/dports/science/rdkit/rdkit-Release_2021_03_5/rdkit/Chem/FeatMaps/ |
H A D | UnitTestFeatMapUtils.py | 45 fm1 = self.p.Parse() 63 fm1 = self.p.Parse() 80 fm1 = self.p.Parse() 98 fm1 = self.p.Parse() 110 fm1 = self.p.Parse() 121 fm1 = self.p.Parse() 141 fm1 = self.p.Parse() 165 fm1 = self.p.Parse() 195 fm1 = self.p.Parse() 214 fm1 = self.p.Parse() [all …]
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/dports/audio/snd/snd-21.2/ |
H A D | fmviolin.clm | 664 0) :fm1-env '(0 1 20 0 100 0) :fm2-rat 0.6875 :reverb-amount 0) 667 0) :fm1-env '(0 1 20 0 100 0) :fm2-rat 0.6875 :reverb-amount 0) 670 0) :fm1-env '(0 1 20 0 100 0) :fm2-rat 0.6875 :reverb-amount 0) 699 …index 2.2165 :amp-env '(0 0 65 1 100 0) :noise-amount 0.004 :fm1-env '(0 0 65 1 100 0) :fm1-rat 1.… 700 …index 2.3234 :amp-env '(0 0 65 1 100 0) :noise-amount 0.004 :fm1-env '(0 0 65 1 100 0) :fm1-rat 3.… 702 …index 1.8667 :amp-env '(0 0 65 1 100 0) :noise-amount 0.004 :fm1-env '(0 0 65 1 100 0) :fm1-rat 3.… 703 …index 1.8523 :amp-env '(0 0 65 1 100 0) :noise-amount 0.004 :fm1-env '(0 0 65 1 100 0) :fm1-rat 3.… 705 …index 1.5187 :amp-env '(0 0 65 1 100 0) :noise-amount 0.004 :fm1-env '(0 0 65 1 100 0) :fm1-rat 3.… 706 …index 2.4074 :amp-env '(0 0 65 1 100 0) :noise-amount 0.004 :fm1-env '(0 0 65 1 100 0) :fm1-rat 3.… 708 …index 2.3069 :amp-env '(0 0 65 1 100 0) :noise-amount 0.004 :fm1-env '(0 0 65 1 100 0) :fm1-rat 3.… [all …]
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/dports/math/R-cran-lme4/lme4/tests/testthat/ |
H A D | test-resids.R | 7 fm1 <- lmer(Reaction ~ Days + (Days|Subject),sleepstudy, globalVar 13 expect_equal(resid(fm1), resid(fm2)) 14 expect_equal(range(resid(fm1)), c(-101.17996, 132.54664), tolerance=1e-6) 16 expect_equal(resid(fm1,"response"),resid(fm1)) 17 expect_equal(resid(fm1,"response"),resid(fm1,type="working")) 18 expect_equal(resid(fm1,"deviance"),resid(fm1,type="pearson")) 19 expect_equal(resid(fm1),resid(fm1,type="pearson")) ## because no weights given 20 expect_error(residuals(fm1,"partial"), 25 fm1NA <- update(fm1,data=sleepstudyNA) 26 fm1NA_exclude <- update(fm1,data=sleepstudyNA,na.action="na.exclude") [all …]
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H A D | test-NAhandling.R | 24 fm2 <- update(fm1, data=sleepstudyNA, 53 expect_error(update(fm1,data=sleepstudyNA, 63 expect_error(update(fm1, data = sleepstudyNA2, 76 fm1 <- update(fm0, data = cakeNA) globalVar 81 fm1_omit <- update(fm1, na.action = na.omit) 86 expect_equal(fm1, fm1_omit) 150 fm1 <- update(fm0, data=d) globalVar 152 expect_false(any(is.na(predict(fm1)))) 153 expect_false(any(is.na(residuals(fm1)))) 154 fm2 <- update(fm1,na.action="na.exclude") [all …]
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H A D | test-lmer.R | 28 expect_equal(VarCorr(fm1),VarCorr(fm1_noCD)) 32 expect_is(fm1@resp, "lmerResp") 33 expect_is(fm1@pp, "merPredD") 41 expect_is(REMLfun <- as.function(fm1), "function") 64 expect_is(Zt <- getME(fm1, "Zt"), "dgCMatrix") 214 expect_is(refit(fm1),"merMod") 218 fm1 <- lmer(z~1|f,d,subset=(z<1e9)) globalVar 222 fm1 <- lmer(z~ as.numeric(f) + 1|f, d) globalVar 223 fm1@optinfo$derivs$Hessian[2,2] <- NA 224 expect_warning(lme4:::checkConv(fm1@optinfo$derivs, [all …]
