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r.d
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r.d
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module betterr.r;
import std.algorithm, std.array, std.conv, std.datetime, std.math;
import std.meta, std.range, std.stdio, std.string, std.sumtype;
import std.traits, std.utf;
import std.exception;
struct AllElements {};
public AllElements _all;
version(gretl) {
import gretl.matrix;
}
struct sexprec {}
alias Robj = sexprec*;
// This enables reference counting of objects allocated by R
// Handles unprotecting for you
// DOES NOT DO THE *PROTECTING* OF AN R OBJECT
// It only stores a protected object and unprotects it when there are no further references to it
// You need to create the ProtectedRObject when you allocate
// It is assumed that you will not touch the .robj directly
// unprotect is needed because only some Robj will need to be unprotected
struct RObjectStorage {
Robj ptr;
bool unprotect;
int refcount;
}
struct ProtectedRObject {
RObjectStorage * data;
alias data this;
// x should already be protected
// ProtectedRObject is for holding an Robj, not for allocating it
this(Robj x, bool u=false) {
data = new RObjectStorage();
data.ptr = x;
data.refcount = 1;
data.unprotect = u;
}
this(this) {
if (data !is null) {
if (data.unprotect) {
enforce(data !is null, "data should never be null inside an ProtectedRObject. You must have created an ProtectedRObject without using the constructor.");
data.refcount += 1;
}
}
}
/* I don't entirely understand this. Sometimes data is null if unprotect is
* false. Maybe the compiler knows unprotect is false so it'll never
* need to execute this part of the code? */
~this() {
if (data !is null) {
if (data.unprotect) {
enforce(data !is null, "Calling the destructor on a ProtectedRObject when data is null. You must have created an ProtectedRObject without using the constructor.");
data.refcount -= 1;
if (data.refcount == 0) {
//~ writeln("unprotecting");
Rf_unprotect_ptr(data.ptr);
}
}
} else {
writeln(&this, " data is null");
}
}
Robj robj() {
return data.ptr;
}
}
extern (C) {
void passToR(Robj x, char * name);
Robj evalInR(char * cmd);
// This needs to be @nogc so I can call it from the destructor
@nogc void evalQuietlyInR(char * cmd);
void setupRinC();
void teardownRinC();
alias startR = setupRinC;
alias closeR = teardownRinC;
}
void toR(T)(T x, string name) {
passToR(x.robj, toUTFz!(char*)(name));
}
void toR(Robj x, string name) {
passToR(x, toUTFz!(char*)(name));
}
void toR(string[] s, string name) {
passToR(s.robj, toUTFz!(char*)(name));
}
Robj evalR(string cmd) {
return evalInR(toUTFz!(char*)(cmd));
}
void evalRQ(string cmd) {
evalQuietlyInR(toUTFz!(char*)(cmd));
}
void evalRQ(string[] cmds) {
foreach(cmd; cmds) {
evalQuietlyInR(toUTFz!(char*)(cmd));
}
}
void assertR(bool test, string msg) {
if (!test) {
Rf_error( toUTFz!(char*)("Error in D code: " ~ msg) );
}
}
void printR(Robj x) {
Rf_PrintValue(x);
}
void printR(ProtectedRObject x) {
Rf_PrintValue(x.robj);
}
void printR(string s) {
evalRQ(`print(` ~ s ~ `)`);
}
void source(string s) {
evalRQ(`source("` ~ s ~ `")`);
}
int length(Robj x) {
return Rf_length(x);
}
bool isVector(Robj x) {
return to!bool(Rf_isVector(x));
}
bool isMatrix(Robj x) {
