE, weighted = TRUE, threads = 1L, h = 0L, nb = NULL, nrows = NULL, na_comp = TRUE) {
+    .Call(`_pc_RcppPC`, source, target, lib, pred, E, tau, style, num_neighbors, zero_tolerance, dist_metric, relative, weighted, threads, h, nb, nrows, na_comp)
 }
 
-RcppPCboot <- function(target, source, libsizes, lib, pred, E, tau, style = 0L, num_neighbors = 4L, zero_tolerance = 0L, dist_metric = "euclidean", boot = 99L, replace_sampling = TRUE, seed = 42L, relative = TRUE, weighted = TRUE, threads = 1L, parallel_level = 0L, verbose = FALSE, h = 0L, nb = NULL, nrows = NULL, na_comp = TRUE) {
-    .Call(`_pc_RcppPCboot`, target, source, libsizes, lib, pred, E, tau, style, num_neighbors, zero_tolerance, dist_metric, boot, replace_sampling, seed, relative, weighted, threads, parallel_level, verbose, h, nb, nrows, na_comp)
+RcppPCboot <- function(source, target, libsizes, lib, pred, E, tau, style = 0L, num_neighbors = 4L, zero_tolerance = 0L, dist_metric = "euclidean", boot = 99L, replace_sampling = TRUE, seed = 42L, relative = TRUE, weighted = TRUE, threads = 1L, parallel_level = 0L, verbose = FALSE, h = 0L, nb = NULL, nrows = NULL, na_comp = TRUE) {
+    .Call(`_pc_RcppPCboot`, source, target, libsizes, lib, pred, E, tau, style, num_neighbors, zero_tolerance, dist_metric, boot, replace_sampling, seed, relative, weighted, threads, parallel_level, verbose, h, nb, nrows, na_comp)
 }
 
-RcppPCops <- function(target, source, lib, pred, E, tau, k, maximize = "positive", style = 0L, zero_tolerance = 0L, dist_metric = "euclidean", relative = TRUE, weighted = TRUE, threads = 1L, parallel_level = 0L, h = 0L, nb = NULL, nrows = NULL, na_comp = TRUE) {
-    .Call(`_pc_RcppPCops`, target, source, lib, pred, E, tau, k, maximize, style, zero_tolerance, dist_metric, relative, weighted, threads, parallel_level, h, nb, nrows, na_comp)
+RcppPCops <- function(source, target, lib, pred, E, tau, k, maximize = "positive", style = 0L, zero_tolerance = 0L, dist_metric = "euclidean", relative = TRUE, weighted = TRUE, threads = 1L, parallel_level = 0L, h = 0L, nb = NULL, nrows = NULL, na_comp = TRUE) {
+    .Call(`_pc_RcppPCops`, source, target, lib, pred, E, tau, k, maximize, style, zero_tolerance, dist_metric, relative, weighted, threads, parallel_level, h, nb, nrows, na_comp)
 }
 

R/ops.R

@@ -1,4 +1,4 @@
-.ops_ts = \(data, target, source, E = 3:5, k = E, tau = 1, style = 1, lib = NULL, pred = NULL,
+.ops_ts = \(data, source, target, E = 3:5, k = E, tau = 1, style = 1, lib = NULL, pred = NULL,
             maximize = c("dark", "positive", "negative"), dist.metric = c("euclidean", "manhattan", "maximum"), 
             zero.tolerance = max(k), relative = TRUE, weighted = TRUE, threads = length(E), higher.parallel = TRUE, h = 0, ...) {
   maximize = match.arg(maximize)
@@ -8,11 +8,11 @@
   if (is.null(lib)) lib = which(!(is.na(tv) | is.na(sv)))
   if (is.null(pred)) pred = lib
 
-  return(RcppPCops(tv, sv, lib, pred, E, tau, k, maximize, style, zero.tolerance,
+  return(RcppPCops(sv, tv, lib, pred, E, tau, k, maximize, style, zero.tolerance,
                    dist.metric, relative, weighted, threads, higher.parallel, h, NULL, NULL))
 }
 
-.ops_lattice = \(data, target, source, E = 3:5, k = E+1, tau = 1, style = 1, lib = NULL, pred = NULL, 
+.ops_lattice = \(data, source, target, E = 3:5, k = E+1, tau = 1, style = 1, lib = NULL, pred = NULL, 
                  maximize = c("dark", "positive", "negative"), dist.metric = c("euclidean", "manhattan", "maximum"), 
                  zero.tolerance = max(k), relative = TRUE, weighted = TRUE, threads = length(E), higher.parallel = TRUE, detrend = FALSE, nb = NULL, ...) {
   if (is.null(nb)) nb = sdsfun::spdep_nb(data)
@@ -23,11 +23,11 @@
   if (is.null(lib)) lib = which(!(is.na(tv) | is.na(sv)))
   if (is.null(pred)) pred = lib
 