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H A D | test-methods.R | 16 fm1 <- fit_sleepstudy_1 globalVar 74 aa <- suppressMessages(anova(fm0,fm1)) 157 aa2 <- anova(fm1,fm0) 307 ci1.w <- confint(fm1,method="Wald") 308 ci1.b <- CI.boot(fm1, nsim=2) 367 s1 <- simulate(fm1) 368 expect_is(refit(fm1,s1), "merMod") 369 s2 <- simulate(fm1,2) 626 expect_equal(df.residual(fm1),176) 762 rfm1 <- rstudent(fm1) [all …]
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/dports/math/R-cran-lme4/lme4/tests/ |
H A D | REMLdev.R | 2 fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) globalVar 3 fm1ML <- refitML(fm1) 4 REMLcrit(fm1) 6 deviance(fm1,REML=FALSE) ## FIXME: not working yet (NA) 7 deviance(fm1,REML=TRUE) 13 … all.equal(REMLcrit(fm1),deviance(fm1,REML=TRUE),deviance(fm1ML,REML=TRUE),oldvals["REML"]), 15 … all.equal(REMLcrit(fm1)/-2,c(logLik(fm1)),c(logLik(fm1ML,REML=TRUE)),c(logLik(fm1,REML=TRUE))),
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H A D | confint.R | 9 fm1 <- fit_sleepstudy_2 globalVar 10 c0 <- confint(fm1, method="Wald") 11 c0B <- confint(fm1, method="Wald",parm="Days") 18 confint(fm1, method="boot", boot.type=bt, nsim=10,quiet=TRUE)) 21 expect_error(confint(fm1, method="boot", boot.type=bt, nsim=10), 25 c1 <- confint(fm1,method="profile",parm=5:6) 28 c2 <- confint(fm1,method="boot",nsim=50,parm=5:6) 35 print(c1B <- confint(fm1, method="profile")) 36 print(c2B <- confint(fm1, method="boot"))
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H A D | predsim.R | 12 fm1 <- lmer(Reaction~Days+(1|Subject),sleepstudy) globalVar 14 pp <- predict(fm1) 15 rr <- range(usim2 <- simulate(fm1,1,use.u=TRUE)[[1]]) 20 points(simulate(fm1,1)[[1]],col=4) 27 ss <- simulate(fm1,1000,use.u=TRUE) 34 pp2 <- predict(fm1,ReForm=NA) 35 ss2 <- simulate(fm1,1000,use.u=FALSE) 69 s1 <- simulate(fm1) 71 s2 <- simulate(fm1,newdata=model.frame(fm1), 72 newparams=getME(fm1,c("theta","beta","sigma"))) [all …]
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H A D | drop.R | 4 fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) globalVar 10 update(fm1, . ~ . - Days) 13 terms(fm1) 14 terms(fm1,fixed.only=FALSE) 16 extractAIC(fm1) 18 drop1(fm1) 19 drop1(fm1, test="Chisq")
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H A D | modFormula.R | 16 fm1 <- mkMerMod(environment(devfun), opt, lmod$reTrms, fr = lmod$fr, globalVar 21 fm1C <- fm1 24 … expect_equal(range(residuals(fm1)), c(-101.18, 132.547), tolerance = 1e-5) # these are "outliers"! 25 expect_is(model.frame(fm1),"data.frame") 27 mfm1 <- model.frame(fm1) 28 expect_equal(formula(fm1), Reaction ~ Days + (Days | Subject)) 39 expect_equal(predict(fm1,newdata=sleepstudy[1:10,],re.form=NULL), 41 expect_equal(predict(fm1,newdata=sleepstudy), 42 predict(fm1))
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H A D | is.R | 3 fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) globalVar 4 stopifnot(isREML(fm1), 5 isLMM(fm1), 6 !isGLMM(fm1), 7 !isNLMM(fm1)) 9 fm1ML <- refitML(fm1)
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H A D | refit.R | 45 fm1 <- fit_sleepstudy_2 globalVar 46 fm1R <- refit(fm1, sleepstudy$Reaction) 47 fm1S <- refit(fm1, simulate(fm1)[[1]]) 49 stopifnot(all.equal(getinfo(fm1 ), 51 all.equal(getinfo(fm1 ), 56 sapply(slotNames(fm1), function(.) argument 57 all.equal( slot(fm1,.), slot(fm1R,.), tolerance=0)) 63 sapply(slotNames(fm1), 65 str(fm1 @ optinfo) 69 fm1ML <- refitML(fm1) [all …]