return to!bool(Rf_isMatrix(x));
}
bool isNumeric(Robj x) {
return to!bool(Rf_isNumeric(x));
}
bool isInteger(Robj x) {
return to!bool(Rf_isInteger(x));
}
/* In case you have to pass an R symbol name to a C function */
Robj RSymbol(string sym) {
return Rf_install(toUTFz!(char*)(sym));
}
Robj RTrue() {
return Rf_ScalarLogical(1);
}
Robj RFalse() {
return Rf_ScalarLogical(0);
}
// RList is for passing data from D to R in a list
// It's the only way to pass multiple values back to R
struct RList {
ProtectedRObject data;
int length; // Length of the underlying Robj, which can never change
string[] names;
int fillPointer = 0;
private int counter = 0; // Used for foreach
this(int n) {
Robj temp;
Rf_protect(temp = Rf_allocVector(19, n));
data = ProtectedRObject(temp, true);
length = n;
names = new string[n];
}
// For an existing list - by default, assumes the list is already protected
// This list is full by construction
this(Robj v, bool u=false) {
enforce(to!bool(Rf_isVectorList(v)), "Cannot pass a non-list to the constructor for an RList");
data = ProtectedRObject(v, u);
length = v.length;
names = v.names;
fillPointer = v.length;
}
version(standalone) {
this(string name) {
this(evalR(name));
}
}
Robj opIndex(int ii) {
enforce(ii < length, "RList index has to be less than the number of elements");
return VECTOR_ELT(data.robj, ii);
}
Robj opIndex(string name) {
auto ind = countUntil!"a == b"(names, name);
if (ind == -1) { enforce(false, "No element in the list with the name " ~ name); }
return opIndex(ind.to!int);
}
void unsafePut(Robj x, int ii) {
enforce(ii < length, "RList index has to be less than the number of elements. Index " ~ to!string(ii) ~ " >= length " ~ to!string(length));
SET_VECTOR_ELT(data.robj, ii, x);
}
void put(Robj x, string name) {
enforce(fillPointer < length, "RList is full - cannot add more elements");
SET_VECTOR_ELT(data.robj, fillPointer, x);
names[fillPointer] = name;
fillPointer += 1;
}
void put(Robj x) {
put(x, "");
}
void opIndexAssign(Robj x, string name) {
put(x, name);
}
// No opIndexAssign(Robj, int): Use unsafePut instead
// Not clear what is going on if we allow rl[3] = x notation
// Should not usually want to put an element into a specific index
void opIndexAssign(RMatrix rm, string name) {
put(rm.robj, name);
}
void opIndexAssign(RVector rv, string name) {
put(rv.robj, name);
}
void opIndexAssign(RString rs, string name) {
put(rs.robj, name);
}
void opIndexAssign(string s, string name) {
put(s.robj, name);
}
void opIndexAssign(string[] sv, string name) {
put(RStringArray(sv).robj, name);
}
void opIndexAssign(double v, string name) {
put(v.robj, name);
}
void opIndexAssign(double[] vec, string name) {
put(vec.robj, name);
}
void opIndexAssign(int v, string name) {
put(v.robj, name);
}
bool empty() {
return counter == length;
}
Robj front() {
return this[counter];
}
void popFront() {
counter += 1;
}
Robj robj() {
setAttrib(data.robj, "names", names.robj);
return data.robj;
}
}
string toString(Robj cstr) {
return to!string(R_CHAR(cstr));
}
string toString(Robj sv, int ii) {
return to!string(R_CHAR(STRING_ELT(sv, ii)));
}
string[] stringArray(Robj sv) {
string[] result;
foreach(ii; 0..Rf_length(sv)) {
result ~= toString(sv, ii);
}
return result;
}