-  return(RcppPCops(tv, sv, lib, pred, E, tau, k, maximize, style, zero.tolerance, 
+  return(RcppPCops(sv, tv, lib, pred, E, tau, k, maximize, style, zero.tolerance, 
                    dist.metric, relative, weighted, threads, higher.parallel, 0, nb, NULL))
 }
 
-.ops_grid = \(data, target, source, E = 3:5, k = E+1, tau = 1, style = 1, lib = NULL, pred = NULL,
+.ops_grid = \(data, source, target, E = 3:5, k = E+1, tau = 1, style = 1, lib = NULL, pred = NULL,
               maximize = c("positive", "negative", "dark"), dist.metric = c("euclidean", "manhattan", "maximum"), 
               zero.tolerance = max(k), relative = TRUE, weighted = TRUE, threads = length(E), higher.parallel = TRUE, detrend = FALSE, ...) {
   maximize = match.arg(maximize)
@@ -37,7 +37,7 @@
   if (is.null(lib)) lib = which(!(is.na(tv) | is.na(sv)))
   if (is.null(pred)) pred = lib
 
-  return(RcppPCops(tv, sv, lib, pred, E, tau, k, maximize, style, zero.tolerance, dist.metric, 
+  return(RcppPCops(sv, tv, lib, pred, E, tau, k, maximize, style, zero.tolerance, dist.metric, 
                    relative, weighted, threads, higher.parallel, 0, NULL, terra::nrow(data)))
 }
 

R/pc.R

@@ -1,4 +1,4 @@
-.pc_ts = \(data, target, source, libsizes = NULL, E = 3, k = E, tau = 1, style = 1, lib = NULL, pred = NULL, boot = 99,
+.pc_ts = \(data, source, target, libsizes = NULL, E = 3, k = E, tau = 1, style = 1, lib = NULL, pred = NULL, boot = 99,
            replace = FALSE, seed = 42L, dist.metric = c("euclidean", "manhattan", "maximum"), zero.tolerance = max(k),
            relative = TRUE, weighted = TRUE, threads = length(libsizes), higher.parallel = TRUE, verbose = TRUE, h = 0, ...) {
   dist.metric = match.arg(dist.metric)
@@ -8,15 +8,15 @@
   if (is.null(pred)) pred = lib
 
   if (is.null(libsizes)) {
-    return(RcppPC(tv, sv, lib, pred, E, tau, style, k, zero.tolerance,
+    return(RcppPC(sv, tv, lib, pred, E, tau, style, k, zero.tolerance,
                   dist.metric, relative, weighted, threads, h, NULL, NULL))
   } else {
-    return(RcppPCboot(tv, sv, libsizes, lib, pred, E, tau, style, k, zero.tolerance, dist.metric, boot,
+    return(RcppPCboot(sv, tv, libsizes, lib, pred, E, tau, style, k, zero.tolerance, dist.metric, boot,
                       replace, seed, relative, weighted, threads, higher.parallel, verbose, h, NULL, NULL))
   }
 }
 
-.pc_lattice = \(data, target, source, libsizes = NULL, E = 3, k = E+1, tau = 1, style = 1, lib = NULL, pred = NULL, boot = 99,
+.pc_lattice = \(data, source, target, libsizes = NULL, E = 3, k = E+1, tau = 1, style = 1, lib = NULL, pred = NULL, boot = 99,
                 replace = FALSE, seed = 42L, dist.metric = c("euclidean", "manhattan", "maximum"), zero.tolerance = max(k), 
                 relative = TRUE, weighted = TRUE, threads = length(libsizes), higher.parallel = TRUE, verbose = TRUE, detrend = FALSE, nb = NULL, ...) {
   if (is.null(nb)) nb = sdsfun::spdep_nb(data)
@@ -27,15 +27,15 @@
   if (is.null(pred)) pred = lib
 
   if (is.null(libsizes)) {
-    return(RcppPC(tv, sv, lib, pred, E, tau, style, k, zero.tolerance,
+    return(RcppPC(sv, tv, lib, pred, E, tau, style, k, zero.tolerance,
                   dist.metric, relative, weighted, threads, 0, nb, NULL))
   } else {
-    return(RcppPCboot(tv, sv, libsizes, lib, pred, E, tau, style, k, zero.tolerance, dist.metric, boot,
+    return(RcppPCboot(sv, tv, libsizes, lib, pred, E, tau, style, k, zero.tolerance, dist.metric, boot,
                       replace, seed, relative, weighted, threads, higher.parallel, verbose, 0, nb, NULL))
   }
 }
 
