diff --git a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/DBeta.java b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/DBeta.java
index d7f3839013c0a57016716592c3618467114164cd..4b60d50296b000f4429f2319139819b1356b9cf7 100644
--- a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/DBeta.java
+++ b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/DBeta.java
@@ -16,7 +16,7 @@ import static com.oracle.truffle.r.library.stats.LBeta.lbeta;
import com.oracle.truffle.r.library.stats.StatsFunctions.Function3_1;
-public class DBeta implements Function3_1 {
+public final class DBeta implements Function3_1 {
@Override
public double evaluate(double x, double a, double b, boolean log) {
/* NaNs propagated correctly */
diff --git a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/DHyper.java b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/DHyper.java
index 5e9496495f0f2323e784fe07a27a48c734b22735..1b569cd453911da9fad0b91b87b5804672d57dba 100644
--- a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/DHyper.java
+++ b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/DHyper.java
@@ -41,24 +41,24 @@ public final class DHyper implements Function4_1 {
return e.result;
}
- x = RMath.forceint(x);
- r = RMath.forceint(r);
- b = RMath.forceint(b);
- n = RMath.forceint(n);
+ double ix = RMath.forceint(x);
+ double ir = RMath.forceint(r);
+ double ib = RMath.forceint(b);
+ double in = RMath.forceint(n);
- if (n < x || r < x || n - x > b) {
+ if (in < ix || ir < ix || in - ix > ib) {
return DPQ.rd0(giveLog);
}
- if (n == 0) {
- return (x == 0) ? DPQ.rd1(giveLog) : DPQ.rd0(giveLog);
+ if (in == 0) {
+ return (ix == 0) ? DPQ.rd1(giveLog) : DPQ.rd0(giveLog);
}
- double p = n / (r + b);
- double q = (r + b - n) / (r + b);
+ double p = in / (ir + ib);
+ double q = (ir + ib - in) / (ir + ib);
- double p1 = dbinomRaw(x, r, p, q, giveLog);
- double p2 = dbinomRaw(n - x, b, p, q, giveLog);
- double p3 = dbinomRaw(n, r + b, p, q, giveLog);
+ double p1 = dbinomRaw(ix, ir, p, q, giveLog);
+ double p2 = dbinomRaw(in - ix, ib, p, q, giveLog);
+ double p3 = dbinomRaw(in, ir + ib, p, q, giveLog);
return (giveLog) ? p1 + p2 - p3 : p1 * p2 / p3;
}
diff --git a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/DNBeta.java b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/DNBeta.java
index 2a6fe146eb926f9c48ad9c23d71add58310e4cb1..c357b66df5d85cd3cc187e6fde1abc17771e07b1 100644
--- a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/DNBeta.java
+++ b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/DNBeta.java
@@ -15,7 +15,7 @@ import static com.oracle.truffle.r.library.stats.GammaFunctions.dpoisRaw;
import com.oracle.truffle.r.library.stats.StatsFunctions.Function4_1;
-public class DNBeta implements Function4_1 {
+public final class DNBeta implements Function4_1 {
private static final double eps = 1.e-15;
private final DBeta dbeta = new DBeta();
diff --git a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/DNChisq.java b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/DNChisq.java
index 55515c3247d87af6f3b93b66b58ba2675f713bb8..8fe5845b3441e24e8921e601459456e7347eb6ac 100644
--- a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/DNChisq.java
+++ b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/DNChisq.java
@@ -17,7 +17,7 @@ import static com.oracle.truffle.r.library.stats.GammaFunctions.dpoisRaw;
import com.oracle.truffle.r.library.stats.Chisq.DChisq;
import com.oracle.truffle.r.library.stats.StatsFunctions.Function3_1;
-public class DNChisq implements Function3_1 {
+public final class DNChisq implements Function3_1 {
private static final double eps = 5e-15;
private final DChisq dchisq = new DChisq();
@@ -85,24 +85,24 @@ public class DNChisq implements Function3_1 {
/* upper tail */
/* LDOUBLE */double sum = mid;
/* LDOUBLE */double term = mid;
- df = dfmid;
+ double df2 = dfmid;
double i = imax;
double x2 = x * ncp2;
double q;
do {
i++;
- q = x2 / i / df;
- df += 2;
+ q = x2 / i / df2;
+ df2 += 2;
term *= q;
sum += term;
} while (q >= 1 || term * q > (1 - q) * eps || term > 1e-10 * sum);
/* lower tail */
term = mid;
- df = dfmid;
+ df2 = dfmid;
i = imax;
while (i != 0) {
- df -= 2;
- q = i * df / x2;
+ df2 -= 2;
+ q = i * df2 / x2;
i--;
term *= q;
sum += term;
diff --git a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Dnf.java b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Dnf.java
index 4b4713273b341e906316620b62f057d411884ea9..2afc8f5e130857118685fbf31b2c191a7e564833 100644
--- a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Dnf.java
+++ b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Dnf.java
@@ -20,7 +20,7 @@ import static com.oracle.truffle.r.library.stats.GammaFunctions.dgamma;
import com.oracle.truffle.r.library.stats.StatsFunctions.Function4_1;
-public class Dnf implements Function4_1 {
+public final class Dnf implements Function4_1 {
private final DNChisq dnchisq = new DNChisq();
private final DNBeta dnbeta = new DNBeta();
diff --git a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Dt.java b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Dt.java
index 7ae62d4958a193eee729c85463648881b25ae187..45eb01fe6b8bd4ead373dccfced2c307d3e50321 100644
--- a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Dt.java
+++ b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Dt.java
@@ -13,7 +13,6 @@
package com.oracle.truffle.r.library.stats;
import static com.oracle.truffle.r.library.stats.GammaFunctions.bd0;
-import static com.oracle.truffle.r.library.stats.GammaFunctions.dnorm;
import static com.oracle.truffle.r.library.stats.GammaFunctions.stirlerr;
import static com.oracle.truffle.r.library.stats.MathConstants.DBL_EPSILON;
import static com.oracle.truffle.r.library.stats.MathConstants.M_1_SQRT_2PI;
@@ -22,6 +21,8 @@ import static com.oracle.truffle.r.library.stats.MathConstants.M_LN_SQRT_2PI;
import com.oracle.truffle.r.library.stats.StatsFunctions.Function2_1;
public final class Dt implements Function2_1 {
+ private static final DNorm dnorm = new DNorm();
+
@Override
public double evaluate(double x, double n, boolean giveLog) {
if (Double.isNaN(x) || Double.isNaN(n)) {
@@ -36,7 +37,7 @@ public final class Dt implements Function2_1 {
return DPQ.rd0(giveLog);
}
if (!Double.isFinite(n)) {
- return dnorm(x, 0., 1., giveLog);
+ return dnorm.evaluate(x, 0., 1., giveLog);
}
double u;
diff --git a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/GammaFunctions.java b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/GammaFunctions.java
index 18c55e3ee9f79d79a4ee41c400b4f66f9d635988..8b221ce9340d4d5f9701d510a3ac14de224879ac 100644
--- a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/GammaFunctions.java
+++ b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/GammaFunctions.java
@@ -1152,7 +1152,7 @@ public abstract class GammaFunctions {
}
f = res12 / elfb;
- np = pnorm(s2pt, 0.0, 1.0, !lowerTail, logp);
+ np = new Pnorm().evaluate(s2pt, 0.0, 1.0, !lowerTail, logp);
if (logp) {
double ndOverP = dpnorm(s2pt, !lowerTail, np);
@@ -1369,45 +1369,6 @@ public abstract class GammaFunctions {
return giveLog ? pr - Math.log(scale) : pr / scale;
}
- //
- // pnorm
- //
-
- static double pnorm(double x, double mu, double sigma, boolean lowerTail, boolean logp) {
- double p;
- double cp = 0;
- double localX = x;
-
- /*
- * Note: The structure of these checks has been carefully thought through. For example, if x
- * == mu and sigma == 0, we get the correct answer 1.