string[] stringArray(string name) {
Robj sv = evalR(name);
string[] result;
foreach(ii; 0..Rf_length(sv)) {
result ~= toString(sv, ii);
}
return result;
}
struct RString {
ProtectedRObject data;
this(string str) {
Robj temp;
Rf_protect(temp = Rf_allocVector(16, 1));
data = ProtectedRObject(temp, true);
SET_STRING_ELT(data.ptr, 0, Rf_mkChar(toUTFz!(char*)(str)));
}
Robj robj() {
return data.ptr;
}
}
Robj getAttrib(Robj x, string attr) {
return Rf_getAttrib(x, RString(attr).robj);
}
Robj getAttrib(ProtectedRObject x, string attr) {
return Rf_getAttrib(x.ptr, RString(attr).robj);
}
Robj getAttrib(Robj x, RString attr) {
return Rf_getAttrib(x, attr.robj);
}
Robj getAttrib(ProtectedRObject x, RString attr) {
return Rf_getAttrib(x.ptr, attr.robj);
}
string[] names(Robj x) {
return stringArray(getAttrib(x, "names"));
}
void setAttrib(Robj x, string attr, ProtectedRObject val) {
Rf_setAttrib(x, RString(attr).robj, val.robj);
}
void setAttrib(Robj x, RString attr, ProtectedRObject val) {
Rf_setAttrib(x, attr.robj, val.robj);
}
void setAttrib(Robj x, string attr, Robj val) {
Rf_setAttrib(x, RString(attr).robj, val);
}
void setAttrib(Robj x, RString attr, Robj val) {
Rf_setAttrib(x, attr.robj, val);
}
Robj robj(double x) {
return Rf_ScalarReal(x);
}
// Copies
Robj robj(double[] v) {
return RVector(v).robj;
}
Robj robj(int x) {
return Rf_ScalarInteger(x);
}
Robj robj(string s) {
return RString(s).robj;
}
Robj robj(string[] sv) {
return RStringArray(sv).robj;
}
// Copies
double[] array(Robj rv) {
enforce(isVector(rv), "In array(Robj rv): Cannot convert non-vector R object to double[]");
enforce(isNumeric(rv), "In array(Robj rv): Cannot convert non-numeric R object to double[]");
double[] result;
result.reserve(rv.length);
double * ptr = REAL(rv);
foreach(ii; 0..rv.length.to!int) {
result ~= ptr[ii];
}
return result;
}
ProtectedRObject RStringArray(string[] sv) {
Robj temp;
Rf_protect(temp = Rf_allocVector(16, to!int(sv.length)));
auto result = ProtectedRObject(temp, true);
foreach(ii; 0..to!int(sv.length)) {
SET_STRING_ELT(result.robj, ii, Rf_mkChar(toUTFz!(char*)(sv[ii])));
}
return result;
}
ulong[3] tsp(Robj rv) {
auto tsprop = RVector(getAttrib(rv, "tsp"));
ulong[3] result;
result[0] = lround(tsprop[0]*tsprop[2])+1;
result[1] = lround(tsprop[1]*tsprop[2])+1;
result[2] = lround(tsprop[2]);
return result;
}
double scalar(Robj rx) {
return Rf_asReal(rx);
}
double scalar(T: double)(Robj rx) {
return Rf_asReal(rx);
}
int scalar(T: int)(Robj rx) {
return Rf_asInteger(rx);
}
long scalar(T: long)(Robj rx) {
return to!long(rx.scalar!int);
}
ulong scalar(T: ulong)(Robj rx) {
return to!ulong(rx.scalar!int);
}
string scalar(T: string)(Robj rx) {
return to!string(R_CHAR(STRING_ELT(rx,0)));
}
double scalar(string name) {
return Rf_asReal(evalR(name));
}
double scalar(T: double)(string name) {
return Rf_asReal(evalR(name));
}
int scalar(T: int)(string name) {
return Rf_asInteger(evalR(name));
}
long scalar(T: long)(string name) {
return to!long(evalR(name).scalar!int);
}
ulong scalar(T: ulong)(string name) {
return to!ulong(evalR(name).scalar!int);
}
string scalar(T: string)(string name) {
return to!string(R_CHAR(STRING_ELT(evalR(name),0)));
}
struct RMatrix {
ProtectedRObject data;
int rows;
int cols;
double * ptr;
