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/dports/science/rdkit/rdkit-Release_2021_03_5/rdkit/Chem/FeatMaps/
H A DUnitTestFeatMapUtils.py45 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()
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/dports/audio/snd/snd-21.2/
H A Dfmviolin.clm664 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 …]
/dports/math/R-cran-lme4/lme4/tests/testthat/
H A Dtest-resids.R7 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")
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H A Dtest-NAhandling.R24 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")
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H A Dtest-lmer.R28 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,
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H A Dtest-methods.R16 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)
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/dports/math/R-cran-lme4/lme4/tests/
H A DREMLdev.R2 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))),
H A Dconfint.R9 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"))
H A Dpredsim.R12 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 …]
H A Ddrop.R4 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")
H A DmodFormula.R16 fm1 <- mkMerMod(environment(devfun), opt, lmod$reTrms, fr = lmod$fr, globalVar
21 fm1C <- fm1
24 … expect_equal(range(residuals(fm1)), c(-101.18, 132.547), tolerance = 1e-5) # these are "outliers"!
25 expect_is(model.frame(fm1),"data.frame")
27 mfm1 <- model.frame(fm1)
28 expect_equal(formula(fm1), Reaction ~ Days + (Days | Subject))
39 expect_equal(predict(fm1,newdata=sleepstudy[1:10,],re.form=NULL),
41 expect_equal(predict(fm1,newdata=sleepstudy),
42 predict(fm1))
H A Dis.R3 fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy) globalVar
4 stopifnot(isREML(fm1),
5 isLMM(fm1),
6 !isGLMM(fm1),
7 !isNLMM(fm1))
9 fm1ML <- refitML(fm1)
H A Drefit.R45 fm1 <- fit_sleepstudy_2 globalVar
46 fm1R <- refit(fm1, sleepstudy$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)
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H A Dmethods.R4 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)
H A Dlmer-1.Rout.save45 + 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))
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/dports/audio/festival/speech_tools/base_class/inst_tmpl/
H A Dvector_dmatrix_t.cc56 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 !=()
H A Dvector_fmatrix_t.cc57 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 !=()
/dports/biology/jalview/jalview/test/jalview/datamodel/features/
H A DFeatureMatcherSetTest.java71 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()
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/dports/finance/R-cran-lmtest/lmtest/R/
H A Dencomptest.R22 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., ...))
/dports/net-mgmt/irrtoolset/irrtoolset-release-5.1.3/src/re2dfa/
H A Dre2dfa.c645 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 …]
/dports/math/R-cran-lme4/lme4/inst/doc/
H A Dlmer.R151 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 …]
/dports/editors/nvi2/nvi2-2.2.0/ex/
H A Dex_move.c34 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()
/dports/editors/vigor/vigor-0.016/ex/
H A Dex_move.c39 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;
/dports/math/tmv/tmv-0.75/examples/
H A DMatrix.cpp187 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()
/dports/math/R-cran-lme4/lme4/man/
H A Dconvergence.Rd132 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)
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