- */
- if (Double.isNaN(localX) || Double.isNaN(mu) || Double.isNaN(sigma)) {
- return localX + mu + sigma;
- }
- if (!RRuntime.isFinite(localX) && mu == localX) {
- return Double.NaN; /* x-mu is NaN */
- }
- if (sigma <= 0) {
- if (sigma < 0) {
- return RMathError.defaultError();
- }
- /* sigma = 0 : */
- return (localX < mu) ? rdt0(lowerTail, logp) : rdt1(lowerTail, logp);
- }
- p = (localX - mu) / sigma;
- if (!RRuntime.isFinite(p)) {
- return (localX < mu) ? rdt0(lowerTail, logp) : rdt1(lowerTail, logp);
- }
- localX = p;
-
- double[] pa = new double[]{p};
- double[] cpa = new double[]{cp};
- pnormBoth(localX, pa, cpa, (lowerTail ? 0 : 1), logp);
-
- return lowerTail ? pa[0] : cpa[0];
- }
-
private static final double SIXTEN = 16; /* Cutoff allowing exact "*" and "/" */
@CompilationFinal private static final double[] pba = new double[]{2.2352520354606839287, 161.02823106855587881, 1067.6894854603709582, 18154.981253343561249, 0.065682337918207449113};
diff --git a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Logis.java b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Logis.java
index a6bc1963fc21cd4d007e14b6d1d66e7f815e5985..b810fbae9f35275e8b574f23c3dfd7c8ac127714 100644
--- a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Logis.java
+++ b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Logis.java
@@ -28,15 +28,15 @@ public final class Logis {
public static final class DLogis implements Function3_1 {
@Override
- public double evaluate(double x, double location, double scale, boolean giveLog) {
- if (Double.isNaN(x) || Double.isNaN(location) || Double.isNaN(scale)) {
- return x + location + scale;
+ public double evaluate(double xIn, double location, double scale, boolean giveLog) {
+ if (Double.isNaN(xIn) || Double.isNaN(location) || Double.isNaN(scale)) {
+ return xIn + location + scale;
}
if (scale <= 0.0) {
return RMathError.defaultError();
}
- x = TOMS708.fabs((x - location) / scale);
+ double x = TOMS708.fabs((xIn - location) / scale);
double e = Math.exp(-x);
double f = 1.0 + e;
return giveLog ? -(x + Math.log(scale * f * f)) : e / (scale * f * f);
@@ -64,31 +64,32 @@ public final class Logis {
}
/* p := logit(p) = Math.log( p / (1-p) ) : */
+ double newP;
if (logP) {
if (lowerTail) {
- p = p - DPQ.rlog1exp(p);
+ newP = p - DPQ.rlog1exp(p);
} else {
- p = DPQ.rlog1exp(p) - p;
+ newP = DPQ.rlog1exp(p) - p;
}
} else {
- p = Math.log(lowerTail ? (p / (1. - p)) : ((1. - p) / p));
+ newP = Math.log(lowerTail ? (p / (1. - p)) : ((1. - p) / p));
}
- return location + scale * p;
+ return location + scale * newP;
}
}
public static final class PLogis implements Function3_2 {
@Override
- public double evaluate(double x, double location, double scale, boolean lowerTail, boolean logP) {
- if (Double.isNaN(x) || Double.isNaN(location) || Double.isNaN(scale)) {
- return x + location + scale;
+ public double evaluate(double xIn, double location, double scale, boolean lowerTail, boolean logP) {
+ if (Double.isNaN(xIn) || Double.isNaN(location) || Double.isNaN(scale)) {
+ return xIn + location + scale;
}
if (scale <= 0.0) {
return RMathError.defaultError();
}
- x = (x - location) / scale;
+ double x = (xIn - location) / scale;
if (Double.isNaN(x)) {
return RMathError.defaultError();
}
diff --git a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/PGamma.java b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/PGamma.java
index 16ab8bd2e3d4479bba0dedb8b614503f661e320a..5886a01b16ae9cf1c6e7ae0f0a9fb72f194d8b1f 100644
--- a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/PGamma.java
+++ b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/PGamma.java
@@ -16,7 +16,7 @@ import static com.oracle.truffle.r.library.stats.GammaFunctions.pgammaRaw;
import com.oracle.truffle.r.library.stats.StatsFunctions.Function3_2;
-public class PGamma implements Function3_2 {
+public final class PGamma implements Function3_2 {
@Override
public double evaluate(double xIn, double alph, double scale, boolean lowerTail, boolean logP) {
if (Double.isNaN(xIn) || Double.isNaN(alph) || Double.isNaN(scale)) {
diff --git a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/PHyper.java b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/PHyper.java
index 5a52dd603231eb1033985c12898d9d46d25b43fe..5a6922a91a1ae2e6f0af36d53bfbb8409d1be409 100644
--- a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/PHyper.java
+++ b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/PHyper.java
@@ -29,21 +29,22 @@ public final class PHyper implements Function4_2 {
private final DHyper dhyper = new DHyper();
@Override
- public double evaluate(double x, double nr, double nb, double n, boolean lowerTail, boolean logP) {
+ public double evaluate(double xIn, double nrIn, double nbIn, double nIn, boolean lowerTailIn, boolean logP) {
/* Sample of n balls from nr red and nb black ones; x are red */
- if (Double.isNaN(x) || Double.isNaN(nr) || Double.isNaN(nb) || Double.isNaN(n)) {
- return x + nr + nb + n;
+ if (Double.isNaN(xIn) || Double.isNaN(nrIn) || Double.isNaN(nbIn) || Double.isNaN(nIn)) {
+ return xIn + nrIn + nbIn + nIn;
}
- x = Math.floor(x + 1e-7);
- nr = RMath.forceint(nr);
- nb = RMath.forceint(nb);
- n = RMath.forceint(n);
+ double x = Math.floor(xIn + 1e-7);
+ double nr = RMath.forceint(nrIn);
+ double nb = RMath.forceint(nbIn);
+ double n = RMath.forceint(nIn);