-.pc_grid = \(data, target, source, libsizes = NULL, E = 3, k = E+1, tau = 1, style = 1, lib = NULL, pred = NULL, boot = 99,
+.pc_grid = \(data, source, target, libsizes = NULL, E = 3, k = E+1, tau = 1, style = 1, lib = NULL, pred = NULL, boot = 99,
              replace = FALSE, seed = 42L, dist.metric = c("euclidean", "manhattan", "maximum"), zero.tolerance = max(k), 
              relative = TRUE, weighted = TRUE, threads = length(libsizes), higher.parallel = TRUE, verbose = TRUE, detrend = FALSE, ...) {
   dist.metric = match.arg(dist.metric)
@@ -45,10 +45,10 @@
   if (is.null(pred)) pred = lib
 
   if (is.null(libsizes)) {
-    return(RcppPC(tv, sv, lib, pred, E, tau, style, k, zero.tolerance, dist.metric,
+    return(RcppPC(sv, tv, lib, pred, E, tau, style, k, zero.tolerance, dist.metric,
                   relative, weighted, threads, 0, NULL, terra::nrow(data)))
   } else {
-    return(RcppPCboot(tv, sv, libsizes, lib, pred, E, tau, style, k, zero.tolerance, dist.metric, boot, replace,
+    return(RcppPCboot(sv, tv, libsizes, lib, pred, E, tau, style, k, zero.tolerance, dist.metric, boot, replace,
                       seed, relative, weighted, threads, higher.parallel, verbose, 0, NULL, terra::nrow(data)))
   }
 }

src/PC.cpp

@@ -12,8 +12,8 @@
 // Wrapper function to perform pattern causality analysis
 // [[Rcpp::export(rng = false)]]
 Rcpp::List RcppPC(
-    const Rcpp::NumericVector& target,
     const Rcpp::NumericVector& source,
+    const Rcpp::NumericVector& target,
     const Rcpp::IntegerVector& lib,
     const Rcpp::IntegerVector& pred,
     const Rcpp::IntegerVector& E,
@@ -31,9 +31,9 @@ Rcpp::List RcppPC(
     bool na_comp = true)
 {
     // --- Input Conversion and Validation ---
-    std::vector<double> tg = Rcpp::as<std::vector<double>>(target);
     std::vector<double> sg = Rcpp::as<std::vector<double>>(source);
-    const size_t n_obs = tg.size();
+    std::vector<double> tg = Rcpp::as<std::vector<double>>(target);
+    const size_t n_obs = sg.size();
 
     // Convert library indices (R 1-based → C++ 0-based)
     std::vector<size_t> lib_std = Rcpp::as<std::vector<size_t>>(lib);
@@ -431,8 +431,8 @@ Rcpp::List RcppPC(
 // Wrapper function to perform bootstrapped pattern causality analysis
 // [[Rcpp::export(rng = false)]]
 Rcpp::List RcppPCboot(
-    const Rcpp::NumericVector& target,
     const Rcpp::NumericVector& source,
+    const Rcpp::NumericVector& target,
     const Rcpp::IntegerVector& libsizes,
     const Rcpp::IntegerVector& lib,
     const Rcpp::IntegerVector& pred,
@@ -456,9 +456,9 @@ Rcpp::List RcppPCboot(
     bool na_comp = true)
 {
     // --- Input Conversion and Validation --------------------------------------
-    std::vector<double> tg = Rcpp::as<std::vector<double>>(target);
     std::vector<double> sg = Rcpp::as<std::vector<double>>(source);
-    const size_t n_obs = tg.size();
+    std::vector<double> tg = Rcpp::as<std::vector<double>>(target);
+    const size_t n_obs = sg.size();
 
     // Convert library indices (R 1-based → C++ 0-based)
     std::vector<size_t> lib_std = Rcpp::as<std::vector<size_t>>(lib);
@@ -1065,8 +1065,8 @@ Rcpp::IntegerVector OptPCparm(const Rcpp::NumericMatrix& Emat,
 // Wrapper function to perform optimal parameters search for pattern causality analysis
 // [[Rcpp::export(rng = false)]]
 Rcpp::List RcppPCops(
-    const Rcpp::NumericVector& target,
     const Rcpp::NumericVector& source,
+    const Rcpp::NumericVector& target,
     const Rcpp::IntegerVector& lib,
     const Rcpp::IntegerVector& pred,
     const Rcpp::IntegerVector& E,
@@ -1086,9 +1086,9 @@ Rcpp::List RcppPCops(
     bool na_comp = true)
 {
     // Input Conversion and Validation --------------------------------------
-    std::vector<double> tg = Rcpp::as<std::vector<double>>(target);
     std::vector<double> sg = Rcpp::as<std::vector<double>>(source);
-    const size_t n_obs = tg.size();
+    std::vector<double> tg = Rcpp::as<std::vector<double>>(target);
+    const size_t n_obs = sg.size();
 
     // Convert library indices (R 1-based → C++ 0-based)
     std::vector<size_t> lib_std = Rcpp::as<std::vector<size_t>>(lib);