head 1.9; access; symbols pkgsrc-2026Q1:1.9.0.12 pkgsrc-2026Q1-base:1.9 pkgsrc-2025Q4:1.9.0.10 pkgsrc-2025Q4-base:1.9 pkgsrc-2025Q3:1.9.0.8 pkgsrc-2025Q3-base:1.9 pkgsrc-2025Q2:1.9.0.6 pkgsrc-2025Q2-base:1.9 pkgsrc-2025Q1:1.9.0.4 pkgsrc-2025Q1-base:1.9 pkgsrc-2024Q4:1.9.0.2 pkgsrc-2024Q4-base:1.9 pkgsrc-2024Q3:1.8.0.6 pkgsrc-2024Q3-base:1.8 pkgsrc-2024Q2:1.8.0.4 pkgsrc-2024Q2-base:1.8 pkgsrc-2024Q1:1.8.0.2 pkgsrc-2024Q1-base:1.8 pkgsrc-2023Q4:1.7.0.6 pkgsrc-2023Q4-base:1.7 pkgsrc-2023Q3:1.7.0.4 pkgsrc-2023Q3-base:1.7 pkgsrc-2023Q2:1.7.0.2 pkgsrc-2023Q2-base:1.7 pkgsrc-2023Q1:1.6.0.8 pkgsrc-2023Q1-base:1.6 pkgsrc-2022Q4:1.6.0.6 pkgsrc-2022Q4-base:1.6 pkgsrc-2022Q3:1.6.0.4 pkgsrc-2022Q3-base:1.6 pkgsrc-2022Q2:1.6.0.2 pkgsrc-2022Q2-base:1.6 pkgsrc-2022Q1:1.5.0.4 pkgsrc-2022Q1-base:1.5 pkgsrc-2021Q4:1.5.0.2 pkgsrc-2021Q4-base:1.5 pkgsrc-2021Q3:1.3.0.18 pkgsrc-2021Q3-base:1.3 pkgsrc-2021Q2:1.3.0.16 pkgsrc-2021Q2-base:1.3 pkgsrc-2021Q1:1.3.0.14 pkgsrc-2021Q1-base:1.3 pkgsrc-2020Q4:1.3.0.12 pkgsrc-2020Q4-base:1.3 pkgsrc-2020Q3:1.3.0.10 pkgsrc-2020Q3-base:1.3 pkgsrc-2020Q2:1.3.0.8 pkgsrc-2020Q2-base:1.3 pkgsrc-2020Q1:1.3.0.4 pkgsrc-2020Q1-base:1.3 pkgsrc-2019Q4:1.3.0.6 pkgsrc-2019Q4-base:1.3 pkgsrc-2019Q3:1.3.0.2 pkgsrc-2019Q3-base:1.3 pkgsrc-2019Q2:1.2.0.10 pkgsrc-2019Q2-base:1.2 pkgsrc-2019Q1:1.2.0.8 pkgsrc-2019Q1-base:1.2 pkgsrc-2018Q4:1.2.0.6 pkgsrc-2018Q4-base:1.2 pkgsrc-2018Q3:1.2.0.4 pkgsrc-2018Q3-base:1.2 pkgsrc-2018Q2:1.2.0.2 pkgsrc-2018Q2-base:1.2 pkgsrc-2018Q1:1.1.0.2 pkgsrc-2018Q1-base:1.1; locks; strict; comment @# @; 1.9 date 2024.10.26.22.01.48; author mef; state Exp; branches; next 1.8; commitid 7K7UVaKwzatCJdvF; 1.8 date 2024.01.24.11.49.19; author mef; state Exp; branches; next 1.7; commitid lhHqFNKxLMGrdHVE; 1.7 date 2023.06.15.10.57.41; author mef; state Exp; branches; next 1.6; commitid ankLPnbqLLpc62tE; 1.6 date 2022.05.21.13.14.49; author mef; state Exp; branches; next 1.5; commitid znQBVZYlwoBsoVED; 1.5 date 2021.10.26.10.55.23; author nia; state Exp; branches; next 1.4; commitid vzl6zVlmjiF3hjeD; 1.4 date 2021.10.07.14.27.46; author nia; state Exp; branches; next 1.3; commitid wLkpKfebF6VS3TbD; 1.3 date 2019.07.31.18.45.22; author brook; state Exp; branches; next 1.2; commitid aP5DjFD63JlsaexB; 1.2 date 2018.06.01.07.10.54; author wen; state Exp; branches; next 1.1; commitid zAKav6NVKPOdZxEA; 1.1 date 2018.01.22.19.22.44; author minskim; state Exp; branches; next ; commitid cjnDDNuWurJcdUnA; desc @@ 1.9 log @(math/R-VGAM) 4 of +TEST_DEPENDS, font issue still exists @ text @$NetBSD: distinfo,v 1.8 2024/01/24 11:49:19 mef Exp $ BLAKE2s (R/VGAM_1.1-12.tar.gz) = f956eea30997f0db97d9ba6ef29a578e61e7a86c09962f5b3ec44f1febef3fba SHA512 (R/VGAM_1.1-12.tar.gz) = 68b0e32b7bcd236e02a075367a2d65591289244a76d4cb822a020bb814225e0b321fe97692c8b255464c810b3971dd4c3c094d602d5be450b714ca05fcb4a08d Size (R/VGAM_1.1-12.tar.gz) = 1682671 bytes @ 1.8 log @ (math/R-VGAM) Updated 1.1.8 to 1.1.9 CHANGES IN VGAM VERSION 1.1-9 NEW FEATURES o Soon: VGAM will require R >= 4.4.0 because plot.profile will move from \pkg{MASS} to \pkg{stats}. Sorry! o Yettodo: modify dgaitdlog() to be like dgaitdpois() in terms of safeguarding against too much deflation and inflation (to return NaN). Ditto to dgaitdzeta() and dgaitdnbinom(). Ditto for the p-type functions. o New family functions: gammaff.mm(), hurea(d). o New generic and/or methods functions: cops(). o acat(), cumulative(), cratio(), propodds(), sratio() handles argument 'thresholds' equalling 'symmetric1' and 'symmetric0'. Note from