if (nr < 0 || nb < 0 || !Double.isFinite(nr + nb) || n < 0 || n > nr + nb) {
return RMathError.defaultError();
}
+ boolean lowerTail = lowerTailIn;
if (x * (nr + nb) > n * nr) {
/* Swap tails. */
double oldNB = nb;
@@ -66,7 +67,7 @@ public final class PHyper implements Function4_2 {
return logP ? DPQ.rdtlog(d + pd, lowerTail, logP) : DPQ.rdlval(d * pd, lowerTail);
}
- static double pdhyper(double x, double nr, double nb, double n, boolean logP) {
+ static double pdhyper(double xIn, double nr, double nb, double n, boolean logP) {
/*
* Calculate
*
@@ -81,6 +82,7 @@ public final class PHyper implements Function4_2 {
/* LDOUBLE */double sum = 0;
/* LDOUBLE */double term = 1;
+ double x = xIn;
while (x > 0 && term >= DBL_EPSILON * sum) {
term *= x * (nb - n + x) / (n + 1 - x) / (nr + 1 - x);
sum += term;
diff --git a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/PNBeta.java b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/PNBeta.java
index 7734338fc8bb15fc79e2ee565225937defd79f91..012c7b2b16d0878f6b2128d164f3c7313b1d370a 100644
--- a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/PNBeta.java
+++ b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/PNBeta.java
@@ -17,7 +17,7 @@ import com.oracle.truffle.r.library.stats.RMathError.MLError;
import com.oracle.truffle.r.library.stats.StatsFunctions.Function4_2;
import com.oracle.truffle.r.library.stats.TOMS708.Bratio;
-public class PNBeta implements Function4_2 {
+public final class PNBeta implements Function4_2 {
@Override
public double evaluate(double x, double a, double b, double ncp, boolean lowerTail, boolean logP) {
if (Double.isNaN(x) || Double.isNaN(a) || Double.isNaN(b) || Double.isNaN(ncp)) {
@@ -99,7 +99,7 @@ public class PNBeta implements Function4_2 {
/* LDOUBLE */double sumq = 1. - q;
/* LDOUBLE */double ans = q * temp;
- /* LDOUBLE */double ax = ans;
+ /* LDOUBLE */double ax;
/* recurse over subsequent terms until convergence is achieved */
double j = Math.floor(x0); // x0 could be billions, and is in package EnvStats
diff --git a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/PNChisq.java b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/PNChisq.java
index 561fd2740d8b730871432f8ce1fa6706ebd45234..c776e2c447895032b09072188ef2f05d050d5db4 100644
--- a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/PNChisq.java
+++ b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/PNChisq.java
@@ -38,7 +38,7 @@ import com.oracle.truffle.r.library.stats.RMathError.MLError;
import com.oracle.truffle.r.library.stats.StatsFunctions.Function3_2;
import com.oracle.truffle.r.runtime.RError.Message;
-public class PNChisq implements Function3_2 {
+public final class PNChisq implements Function3_2 {
private static final double _dbl_min_exp = M_LN2 * DBL_MIN_EXP;
private final PChisq pchisq = new PChisq();
@@ -284,7 +284,8 @@ public class PNChisq implements Function3_2 {
}
}
- private void debugPrintf(@SuppressWarnings("unused") String fmt, @SuppressWarnings("unused") Object... args) {
+ @SuppressWarnings("unused")
+ private void debugPrintf(String fmt, Object... args) {
// System.out.printf(fmt + "\n", args);
}
diff --git a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/PPois.java b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/PPois.java
index 1d15fa313533e6f9ffe2d39751405c0c3b4dbe3e..1ad3492f1ffb50c308b4f932f294dfc9bcd34c3f 100644
--- a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/PPois.java
+++ b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/PPois.java
@@ -15,7 +15,7 @@ import static com.oracle.truffle.r.library.stats.GammaFunctions.pgamma;
import com.oracle.truffle.r.library.stats.StatsFunctions.Function2_2;
-public class PPois implements Function2_2 {
+public final class PPois implements Function2_2 {
@Override
public double evaluate(double x, double lambda, boolean lowerTail, boolean logP) {
if (Double.isNaN(x) || Double.isNaN(lambda) || lambda < 0.) {
@@ -30,8 +30,8 @@ public class PPois implements Function2_2 {
if (!Double.isFinite(x)) {
return DPQ.rdt1(lowerTail, logP);
}
- x = Math.floor(x + 1e-7);
+ double floorX = Math.floor(x + 1e-7);
- return pgamma(lambda, x + 1, 1., !lowerTail, logP);
+ return pgamma(lambda, floorX + 1, 1., !lowerTail, logP);
}
}
diff --git a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Pnf.java b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Pnf.java
index 56ff4406e9a194b3fd901926ce30bf814d414e11..a48d487b9d972af9bb63f87a42f635fa67e2352e 100644
--- a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Pnf.java
+++ b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Pnf.java
@@ -14,7 +14,7 @@ package com.oracle.truffle.r.library.stats;
import com.oracle.truffle.r.library.stats.DPQ.EarlyReturn;
import com.oracle.truffle.r.library.stats.StatsFunctions.Function4_2;
-public class Pnf implements Function4_2 {
+public final class Pnf implements Function4_2 {
private final PNChisq pnchisq = new PNChisq();
private final PNBeta pnbeta = new PNBeta();
diff --git a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Pt.java b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Pt.java
index fd2e60684a0cef5f1b32e4445056eabe88f48251..f1ef9bf8a51c42b38e04316414d2ced717bcf10a 100644
--- a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Pt.java
+++ b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Pt.java