this(int r, int c) {
Robj temp;
Rf_protect(temp = Rf_allocMatrix(14, r, c));
data = ProtectedRObject(temp, true);
ptr = REAL(temp);
rows = r;
cols = c;
}
version(gretl) {
this(T)(T m) if (is(T == DoubleMatrix) || is(T == GretlMatrix)) {
Robj temp;
Rf_protect(temp = Rf_allocMatrix(14, m.rows, m.cols));
data = ProtectedRObject(temp, true);
ptr = REAL(temp);
rows = m.rows;
cols = m.cols;
ptr[0..m.rows*m.cols] = m.ptr[0..m.rows*m.cols];
}
}
version(gretl) {
GretlMatrix mat() {
GretlMatrix result;
result.rows = this.rows;
result.cols = this.cols;
result.ptr = this.ptr;
return result;
}
alias mat this;
}
/* Normally this will be a matrix allocated inside R, and as such, it will already be protected. Nonetheless you have the option to protect by setting the second argument to false. */
this(Robj rm, bool u=false) {
enforce(isMatrix(rm), "Constructing RMatrix from something not a matrix");
enforce(isNumeric(rm), "Constructing RMatrix from something that is not numeric");
data = ProtectedRObject(rm, u);
ptr = REAL(rm);
rows = Rf_nrows(rm);
cols = Rf_ncols(rm);
}
version(standalone) {
this(string name) {
this(evalR(name));
}
}
// Use this only with objects that don't need protection
// For "normal" use that's not an issue
this(ProtectedRObject rm) {
this(rm.ptr);
}
this(RVector v) {
data = v.data;
rows = v.rows;
cols = 1;
ptr = v.ptr;
}
double opIndex(int r, int c) {
enforce(r < this.rows, "First index exceeds the number of rows");
enforce(c < this.cols, "Second index exceeds the number of columns");
return ptr[c*this.rows+r];
}
void opIndexAssign(double v, int r, int c) {
ptr[c*rows+r] = v;
}
void opAssign(double val) {
ptr[0..this.rows*this.cols] = val;
}
void opAssign(RMatrix m) {
Robj temp;
Rf_protect(temp = Rf_allocMatrix(14, m.rows, m.cols));
data = ProtectedRObject(temp, true);
ptr = REAL(temp);
rows = m.rows;
cols = m.cols;
ptr[0..m.rows*m.cols] = m.ptr[0..m.rows*m.cols];
}
version(gretl) {
void opAssign(T)(T m) if (is(T == DoubleMatrix) || is(T == GretlMatrix)) {
enforce(rows == m.rows, "Number of rows in source (" ~ to!string(m.rows) ~ ") is different from number of rows in destination (" ~ rows ~ ").");
enforce(cols == m.cols, "Number of columns in source (" ~ to!string(m.rows) ~ ") is different from number of columns in destination (" ~ rows ~ ").");
ptr[0..m.rows*m.cols] = m.ptr[0..m.rows*m.cols];
}
}
RMatrix opBinary(string op)(double a) {
static if(op == "+") {
return matrixAddition(this, a);
}
static if(op == "-") {
return matrixSubtraction(this, a);
}
static if(op == "*") {
return matrixMultiplication(this, a);
}
static if(op == "/") {
return matrixDivision(this, a);
}
}
RMatrix opBinaryRight(string op)(double a) {
static if(op == "+") {
return matrixAddition(this, a);
}
static if(op == "-") {
return matrixSubtraction(a, this);
}
static if(op == "*") {
return matrixMultiplication(this, a);
}
static if(op == "/") {
return matrixDivision(a, this);
}
}
RMatrix matrixAddition(RMatrix m, double a) {
auto result = RMatrix(m.rows, m.cols);
foreach(ii; 0..m.rows*m.cols) {
result.ptr[ii] = m.ptr[ii] + a;
}
return result;
}
RMatrix matrixSubtraction(RMatrix m, double a) {
auto result = RMatrix(m.rows, m.cols);
foreach(ii; 0..m.rows*m.cols) {
result.ptr[ii] = m.ptr[ii] - a;
}
return result;
}