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H A D | methods.R | 4 fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) globalVar 5 expect_equal(colnames(model.frame(fm1)),c("Reaction","Days","Subject")) 6 expect_equal(colnames(model.frame(fm1,fixed.only=TRUE)),c("Reaction","Days")) 7 expect_equal(formula(fm1),Reaction ~ Days + (Days | Subject)) 8 expect_equal(formula(fm1,fixed.only=TRUE),Reaction ~ Days)
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H A D | lmer-1.Rout.save | 45 + anova(fm1, fm2) 52 + stopifnot(all.equal(fm1, fm1.)) 55 + #stopifnot(all.equal(fm1@devcomp$cmp['REML'], fm1.@devcomp$cmp['REML']), 56 + # all.equal(fixef(fm1), fixef(fm1.)), 57 + # all.equal(fm1@re@theta, fm1.@theta, tolerance = 1.e-7), 58 + # all.equal(ranef(fm1), ranef(fm1.))) 64 + ## stopifnot(all.equal(fm1@devcomp$cmp['REML'], fm1.@devcomp$cmp['REML']), 65 + ## all.equal(fixef(fm1), fixef(fm1.)), 66 + ## all.equal(fm1@re@theta, fm1.@re@theta, tolerance = 1.e-7), 67 + ## all.equal(ranef(fm1), ranef(fm1.), tolerance = 1.e-7)) [all …]
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/dports/audio/festival/speech_tools/base_class/inst_tmpl/ |
H A D | vector_dmatrix_t.cc | 56 int operator !=(const EST_DMatrix &fm1, in operator !=() argument 60 if(fm1.num_rows() != fm2.num_rows() || in operator !=() 61 fm1.num_columns() != fm2.num_columns() ) in operator !=() 64 for(i=0;i<fm1.num_rows();i++) in operator !=() 65 for(j=0;j<fm1.num_columns();j++) in operator !=() 66 if(fm1.a_no_check(i,j) != fm1.a_no_check(i,j)) in operator !=()
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H A D | vector_fmatrix_t.cc | 57 int operator !=(const EST_FMatrix &fm1, in operator !=() argument 61 if(fm1.num_rows() != fm2.num_rows() || in operator !=() 62 fm1.num_columns() != fm2.num_columns() ) in operator !=() 65 for(i=0;i<fm1.num_rows();i++) in operator !=() 66 for(j=0;j<fm1.num_columns();j++) in operator !=() 67 if(fm1.a_no_check(i,j) != fm1.a_no_check(i,j)) in operator !=()
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/dports/biology/jalview/jalview/test/jalview/datamodel/features/ |
H A D | FeatureMatcherSetTest.java | 71 assertTrue(fm1.matches(sf)); in testAnd() 76 fms.and(fm1); in testAnd() 131 fms.and(fm1); in testToString() 142 fms.or(fm1); in testToString() 150 fms.and(fm1); in testToString() 177 fms.or(fm1); in testOr() 185 fms.or(fm1); in testOr() 225 fms.and(fm1); in testGetMatchers() 310 fms.and(fm1); in testToStableString() 323 fms.or(fm1); in testToStableString() [all …]
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/dports/finance/R-cran-lmtest/lmtest/R/ |
H A D | encomptest.R | 22 fm1 <- lm(formula1, data = data) functionVar 26 fm1 <- if(inherits(formula1, "formula")) lm(formula1, data = data, ...) else formula1 28 fm2 <- update(fm1, formula2) 31 if(deparse(terms(fm1)[[2]]) != deparse(terms(fm2)[[2]])) 33 if(length(fm1$residuals) != length(fm2$residuals)) 39 fm <- fm[!(fm %in% attr(terms(fm1), "term.labels"))] 42 fm <- update(fm1, fm) 44 m1 <- paste("Model 1:", paste(deparse(formula(fm1)), collapse = "\n")) 51 rval1 <- as.data.frame(waldtest(fm, fm1, vcov = vcov., ...))