@@ -11,7 +11,6 @@
*/
package com.oracle.truffle.r.library.stats;
-import static com.oracle.truffle.r.library.stats.GammaFunctions.pnorm;
import static com.oracle.truffle.r.library.stats.LBeta.lbeta;
import static com.oracle.truffle.r.library.stats.MathConstants.M_LN2;
import static com.oracle.truffle.r.library.stats.Pbeta.pbeta;
@@ -19,8 +18,9 @@ import static com.oracle.truffle.r.library.stats.Pbeta.pbeta;
import com.oracle.truffle.api.profiles.BranchProfile;
import com.oracle.truffle.r.library.stats.StatsFunctions.Function2_2;
-public class Pt implements Function2_2 {
+public final class Pt implements Function2_2 {
private final BranchProfile pbetaNanProfile = BranchProfile.create();
+ private final Pnorm pnorm = new Pnorm();
@Override
public double evaluate(double x, double n, boolean lowerTail, boolean logP) {
@@ -41,7 +41,7 @@ public class Pt implements Function2_2 {
return (x < 0) ? DPQ.rdt0(lowerTail, logP) : DPQ.rdt1(lowerTail, logP);
}
if (!Double.isFinite(n)) {
- return pnorm(x, 0.0, 1.0, lowerTail, logP);
+ return pnorm.evaluate(x, 0.0, 1.0, lowerTail, logP);
}
double nx = 1 + (x / n) * x;
@@ -66,19 +66,17 @@ public class Pt implements Function2_2 {
}
/* Use "1 - v" if lower_tail and x > 0 (but not both): */
- if (x <= 0.) {
- lowerTail = !lowerTail;
- }
+ boolean newLowerTail = x <= 0. ? !lowerTail : lowerTail;
if (logP) {
- if (lowerTail) {
+ if (newLowerTail) {
return RMath.log1p(-0.5 * Math.exp(val));
} else {
return val - M_LN2; /* = Math.log(.5* pbeta(....)) */
}
} else {
val /= 2.;
- return DPQ.rdcval(val, lowerTail);
+ return DPQ.rdcval(val, newLowerTail);
}
}
diff --git a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/QBeta.java b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/QBeta.java
index c704b4b59411031634a7d966c5ed60de81e2d7fd..8e8c7512edb90b564a5677756a68258f040b6c3a 100644
--- a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/QBeta.java
+++ b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/QBeta.java
@@ -61,7 +61,8 @@ public final class QBeta implements Function3_2 {
/**
* Debugging printfs should print exactly the same output as GnuR, this can help with debugging.
*/
- private static void debugPrintf(@SuppressWarnings("unused") String fmt, @SuppressWarnings("unused") Object... args) {
+ @SuppressWarnings("unused")
+ private static void debugPrintf(String fmt, Object... args) {
// System.out.printf(fmt + "\n", args);
}
@@ -84,7 +85,7 @@ public final class QBeta implements Function3_2 {
// The fields and variables are named after local variables from GnuR, we keep the original
// names for the ease of debugging
// Checkstyle: stop field name check
- private static class QBetaRawMethod {
+ private static final class QBetaRawMethod {
private boolean give_log_q;
private boolean use_log_x;
private boolean add_N_step;
diff --git a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/QNBeta.java b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/QNBeta.java
index ea00bc27cf0cd1b62cd7f87db5e6e7439f7263e1..ccbd2f19b13549768e8656333228e3b19e8c22bd 100644
--- a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/QNBeta.java
+++ b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/QNBeta.java
@@ -16,16 +16,16 @@ import static com.oracle.truffle.r.library.stats.MathConstants.DBL_MIN;
import com.oracle.truffle.r.library.stats.DPQ.EarlyReturn;
import com.oracle.truffle.r.library.stats.StatsFunctions.Function4_2;
-public class QNBeta implements Function4_2 {
+public final class QNBeta implements Function4_2 {
private static final double accu = 1e-15;
private static final double Eps = 1e-14; /* must be > accu */
private final PNBeta pnbeta = new PNBeta();
@Override
- public double evaluate(double p, double a, double b, double ncp, boolean lowerTail, boolean logP) {
- if (Double.isNaN(p) || Double.isNaN(a) || Double.isNaN(b) || Double.isNaN(ncp)) {
- return p + a + b + ncp;
+ public double evaluate(double pIn, double a, double b, double ncp, boolean lowerTail, boolean logP) {
+ if (Double.isNaN(pIn) || Double.isNaN(a) || Double.isNaN(b) || Double.isNaN(ncp)) {
+ return pIn + a + b + ncp;
}
if (!Double.isFinite(a)) {
return RMathError.defaultError();
@@ -36,12 +36,12 @@ public class QNBeta implements Function4_2 {
}
try {
- DPQ.rqp01boundaries(p, 0, 1, lowerTail, logP);
+ DPQ.rqp01boundaries(pIn, 0, 1, lowerTail, logP);
} catch (EarlyReturn e) {
return e.result;
}
- p = DPQ.rdtqiv(p, lowerTail, logP);
+ double p = DPQ.rdtqiv(pIn, lowerTail, logP);
/*
* Invert pnbeta(.) : 1. finding an upper and lower bound
diff --git a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/QNChisq.java b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/QNChisq.java
index 897f0875c98f71d88f6393779ab981589b33aa01..6673c76ce1cae3cb9c37a56ed8c5bc2e16d7b8f4 100644
--- a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/QNChisq.java
+++ b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/QNChisq.java
@@ -21,7 +21,7 @@ import com.oracle.truffle.r.library.stats.DPQ.EarlyReturn;
import com.oracle.truffle.r.library.stats.RMathError.MLError;
import com.oracle.truffle.r.library.stats.StatsFunctions.Function3_2;
-public class QNChisq implements Function3_2 {
+public final class QNChisq implements Function3_2 {
private static final double accu = 1e-13;
private static final double racc = 4 * DBL_EPSILON;