version 1.1-8 that 'equidistant' was added. o Tested okay on R 4.3.0. BUG FIXES and CHANGES o wald.stat(..., orig.SE = TRUE, values0 = values0) assumed that values0 == 0. o [rq]zinegbin() did not handle the case 'munb = NULL' when 'prob' was specified. Thanks to Giuseppe D for finding this bug. o acat(), cumulative(), cratio(), propodds(), sratio() must have an intercept term. o For vglm.fit(), slot "middle" is now "middle1", "fini" is now "fini1", and a new "start1" slot added. o bigamma.mckay() moved into VGAMdata 1.1-9. o nakagami() has a zero = "shape" argument. o [dp]gaitdpois() have more range checking, e.g., for too much deflation and inflation. o For more speed, several slow-checking .Rd files have been changed by using \dontrun{}. o summary(posbernoulli.tb()) failed to print the confidence interval. Thanks to Carl Schwarz for picking this up. o DFLOAT() changed to DBLE() in some .f files. @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.7 2023/06/15 10:57:41 mef Exp $ d3 3 a5 3 BLAKE2s (R/VGAM_1.1-9.tar.gz) = 137bc8a6eacfa54fe869bcd8ba47fc3feb4615c59f6588010f78985f1930c0e8 SHA512 (R/VGAM_1.1-9.tar.gz) = 4ac3eff60096408885ddaeaf0e6637f10160a8dd19c9a4231713c111465ced92ae72a1aacd7785f6941dab537030d6780772b3f810482cbe1114cfb8d35e2c74 Size (R/VGAM_1.1-9.tar.gz) = 1644850 bytes @ 1.7 log @(math/R-VGAM) Updated 1.1.6 to 1.1.8 CHANGES IN VGAM VERSION 1.1-8 NEW FEATURES o Warnings from R-devel addressed. o acat(), cumulative(), cratio(), sratio() have arguments 'thresholds', 'Tref', 'Treverse'. o hdeffsev() has been edited. o margeff() works for poissonff(), negbinomial() and posnegbinomial() objects. o multilogit() did not handle 1-row arguments correctly when 'inverse = FALSE'. Now vglm(y, multinomial) handles a 1-row y, as well as acat and cumulative and [cs]ratio. o rrvglm.fit() is more robust with respect to 'one.more'. o plot.vgam() issues an error if sm.os()/sm.ps() is used with deriv.arg > 0. o New data set: budworm. BUG FIXES and CHANGES o rainbow.sky has a new green. o zoabetaR() handles the argument 'constraints'. Thanks to Riccardo Lo Martire for helping to find the bug. CHANGES IN VGAM VERSION 1.1-7 NEW FEATURES o Slot 'rqresslot' added to VGAM family functions, for implementing randomized quantile residuals. Available in about 50 family functions such as poissonff() currently. o Slot 'rqresslot' added to VGAM family functions, for implementing o Argument 'label.it' added to model.matrixvlm(). o New generic and/or methods functions: rqresid(), rqresiduals(). o New data set: lpossums. o Tested okay on R 4.2.1. BUG FIXES and CHANGES o cumulative() has been replaced by its version prior to 2021-05. Evidently some so-called improvements created some bugs. Thanks to Johanna Neslehova for alerting me to this. o bistudentt() was documented wrong; thanks to Iago Gine Vazquez for finding this. o fill() now deprecated; replaced by fill4(). @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.6 2022/05/21 13:14:49 mef Exp $ d3 3 a5 3 BLAKE2s (R/VGAM_1.1-8.tar.gz) = 43a729998f03a69cb990acf95f904270f4ffbb28c6482c04b50a3a4669a9a1e3 SHA512 (R/VGAM_1.1-8.tar.gz) = cbb4d398b8f3daab4613d80a67aeb1f7bc30933ad4e8b41570c43deea421ac4bc89542df2651010583d6e928ddc63598ca5c72a7efe799cd94c6bc1cf6bff6b2 Size (R/VGAM_1.1-8.tar.gz) = 1638263 bytes @ 1.6 log @(math/R-VGAM) Updated 1.1.1 to 1.1.6 CHANGES IN VGAM VERSION 1.1-6 NEW FEATURES o Most of the GAIT regression code have new arguments 'd.mlm' and 'd.mix' but mainly only the dpqr-type functions work! Some other functions should