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/dports/net-mgmt/irrtoolset/irrtoolset-release-5.1.3/src/re2dfa/ |
H A D | re2dfa.c | 645 if (RD_ACCEPTS_EMPTY_STRING(fm1) && !fm1->eolexp) { in rd_concatenate() 647 fm1 = fm2; in rd_concatenate() 669 RDQ_LIST_START(&(fm1->rf_final), fm1, rs, rd_state) { in rd_concatenate() 671 } RDQ_LIST_END(&(fm1->rf_final), fm1, rs, rd_state); in rd_concatenate() 687 RDQ_UNLINK_LIST(&(fm1->rf_final), fm1); in rd_concatenate() 715 fm1 = rd_make_bol(fm1); in rd_alternate() 720 fm1 = rd_make_eol(fm1); in rd_alternate() 778 if (fm1->bolexp || fm1->eolexp) in rd_one_or_more() 783 RDQ_LIST_START(&(fm1->rf_final), fm1, rs, rd_state) { in rd_one_or_more() 785 } RDQ_LIST_END(&(fm1->rf_final), fm1, rs, rd_state); in rd_one_or_more() [all …]
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/dports/math/R-cran-lme4/lme4/inst/doc/ |
H A D | lmer.R | 151 RX <- getME(fm1, "RX") 152 sigma2 <- sigma(fm1)^2 176 ss <- summary(fm1) 197 as.data.frame(VarCorr(fm1)) 207 plot(fm1, type = c("p", "smooth")) 214 qqmath(fm1, id = 0.05) 231 anova(fm1, fm2, fm3) 236 fm1ML <- refitML(fm1) 245 ccw <- confint(fm1, method = "Wald") 247 ccb <- confint(fm1, method = "boot") [all …]
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/dports/editors/nvi2/nvi2-2.2.0/ex/ |
H A D | ex_move.c | 34 MARK fm1, fm2, m, tm; in ex_copy() local 47 fm1 = cmdp->addr1; in ex_copy() 50 for (cnt = fm1.lno; cnt <= fm2.lno; ++cnt) in ex_copy() 68 cnt = (fm2.lno - fm1.lno) + 1; in ex_copy() 86 MARK fm1, fm2; in ex_move() local 99 fm1 = cmdp->addr1; in ex_move() 101 if (cmdp->lineno >= fm1.lno && cmdp->lineno <= fm2.lno) { in ex_move() 117 fl = fm1.lno; in ex_move() 134 diff = (fm2.lno - fm1.lno) + 1; in ex_move()
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/dports/editors/vigor/vigor-0.016/ex/ |
H A D | ex_move.c | 39 MARK fm1, fm2, m, tm; local 52 fm1 = cmdp->addr1; 56 for (cnt = fm1.lno; cnt <= fm2.lno; ++cnt) 74 cnt = (fm2.lno - fm1.lno) + 1; 94 MARK fm1, fm2; local 106 fm1 = cmdp->addr1; 108 if (cmdp->lineno >= fm1.lno && cmdp->lineno <= fm2.lno) { 124 fl = fm1.lno; 141 diff = (fm2.lno - fm1.lno) + 1;
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/dports/math/tmv/tmv-0.75/examples/ |
H A D | Matrix.cpp | 187 tmv::Matrix<double,tmv::FortranStyle> fm1 = m1; in main() local 188 std::cout<<"fm1 = m1 =\n"<<fm1; in main() 195 std::cout<<"fm1(1,1) = "<<fm1(1,1)<<std::endl; in main() 197 std::cout<<"fm1(4,3) = "<<fm1(4,3)<<std::endl; in main() 199 std::cout<<"fm1.row(1) = "<<fm1.row(1)<<std::endl; in main() 201 std::cout<<"fm1.col(3) = "<<fm1.col(3)<<std::endl; in main() 203 std::cout<<"fm1.subMatrix(2,3,1,2) =\n"<<fm1.subMatrix(2,3,1,2); in main() 208 std::cout<<"fm1.subMatrix(1,3,2,3,2,1) =\n"<<fm1.subMatrix(1,3,2,3,2,1); in main() 213 std::cout<<"fm1.colRange(1,2) =\n"<<fm1.colRange(1,2); in main() 220 std::cout<<"fm1.rowPair(4,1) =\n"<<fm1.rowPair(4,1); in main()
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/dports/math/R-cran-lme4/lme4/man/ |
H A D | convergence.Rd | 132 fm1.tol <- update(fm1, control=strict_tol) 137 fm1.CS <- update(fm1, data=ss.CS) 140 devfun <- update(fm1, devFunOnly=TRUE) 141 if (isLMM(fm1)) { 142 pars <- getME(fm1,"theta") 145 pars <- getME(fm1, c("theta","fixef")) 154 fm1@optinfo$derivs 158 fm1.restart <- update(fm1, start=pars) 161 fm1.restart2 <- update(fm1, start=pars_x, 166 fm1.all <- allFit(fm1) [all …]
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