/* these two are for the "search" loops, can have less accuracy: */
@@ -32,21 +32,21 @@ public class QNChisq implements Function3_2 {
private final PNChisq pnchisq = new PNChisq();
@Override
- public double evaluate(double p, double df, double ncp, boolean lowerTail, boolean logP) {
- if (Double.isNaN(p) || Double.isNaN(df) || Double.isNaN(ncp)) {
- return p + df + ncp;
+ public double evaluate(double pIn, double df, double ncp, boolean lowerTail, boolean logP) {
+ if (Double.isNaN(pIn) || Double.isNaN(df) || Double.isNaN(ncp)) {
+ return pIn + df + ncp;
}
if (!Double.isFinite(df) || df < 0 || ncp < 0) {
return RMathError.defaultError();
}
try {
- DPQ.rqp01boundaries(p, 0, Double.POSITIVE_INFINITY, lowerTail, logP);
+ DPQ.rqp01boundaries(pIn, 0, Double.POSITIVE_INFINITY, lowerTail, logP);
} catch (EarlyReturn e) {
return e.result;
}
- double pp = DPQ.rdqiv(p, logP);
+ double pp = DPQ.rdqiv(pIn, logP);
if (pp > 1 - DBL_EPSILON) {
return lowerTail ? Double.POSITIVE_INFINITY : 0.0;
}
@@ -61,30 +61,32 @@ public class QNChisq implements Function3_2 {
double b = (ncp * ncp) / (df + 3 * ncp);
double c = (df + 3 * ncp) / (df + 2 * ncp);
double ff = (df + 2 * ncp) / (c * c);
- double ux = b + c * qchisq.evaluate(p, ff, lowerTail, logP);
+ double ux = b + c * qchisq.evaluate(pIn, ff, lowerTail, logP);
if (ux < 0) {
ux = 1;
}
double ux0 = ux;
- if (!lowerTail && ncp >= 80) {
+ double p = pIn;
+ boolean newLowerTail = lowerTail;
+ if (!newLowerTail && ncp >= 80) {
/* in this case, pnchisq() works via lower_tail = true */
if (pp < 1e-10) {
RMathError.error(MLError.PRECISION, "qnchisq");
}
- p = DPQ.rdtqiv(p, lowerTail, logP);
- lowerTail = true;
+ p = DPQ.rdtqiv(p, newLowerTail, logP);
+ newLowerTail = true;
} else {
p = pp;
}
pp = RMath.fmin2(1 - DBL_EPSILON, p * (1 + Eps));
- while (ux < DBL_MAX && isLower(lowerTail, pnchisq.pnchisqRaw(ux, df, ncp, Eps, rEps, 10000, lowerTail, false), pp)) {
+ while (ux < DBL_MAX && isLower(newLowerTail, pnchisq.pnchisqRaw(ux, df, ncp, Eps, rEps, 10000, newLowerTail, false), pp)) {
ux *= 2;
}
pp = p * (1 - Eps);
double lx = RMath.fmin2(ux0, DBL_MAX);
- while (lx > DBL_MIN && isGreater(lowerTail, pnchisq.pnchisqRaw(lx, df, ncp, Eps, rEps, 10000, lowerTail, false), pp)) {
+ while (lx > DBL_MIN && isGreater(newLowerTail, pnchisq.pnchisqRaw(lx, df, ncp, Eps, rEps, 10000, newLowerTail, false), pp)) {
lx *= 0.5;
}
@@ -92,8 +94,8 @@ public class QNChisq implements Function3_2 {
double nx;
do {
nx = 0.5 * (lx + ux);
- double raw = pnchisq.pnchisqRaw(nx, df, ncp, accu, racc, 100000, lowerTail, false);
- if (isGreater(lowerTail, raw, p)) {
+ double raw = pnchisq.pnchisqRaw(nx, df, ncp, accu, racc, 100000, newLowerTail, false);
+ if (isGreater(newLowerTail, raw, p)) {
ux = nx;
} else {
lx = nx;
diff --git a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/QPois.java b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/QPois.java
index 34cbad5586728c66abb3153db046256b3f62d13d..95f1096a5de95f3192ba8b7460bf39c22932f149 100644
--- a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/QPois.java
+++ b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/QPois.java
@@ -16,14 +16,14 @@ import static com.oracle.truffle.r.library.stats.MathConstants.DBL_EPSILON;
import com.oracle.truffle.r.library.stats.DPQ.EarlyReturn;
import com.oracle.truffle.r.library.stats.StatsFunctions.Function2_2;
-public class QPois implements Function2_2 {
+public final class QPois implements Function2_2 {
private final Qnorm qnorm = new Qnorm();
private final PPois ppois = new PPois();
@Override
- public double evaluate(double p, double lambda, boolean lowerTail, boolean logP) {
- if (Double.isNaN(p) || Double.isNaN(lambda)) {
- return p + lambda;
+ public double evaluate(double pIn, double lambda, boolean lowerTail, boolean logP) {
+ if (Double.isNaN(pIn) || Double.isNaN(lambda)) {
+ return pIn + lambda;
}
if (!Double.isFinite(lambda)) {
return RMathError.defaultError();
@@ -36,7 +36,7 @@ public class QPois implements Function2_2 {
}
try {
- DPQ.rqp01boundaries(p, 0, Double.POSITIVE_INFINITY, lowerTail, logP);
+ DPQ.rqp01boundaries(pIn, 0, Double.POSITIVE_INFINITY, lowerTail, logP);
} catch (EarlyReturn e) {
return e.result;
}
@@ -50,6 +50,7 @@ public class QPois implements Function2_2 {
* Note : "same" code in qpois.c, qbinom.c, qnbinom.c -- FIXME: This is far from optimal
* [cancellation for p ~= 1, etc]:
*/
+ double p = pIn;
if (!lowerTail || logP) {
p = DPQ.rdtqiv(p, lowerTail, logP); /* need check again (cancellation!): */
if (p == 0.) {
@@ -109,7 +110,7 @@ public class QPois implements Function2_2 {
double y = yIn;
for (;;) {
y = y + incr;
- double z = zIn;
+ double z;
if ((z = ppois.evaluate(y, lambda, /* l._t. */true, /* log_p */false)) >= p) {
return new SearchResult(y, z);
}
diff --git a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Qf.java b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Qf.java
index 4c0274673717603470b161e05700b6789d0bfeaa..94d0967d1c800f55b0e4636aa4d8d84f5c178279 100644
--- a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Qf.java
+++ b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Qf.java
@@ -54,7 +54,7 @@ public final class Qf implements Function3_2 {
}
// FIXME: (1/qb - 1) = (1 - qb)/qb; if we know qb ~= 1, should use other tail
- p = (1. / qbeta.evaluate(p, df2 / 2, df1 / 2, !lowerTail, logP) - 1.) * (df2 / df1);