work such as gaitdpoisson() and dgaitplot(). Also, is.deflated() and goffset() are new. o New family function: gaitdnbinomial(). o Upgraded family functions: gaitpoisson() becomes gaitdpoisson(), gaitlog() becomes gaitdlog(), gaitzeta() becomes gaitdzeta(). o New generic and/or methods functions: KLD(), Pheapseep(). o Some colours are pre-defined for GAITD regression, and the default colour scheme has changed. o trim.constraints() has a new 'intercepts = TRUE' argument. o Many family functions have a 'dpqrfun' component in the @@infos slot. Useful to tie in the modelling function with its density, etc. o binormal() has a new 'rho.arg' argument. o Some link functions handle deriv = 4: e.g., loglink(), logitlink(). o vglmfit@@misc$history gives the convergence history. o Improvements to clogloglink() at the boundary 1. o hdeff.vglm() has a new argument 'theta0'. o wald.stat() cleaned up internally. o Tested okay on R 4.1.2. BUG FIXES and CHANGES o All GAIT regression code has arguments 'alt.mlm' changed to 'a.mlm', 'inf.mix' changed to 'i.mix', etc. Colours have changed. [dpqr]gaitpois() have been renamed to [dpqr]gaitdpois(), and gaitpoisson() to gaitdpoisson(). o [dpqr]zanegbin() no longer supports argument 'prob'. o hdeff() makes a recursive call if any NAs are in the answer and fd.only == FALSE. So the answer should then be a 'proper' one. o Code involving anova() for VGLMs/VGAMs changed to avoid an error when loading in \pkg{semTools}. o spikeplot(..., use.table = TRUE) failed wrt x.use and y.use. o vcov() slightly faster for "vglm" objects. Thanks to Frank Harrell for comments that led to this. o linkfun.vglm() changed to linkfunvglm(). CHANGES IN VGAM VERSION 1.1-5 NEW FEATURES o New functions: meangait(), spikeplot(), trim.constraints(). o iam(i, 1:M, M = M) now works, for selecting a whole row, and similarly for a column. o Tested okay on R 4.0.3. BUG FIXES and CHANGES o gait[log,poisson,zeta](): arguments llambda.[ai] and lshape.[ai] equal llambda.p and lshape.p by default. This means only one argument needs be assigned in order to change them all. o [dpqr]genpois[12]() has argument 'mean' changed to 'meanpar'. o gait[log,zeta]() bug fixed wrt missing 'allprobs'. o qfoldnorm() now uses the bisection method. Thanks to Mauricio Romero for a suggestion that led to this. o gait[log,poisson,zeta]() compute the sandwich formula explicitly for the working weights; this has speed gains. Their @@deriv avoids nested for() loops too. Their initial value grids have become coarser. o Functions moved to VGAMdata 1.1-5: yip88, bellff(dr), tikuv(dpqr). CHANGES IN VGAM VERSION 1.1-4 NEW FEATURES o Functions score.stat() and wald.stat() offer greater flexibility by some new arguments, and 'as.summary' changed to 'orig.SE'. o Influence() computes the influence functions of a "vglm" object. o Methods functions hdeff.matrix() and hdeff.numeric() are new. o Family function slot genpoisson()@@ weight was updated with the EIM derived by Easton Huch, and after major changes, genpoisson() was renamed to genpoisson0(). o New functions: [dpqr]gaitnbinom(), [dpqr]gaitgenpois[012](), [dpqr]gaitbinom(), dgaitplot(), plotdgait.vglm(), Trunc(). o New family functions: genpoisson[12](dpqr), gaitpoisson() so that gaitpoisson.mix() and gaitpoisson.mlm() were removed, gaitlog() so that gaitlog.mix() was removed, gaitzeta() so that gaitzeta.mix() was removed. o Tested okay on R 4.0.3. BUG FIXES and CHANGES o Deprecated: dgenpois(), genpoisson(), [dpqr]gaitnbinom.m[ix,lm](). gatnbinomial.m[ix,lm](dpqr), [dpqr]gaitbinom.mlm(), gaitpoisson.mix(), gaitpoisson.mlm(), gabinomial.mlm(), gtbinomial(). o 'lhs.prob' changed to 'cdf.max.s'. o Argument changes for all GAIT code, e.g., 'alter' changed to 'alt.mix' or 'alt.mlm', 'byrow.arg' to 'byrow.ai', etc. o Functions moved to VGAMdata 1.1-4: oalog, oilog, otlog, oapospois, oipospois, otpospois, oazeta, oizeta, otzeta, oizipf, oiposbinomial(dpqr), [dpqr]posbinom, [dpqr]pospois, [dpqr]posnegbin. o Pearson residuals no longer printed by default in a summary of a "vglm" object: presid = FALSE. o Some changes made to plot(vgam()) code for changes in R 4.0.0, especially if the covariate is a character/factor. Now avoids "coercing argument of type 'double' to logical" warning. o negbinomial(lmu = "nbcanlink") had an error relating to "newemu". CHANGES IN VGAM VERSION 1.1-3 NEW FEATURES o New functions: [dpqr]gaitpois(), [dpqr]gaitlog(), [dpqr]gaitzeta(), dextlogF(). o New family functions: gatnbinomial.mix(dpqr), gaitlog.mix(dpqr), gaitpoisson.mix(dpqr), gaitpoisson.mlm(dpqr), extlogF1(d). o New generic and/or methods functions: altered(), inflated(), truncated(), specialsvglm(), fix.crossing(), is.crossing(). o Coef.vlm() handles models with contiguous "multilogitlink"s, e.g., gaitpoisson.mlm(). o get.offset() is now defined as a generic function (returns the n x M matrix of offsets by default). o Some .f files have been pruned of unnecessary code. o New data set: V2. o Tested okay on R 4.0.0. BUG FIXES and CHANGES o Another attempt to .Deprecated() all link function names which do not end in "link", e.g., loglink() replaces loge(), logitlink() replaces logit(). o gatpoisson.mix() (now merged into gaitpoisson.mix()) reorders its linear/additive predictors and now handles length(alter) == 0 (default, so equivalent to poissonff()) and length(alter) == 1. Ditto for gatnbinomial.mlm(), etc. o Three argument mismatches found in .f and .c code. o qlog() and qyules() buggy wrt interval selection prior to applying bisection. o 'Rank mismatches' flagged by gfortran10 fixed, by not calling two subroutines. o [dpqr]gaitpois.mlm() and [dpqr]gaitpois.mix() have been combined into [dpqr]gaitpois(). CHANGES IN VGAM VERSION 1.1-2 NEW FEATURES o New generic and/or methods functions: add1.vglm(), dfterms(), drop1.vglm(), extractAIC.vglm(), rootogram4vglm() [based on \pkg{countreg}], step4vglm(). o New family functions: gabinomial.mlm(), gatnbinomial.mlm(dpqr), gatpoisson.mix(dpqr), gatpoisson.mlm(dpqr). o New functions: [dpqr]zipfmb(), [dpqr]gaitbinom.mlm(), [dpqr]gaitnbinom.mlm(), [dpqr]gaitpois.mlm(), [dpqr]gaitnbinom.mix(), [dpqr]gaitpois.mix(). Note that the naming conventions have changed somewhat, especially regarding the negative binomial distribution. o Decommissioned functions: gapoisson(), gtpoisson(), [dpqr]gabinom(), [dpqr]gapois(), [dpqr]gibinom(), [dpqr]gipois(), [dpqr]gtbinom(), [dpqr]gtpois(). o eta2theta() should be able to handle links for, e.g., gatpoisson.mlm(), gibinomial(). o posbernoulli.t() has a 'type.fitted' argument. o gtpoisson.mlm() supports type.fitted = "Pobs.a", gipoisson.mlm() supports type.fitted = "Pstr.i". o New data set: backPain2. o Cleve Moler added to DESCRIPTION as a contributor, to reflect the use of LINPACK. o Tested okay on R 3.6.1. BUG FIXES and CHANGES o Use of old link function names now result in a call to .Deprecated(), except for a selected few such as logit() and probitlink()---this will only be allowed for a limited time. o negbinomial()@@initialize bug fixed for "nbcanlink()" and multiple responses; thanks