RMatrix matrixSubtraction(double a, RMatrix m) {
auto result = RMatrix(m.rows, m.cols);
foreach(ii; 0..m.rows*m.cols) {
result.ptr[ii] = a - m.ptr[ii];
}
return result;
}
RMatrix matrixMultiplication(RMatrix m, double a) {
auto result = RMatrix(m.rows, m.cols);
foreach(ii; 0..m.rows*m.cols) {
result.ptr[ii] = a*m.ptr[ii];
}
return result;
}
RMatrix matrixDivision(RMatrix m, double a) {
auto result = RMatrix(m.rows, m.cols);
foreach(ii; 0..m.rows*m.cols) {
result.ptr[ii] = m.ptr[ii]/a;
}
return result;
}
RMatrix matrixDivision(double a, RMatrix m) {
auto result = RMatrix(m.rows, m.cols);
foreach(ii; 0..m.rows*m.cols) {
result.ptr[ii] = a/m.ptr[ii];
}
return result;
}
RMatrix sameSize() {
return RMatrix(rows, cols);
}
Robj robj() {
return data.robj;
}
}
void print(RMatrix m, string msg="") {
writeln(msg);
foreach(row; 0..m.rows) {
foreach(col; 0..m.cols) {
write(m[row,col], " ");
}
writeln("");
}
}
// Copies
RMatrix dup(RMatrix rm) {
RMatrix result = RMatrix(Rf_protect(Rf_duplicate(rm.robj)), true);
return result;
}
struct MatrixIndex {
int rows;
int cols;
int currentRow=0;
int currentCol=0;
this(RMatrix rm) {
rows = rm.rows;
cols = rm.cols;
}
bool empty() {
return currentCol >= cols;
}
int[2] front() {
return [currentRow, currentCol];
}
void popFront() {
if (currentRow >= rows-1) {
currentCol += 1;
currentRow = 0;
} else {
currentRow += 1;
}
}
}
struct TransposeIndex {
int rows;
int cols;
int currentRow=0;
int currentCol=0;
this(RMatrix rm) {
rows = rm.rows;
cols = rm.cols;
}
bool empty() {
return currentCol >= cols;
}
int[2] front() {
return [currentCol, currentRow];
}
void popFront() {
if (currentRow >= rows-1) {
currentCol += 1;
currentRow = 0;
} else {
currentRow += 1;
}
}
}
struct DiagonalIndex {
int rows;
int cols;
int currentRow=0;
int currentCol=0;
this(RMatrix rm) {
rows = rm.rows;
cols = rm.cols;
}
bool empty() {
return (currentCol >= cols) | (currentRow >= rows);
}
int[2] front() {
return [currentRow, currentCol];
}
void popFront() {
currentCol += 1;
currentRow += 1;
}
}
struct BelowDiagonalIndex {
int rows;
int cols;
int currentRow=1;
int currentCol=0;
this(RMatrix rm) {
rows = rm.rows;
cols = rm.cols;
}
bool empty() {
return currentCol >= cols;
}
int[2] front() {
return [currentRow, currentCol];
}
void popFront() {
if (currentRow >= rows) {
currentCol += 1;
currentRow = currentCol+1;
} else {
currentRow += 1;
}
}
}
struct AboveDiagonalIndex {
int rows;
int cols;
int currentRow=0;
int currentCol=1;
this(RMatrix rm) {
rows = rm.rows;
cols = rm.cols;
}
bool empty() {
return currentCol >= cols;
}
int[2] front() {
return [currentRow, currentCol];
}
void popFront() {
if (currentRow >= currentCol-1) {
currentCol += 1;
currentRow = 0;
} else {
currentRow += 1;
}
}
}
struct RVector {
int rows;
double * ptr;
ProtectedRObject data;
version(gretl) {
GretlMatrix mat() {
GretlMatrix result;
result.rows = this.rows;
result.cols = 1;
result.ptr = this.ptr;
return result;
}
alias mat this;
}
this(int r) {
Robj temp;
Rf_protect(temp = Rf_allocVector(14,r));
data = ProtectedRObject(temp, true);
rows = r;
ptr = REAL(temp);
}
this(Robj rv, bool u=false) {
enforce(isVector(rv), "In RVector constructor: Cannot convert non-vector R object to RVector");