- return RMath.mlValid(p) ? p : Double.NaN;
+ double newP = (1. / qbeta.evaluate(p, df2 / 2, df1 / 2, !lowerTail, logP) - 1.) * (df2 / df1);
+ return RMath.mlValid(newP) ? newP : Double.NaN;
}
}
diff --git a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Qnf.java b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Qnf.java
index 7f06ef8e578ab80d6f28e4a67ba58ba53a8b45ae..54a6acf636c3f2224d467dd98b754912cff380ea 100644
--- a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Qnf.java
+++ b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Qnf.java
@@ -13,7 +13,7 @@ package com.oracle.truffle.r.library.stats;
import com.oracle.truffle.r.library.stats.DPQ.EarlyReturn;
import com.oracle.truffle.r.library.stats.StatsFunctions.Function4_2;
-public class Qnf implements Function4_2 {
+public final class Qnf implements Function4_2 {
private final QNChisq qnchisq = new QNChisq();
private final QNBeta qnbeta = new QNBeta();
diff --git a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Qt.java b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Qt.java
index 2c4fd0191a3882cb62a484eac535e06cc20411e4..5c527504357c63d421a371b0f3df14191f277cbd 100644
--- a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Qt.java
+++ b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Qt.java
@@ -24,7 +24,7 @@ import static com.oracle.truffle.r.library.stats.MathConstants.M_SQRT2;
import com.oracle.truffle.r.library.stats.DPQ.EarlyReturn;
import com.oracle.truffle.r.library.stats.StatsFunctions.Function2_2;
-public class Qt implements Function2_2 {
+public final class Qt implements Function2_2 {
private static final double eps = 1.e-12;
private static final double accu = 1e-13;
private static final double Eps = 1e-11; /* must be > accu */
@@ -34,14 +34,14 @@ public class Qt implements Function2_2 {
private final Pt pt = new Pt();
@Override
- public double evaluate(double p, double ndf, boolean lowerTail, boolean logP) {
+ public double evaluate(double pIn, double ndf, boolean lowerTail, boolean logP) {
- if (Double.isNaN(p) || Double.isNaN(ndf)) {
- return p + ndf;
+ if (Double.isNaN(pIn) || Double.isNaN(ndf)) {
+ return pIn + ndf;
}
try {
- DPQ.rqp01boundaries(p, Double.NEGATIVE_INFINITY, Double.POSITIVE_INFINITY, lowerTail, logP);
+ DPQ.rqp01boundaries(pIn, Double.NEGATIVE_INFINITY, Double.POSITIVE_INFINITY, lowerTail, logP);
} catch (EarlyReturn earlyReturn) {
return earlyReturn.result;
}
@@ -50,6 +50,7 @@ public class Qt implements Function2_2 {
return RMathError.defaultError();
}
+ double p = pIn;
if (ndf < 1) { /* based on qnt */
int iter = 0;
diff --git a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/RBeta.java b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/RBeta.java
index 7fab48d93886d5aec51fc209396f7eeef3442128..cc59560caa6b01c6559d67e1f37e6559e0e4e3ea 100644
--- a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/RBeta.java
+++ b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/RBeta.java
@@ -24,6 +24,15 @@ public final class RBeta extends RandFunction2_Double {
private static final double expmax = (DBL_MAX_EXP * M_LN2); /* = log(DBL_MAX) */
+ // TODO: state variables
+ private static double beta = 0;
+ private static double gamma = 1;
+ private static double delta;
+ private static double k1 = 0;
+ private static double k2 = 0;
+ private static double olda = -1.0;
+ private static double oldb = -1.0;
+
@Override
public double execute(double aa, double bb, RandomNumberProvider rand) {
if (Double.isNaN(aa) || Double.isNaN(bb) || aa < 0. || bb < 0.) {
@@ -43,18 +52,6 @@ public final class RBeta extends RandFunction2_Double {
return 0.0;
}
- double v = 0;
- double w = 0;
-
- // TODO: state variables
- double beta = 0;
- double gamma = 1;
- double delta;
- double k1 = 0;
- double k2 = 0;
- double olda = -1.0;
- double oldb = -1.0;
-
/* Test if we need new "initializing" */
boolean qsame = (olda == aa) && (oldb == bb);
if (!qsame) {
@@ -66,6 +63,9 @@ public final class RBeta extends RandFunction2_Double {
double b = fmax2(aa, bb); /* a <= b */
double alpha = a + b;
+ double v;
+ double w;
+
if (a <= 1.0) { /* --- Algorithm BC --- */
/* changed notation, now also a <= b (was reversed) */
if (!qsame) { /* initialize */
diff --git a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/RGamma.java b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/RGamma.java
index 8d344b1625e7e68963c496047d185e8fd2603b6b..f3546d5e1a7b174d106d48e902dfef71e6a1aa83 100644
--- a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/RGamma.java
+++ b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/RGamma.java
@@ -16,7 +16,7 @@ import static com.oracle.truffle.r.library.stats.TOMS708.fabs;
import com.oracle.truffle.r.library.stats.RandGenerationFunctions.RandFunction2_Double;
import com.oracle.truffle.r.library.stats.RandGenerationFunctions.RandomNumberProvider;
-public class RGamma extends RandFunction2_Double {
+public final class RGamma extends RandFunction2_Double {
private static final double sqrt32 = 5.656854;
private static final double exp_m1 = 0.36787944117144232159; /* exp(-1) = 1/e */
@@ -44,8 +44,8 @@ public class RGamma extends RandFunction2_Double {
public double execute(double a, double scale, RandomNumberProvider rand) {
// TODO: state variables
- double aa = 0.;
- double aaa = 0.;
+ double aa = Double.NaN;
+ double aaa = Double.NaN;
double s = 0;
double s2 = 0;
double d = 0; /* no. 1 (step 1) */
diff --git a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/RHyper.java b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/RHyper.java
index a233c0c549c1faa414ec875030ad7d5d56845c0b..fb549a90f9e39d7262d5793b9ef3b3cdff6ddfe4 100644
--- a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/RHyper.java
+++ b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/RHyper.java
@@ -73,7 +73,14 @@ public final class RHyper extends RandFunction3_Double {
private static double w;
// III:
// Checkstyle: stop
- private static double a, d, s, xl, xr, kl, kr, lamdl, lamdr, p1, p2, p3;
+ private static double a;
+ private static double xl;
+ private static double xr;
+ private static double lamdl;
+ private static double lamdr;
+ private static double p1;
+ private static double p2;
+ private static double p3;
// // Checkstyle: resume
private static final double scale = 1e25; // scaling factor against (early) underflow
@@ -201,18 +208,19 @@ public final class RHyper extends RandFunction3_Double {
double u;
double v;
+ double s;
if (setup1 || setup2) {
s = Math.sqrt((tn - k) * k * n1 * n2 / (tn - 1) / tn / tn);
/* remark: d is defined in reference without int. */
/* the truncation centers the cell boundaries at 0.5 */
- d = (int) (1.5 * s) + .5;
+ double d = (int) (1.5 * s) + .5;
xl = m - d + .5;
xr = m + d + .5;
a = afc(m) + afc(n1 - m) + afc(k - m) + afc(n2 - k + m);
- kl = Math.exp(a - afc((int) (xl)) - afc((int) (n1 - xl)) - afc((int) (k - xl)) - afc((int) (n2 - k + xl)));
- kr = Math.exp(a - afc((int) (xr - 1)) - afc((int) (n1 - xr + 1)) - afc((int) (k - xr + 1)) - afc((int) (n2 - k + xr - 1)));
+ double kl = Math.exp(a - afc((int) (xl)) - afc((int) (n1 - xl)) - afc((int) (k - xl)) - afc((int) (n2 - k + xl)));
+ double kr = Math.exp(a - afc((int) (xr - 1)) - afc((int) (n1 - xr + 1)) - afc((int) (k - xr + 1)) - afc((int) (n2 - k + xr - 1)));
lamdl = -Math.log(xl * (n2 - k + xl) / (n1 - xl + 1) / (k - xl + 1));
lamdr = -Math.log((n1 - xr + 1) * (k - xr + 1) / xr / (n2 - k + xr));
p1 = d + d;
@@ -329,11 +337,7 @@ public final class RHyper extends RandFunction3_Double {
/*
* * Stirling's formula to machine accuracy
*/
- if (alv <= (a - afc(ix) - afc(n1 - ix) - afc(k - ix) - afc(n2 - k + ix))) {
- reject = false;
- } else {
- reject = true;
- }
+ reject = !(alv <= (a - afc(ix) - afc(n1 - ix) - afc(k - ix) - afc(n2 - k + ix)));
}
}
} // else
diff --git a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/RMath.java b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/RMath.java
index a7f1cd01da654d6c683b5f33d355995655b0e976..68347359d023a0f292c66d2618558cbe1c009954 100644
--- a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/RMath.java
+++ b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/RMath.java
@@ -27,7 +27,7 @@ import com.oracle.truffle.r.runtime.RRuntime;
* @see RMathError
* @see MathConstants
*/
-public class RMath {
+public final class RMath {
public static boolean mlValid(double d) {
return !Double.isNaN(d);
diff --git a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/RMultinom.java b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/RMultinom.java
index f6ec7325bbd3dff6af4f600aa1afdfea39ea27d8..9a0f80cd9a3702d9990ca94a00aeb02b60e4c37a 100644
--- a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/RMultinom.java
+++ b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/RMultinom.java
@@ -13,10 +13,10 @@
package com.oracle.truffle.r.library.stats;
import static com.oracle.truffle.r.nodes.builtin.CastBuilder.Predef.notIntNA;
-import static com.oracle.truffle.r.runtime.RError.SHOW_CALLER;
import static com.oracle.truffle.r.runtime.RError.Message.NA_IN_PROB_VECTOR;
import static com.oracle.truffle.r.runtime.RError.Message.NEGATIVE_PROBABILITY;
import static com.oracle.truffle.r.runtime.RError.Message.NO_POSITIVE_PROBABILITIES;
+import static com.oracle.truffle.r.runtime.RError.SHOW_CALLER;
import java.math.BigDecimal;
import java.math.RoundingMode;
@@ -89,16 +89,16 @@ public abstract class RMultinom extends RExternalBuiltinNode.Arg3 {
private static void fixupProb(double[] p) {
double sum = 0.0;
int npos = 0;
- for (int i = 0; i < p.length; i++) {
- if (!Double.isFinite(p[i])) {
+ for (double prob : p) {
+ if (!Double.isFinite(prob)) {
throw RError.error(SHOW_CALLER, NA_IN_PROB_VECTOR);
}
- if (p[i] < 0.0) {
+ if (prob < 0.0) {
throw RError.error(SHOW_CALLER, NEGATIVE_PROBABILITY);
}
- if (p[i] > 0.0) {
+ if (prob > 0.0) {
npos++;
- sum += p[i];
+ sum += prob;
}
}
if (npos == 0) {
diff --git a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/RPois.java b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/RPois.java
index 8ed6d66484b423f7b4c830ec6660764b4c9bb56f..36759275c32b8477b5fd67b7a68502abfa804f70 100644
--- a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/RPois.java
+++ b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/RPois.java
@@ -40,8 +40,6 @@ public final class RPois extends RandFunction1_Double {
// TODO: state variables
private static int l = 0;
private static int m = 0;
- private static double b1;
- private static double b2;
private static double c = 0;
private static double c0 = 0;
private static double c1 = 0;
@@ -193,8 +191,8 @@ public final class RPois extends RandFunction1_Double {
* discrete normal probabilities fk.