enforce(isNumeric(rv), "In RVector constructor: Cannot convert non-numeric R object to RVector");
data = ProtectedRObject(rv, u);
rows = rv.length;
ptr = REAL(rv);
}
this(string name) {
this(evalR(name));
}
this(ProtectedRObject rv, bool u=false) {
this(rv.robj, u);
}
this(T)(T v) {
Robj temp;
Rf_protect(temp = Rf_allocVector(14, to!int(v.length)));
data = ProtectedRObject(temp, true);
rows = to!int(v.length);
ptr = REAL(temp);
foreach(ii; 0..to!int(v.length)) {
ptr[ii] = v[ii];
}
}
double opIndex(int r) {
enforce(r < rows, "Index out of range: index on RVector is too large");
return ptr[r];
}
RVector opIndex(int[] obs) {
auto result = RVector(to!int(obs.length));
foreach(ii; 0..to!int(obs.length)) {
result[ii] = this[obs[ii]];
}
return result;
}
void opIndexAssign(double v, int r) {
enforce(r < rows, "Index out of range: index on RVector is too large");
ptr[r] = v;
}
void opAssign(T)(T x) {
enforce(x.length == rows, "Cannot assign to RVector from an object of a different length");
foreach(ii; 0..to!int(x.length)) {
this[ii] = x[ii];
}
}
RVector opSlice(int i, int j) {
enforce(j <= rows, "Index out of range: index on RVector slice is too large. index=" ~ to!string(j) ~ " # rows=" ~ to!string(rows));
enforce(i < j, "First index has to be less than second index");
RVector result = this;
result.rows = j-i;
result.ptr = &ptr[i];
result.data = data;
return result;
}
void print(string msg="") {
if (msg != "") { writeln(msg, ":"); }
foreach(val; this) {
writeln(val);
}
}
int length() {
return rows;
}
bool empty() {
return rows == 0;
}
double front() {
return this[0];
}
void popFront() {
ptr = &ptr[1];
rows -= 1;
}
double[] array() {
double[] result;
result.reserve(rows);
foreach(val; this) {
result ~= val;
}
return result;
}
Robj robj() {
return data.robj;
}
}
double fromLast(RVector rv, int ii) {
return rv[rv.length-ii-1];
}
double last(RVector rv) {
return rv[rv.length-1];
}
struct RIntVector {
ProtectedRObject data;
ulong length;
int * ptr;
this(int r) {
Robj temp;
Rf_protect(temp = Rf_allocVector(13, r));
data = ProtectedRObject(temp, true);
length = r;
ptr = INTEGER(temp);
}
this(int[] v) {
Robj temp;
Rf_protect(temp = Rf_allocVector(13, to!int(v.length)));
data = ProtectedRObject(temp);
length = v.length;
ptr = INTEGER(temp);
foreach(ii, val; v) {
this[ii.to!int] = val;
}
}
this(Robj rv, bool u=false) {
enforce(isVector(rv), "In RVector constructor: Cannot convert non-vector R object to RVector");
enforce(isInteger(rv), "In RVector constructor: Cannot convert non-integer R object to RVector");
data = ProtectedRObject(rv);
length = rv.length;
ptr = INTEGER(rv);
}
int opIndex(int obs) {
enforce(obs < length, "Index out of range: index on RIntVector is too large");
return ptr[obs];
}
void opIndexAssign(int val, int obs) {
enforce(obs < length, "Index out of range: index on RIntVector is too large");
ptr[obs] = val;
}
void opAssign(int[] v) {
foreach(ii, val; v) {
this[ii.to!int] = val;
}
}
RIntVector opSlice(int i, int j) {
enforce(j < length, "Index out of range: index on RIntVector slice is too large");
enforce(i < j, "First index on RIntVector slice has to be less than the second index");
RIntVector result;
result.data = data;
result.length = j-i;
result.ptr = &ptr[i];
return result;
}
int[] array() {
int[] result;
result.reserve(length);