*/
- b1 = one_24 / mu;
- b2 = 0.3 * b1 * b1;
+ double b1 = one_24 / mu;
+ double b2 = 0.3 * b1 * b1;
c3 = one_7 * b1 * b2;
c2 = b2 - 15. * c3;
c1 = b1 - 6. * b2 + 45. * c3;
diff --git a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/RandGenerationFunctions.java b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/RandGenerationFunctions.java
index 19717a9b865e7c364a7b4c24cc8de51b0e1824a1..61aae8184e43a191d9c6f38f7941902da30f50dd 100644
--- a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/RandGenerationFunctions.java
+++ b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/RandGenerationFunctions.java
@@ -184,8 +184,7 @@ public final class RandGenerationFunctions {
RandGenerationNodeData nodeData) {
int length = nodeData.resultVectorLengthProfile.profile(convertToLength.execute(lengthVec));
RNode.reportWork(this, length);
- Object result = evaluate(length, a, b, c, nodeData, rand);
- return result;
+ return evaluate(length, a, b, c, nodeData, rand);
}
@SuppressWarnings("unused")
@@ -308,12 +307,14 @@ public final class RandGenerationFunctions {
return RandFunction3NodeGen.create(RandGenerationFunctionsFactory.RandFunctionIntExecutorNodeGen.create(function));
}
+ // Note: for completeness of the API
+ @SuppressWarnings("unused")
public static RandFunction3Node createDouble(RandFunction3_Double function) {
return RandFunction3NodeGen.create(RandGenerationFunctionsFactory.RandFunctionDoubleExecutorNodeGen.create(function));
}
@Override
- protected void createCasts(CastBuilder casts) {
+ protected final void createCasts(CastBuilder casts) {
ConvertToLength.addLengthCast(casts);
casts.arg(1).asDoubleVector();
casts.arg(2).asDoubleVector();
@@ -343,7 +344,7 @@ public final class RandGenerationFunctions {
}
@Override
- protected void createCasts(CastBuilder casts) {
+ protected final void createCasts(CastBuilder casts) {
ConvertToLength.addLengthCast(casts);
casts.arg(1).asDoubleVector();
casts.arg(2).asDoubleVector();
@@ -372,7 +373,7 @@ public final class RandGenerationFunctions {
}
@Override
- protected void createCasts(CastBuilder casts) {
+ protected final void createCasts(CastBuilder casts) {
ConvertToLength.addLengthCast(casts);
casts.arg(1).asDoubleVector();
}
diff --git a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Random2.java b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Random2.java
index 729f0d0833ed777de42e12fc552206ce7d12f58d..de77422aefb34b79d6788ebc94672fe500c0c1be 100644
--- a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Random2.java
+++ b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Random2.java
@@ -17,7 +17,10 @@ import static com.oracle.truffle.r.library.stats.DPQ.rdtqiv;
/*
* Logic derived from GNU-R, see inline comments.
*/
-public class Random2 {
+public final class Random2 {
+ private Random2() {
+ // only static members
+ }
// from GNUR: qnorm.c
public static double qnorm5(double p, double mu, double sigma, boolean lowerTail, boolean logP) {
diff --git a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Rbinom.java b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Rbinom.java
index 37964392e6762bbac3cebd294e474e15b73c57cc..4f9080aae6e2193cc0313879512fbe35dcdd331c 100644
--- a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Rbinom.java
+++ b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/Rbinom.java
@@ -22,6 +22,9 @@ public final class Rbinom extends RandFunction2_Double {
private final Qbinom qbinom = new Qbinom();
+ // TODO: some of the variables below are static in GnuR, because they cache intermediate results
+ // that depend on paremeters that often do not change between calls.
+
@Override
public double execute(double nin, double pp, RandomNumberProvider rand) {
double psave = -1.0;
diff --git a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/TOMS708.java b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/TOMS708.java
index f335b9f7b1c29ec9b320e822ce49d48e54e6c971..9f0ee17d7b44b2a40a399ec10a63b0beccd7c870 100644
--- a/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/TOMS708.java
+++ b/com.oracle.truffle.r.library/src/com/oracle/truffle/r/library/stats/TOMS708.java
@@ -25,7 +25,10 @@ import com.oracle.truffle.r.runtime.RRuntime;
* transcribed from toms708.c - as the original file contains no copyright header, we assume that it is copyright R code and R foundation.
*/
-public class TOMS708 {
+public final class TOMS708 {
+ private TOMS708() {
+ // only static members
+ }
@SuppressWarnings("unused")
private static void debugPrintf(String format, Object... args) {
diff --git a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RErrorHandling.java b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RErrorHandling.java
index 9fcf43914e98f05039582e68d6acd43abf911c10..6b055c7debfdeefaa0b4d6e0bf930a149c029d47 100644
--- a/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RErrorHandling.java
+++ b/com.oracle.truffle.r.runtime/src/com/oracle/truffle/r/runtime/RErrorHandling.java
@@ -634,7 +634,7 @@ public class RErrorHandling {
throw RInternalError.unimplemented();
} else if (w == 1) {
Utils.writeStderr(message, true);
- } else if (w == 0) {
+ } else if (w == 0 && errorHandlingState.warnings.size() < errorHandlingState.maxWarnings) {
errorHandlingState.warnings.add(new Warning(fmsg, call));
}
} finally {
@@ -695,7 +695,7 @@ public class RErrorHandling {
if (nWarnings < errorHandlingState.maxWarnings) {
Utils.writeStderr(String.format("There were %d warnings (use warnings() to see them)", nWarnings), true);
} else {
- nWarnings = errorHandlingState.maxWarnings;
+ assert nWarnings == errorHandlingState.maxWarnings : "warnings above the limit should not have been added";
Utils.writeStderr(String.format("There were %d or more warnings (use warnings() to see the first %d)", nWarnings, nWarnings), true);
}
}
diff --git a/com.oracle.truffle.r.test/src/com/oracle/truffle/r/test/library/stats/TestDistributions.java b/com.oracle.truffle.r.test/src/com/oracle/truffle/r/test/library/stats/TestDistributions.java
index 54841d07cd4906fc83f11d5136cf5efe764a9c62..b372e721801c039ad33509331914c61ad6b62b46 100644
--- a/com.oracle.truffle.r.test/src/com/oracle/truffle/r/test/library/stats/TestDistributions.java
+++ b/com.oracle.truffle.r.test/src/com/oracle/truffle/r/test/library/stats/TestDistributions.java
@@ -228,6 +228,12 @@ public class TestDistributions extends TestBase {
return this;
}
+ /**
+ * Removes the predefined "error" values for parameters. These are so far always the same,
+ * but this method is here to make the API "complete". May be removed if all distributions
+ * already have tests and non of them needs it.
+ */
+ @SuppressWarnings("unused")
public DistrTest clearDefaultErrorParamValues() {
errorParamValues.clear();
return this;