to Victor Miranda. o cens.poisson() gave a warning upon a summary(). Thanks to Jens Heumann for picking this up. o bisection.basic() returns a warning, not an error, if it cannot find an interval which covers the root. o Rank() has an improved implementation and documentation. o anova.vglm() had some bugs---thanks to Thamron Keowmani for finding them. o posnormal() failed when 'constraints' was inputted---thanks to Michael Zamo for picking this up. o Improvements to yules(dq). @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.5 2021/10/26 10:55:23 nia Exp $ d3 3 a5 3 BLAKE2s (R/VGAM_1.1-6.tar.gz) = 0d42857e240e3d5e2b72976e8a3dcac141a1682bc9146373f183f760a186c5e2 SHA512 (R/VGAM_1.1-6.tar.gz) = fc05040324ab32271a1b6e95e20a42fbe154540651e356cb61030333c928a4d32f46e29fdfb98fa5e62010cd782441c09240c59bd36e533cc8cf864f0de7be41 Size (R/VGAM_1.1-6.tar.gz) = 1713153 bytes @ 1.5 log @math: Replace RMD160 checksums with BLAKE2s checksums All checksums have been double-checked against existing RMD160 and SHA512 hashes @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.4 2021/10/07 14:27:46 nia Exp $ d3 3 a5 3 BLAKE2s (R/VGAM_1.1-1.tar.gz) = 60696739cd8556cd20e6bb684bdff8625bd8d2d956a29be536f70bf278691b70 SHA512 (R/VGAM_1.1-1.tar.gz) = c868bd0ccde59d6d9b15446331c3fc4762d3356bda7063e6b38b7e1bfd7bbedddedb5a94b4e3812173fefc6f8b806123201f6a2a619d8bd038bcb4b4ec268b8e Size (R/VGAM_1.1-1.tar.gz) = 2624046 bytes @ 1.4 log @math: Remove SHA1 hashes for distfiles @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.3 2019/07/31 18:45:22 brook Exp $ d3 1 a3 1 RMD160 (R/VGAM_1.1-1.tar.gz) = 264d8486c35869c1de9ab5f232978b64e5b565ee @ 1.3 log @R-VGAM: update to version 1.1.1. Update to the canonical form of an R package and fix the LICENSE field. @ text @d1 1 a1 1 $NetBSD$ a2 1 SHA1 (R/VGAM_1.1-1.tar.gz) = 535566d53110d7f58e4667fdca5b8f200bae8fb8 @ 1.2 log @Update to 1.0.5 Upstream changes: CHANGES IN VGAM VERSION 1.0-5 NEW FEATURES o extlogit() now handles 'deriv = 3'. o Generic function hdeff() implements an analytic solution for the following families: borel.tanner(), felix(), lindley(). For almost all other families, finite-difference approximations to derivatives means that first and second derivatives can be computed, even with models with 'xij' terms. o Generic function wald.stat() implements Wald tests with SEs evaluated at the null values, not at the original MLE, so do not suffer from the Hauck-Donner effect. o "vglm" objects have a new "charfun" slot, for the characteristic function. o "summary.vglm" and "summary.vlm" objects have new "coef4lrt0", "coef4score0", "coef4wald0" slots, for storing the 'Wald table' equivalent of LRTs, score tests and modified Wald tests. The latter has its SEs computed at the null values with the other coefficients obtained by further IRLS iterations, etc. Function summaryvglm() has arguments 'lrt0.arg', 'score0.arg', 'wald0.arg'. o TIC() is new, for the Takeuchi's Information Criterion. Thanks to Khedhaouiria Dikra for suggesting this. o mills.ratio() and mills.ratio2() are exported. o New functions: lrt.stat(), score.stat(), wald.stat(), which.etas(), which.xij(). o cauchy1() and cauchy() handle multiple responses and have been modernized a bit. o Tested okay on R 3.4.3. BUG FIXES and CHANGES o Setting 'deriv.arg' a positive value in plotvgam() when there are no s() terms results in a warning. Thanks to Barry Goodwin for detecting this. o cens.poisson() can better handle large lambda values, at least for left and right censored data (but not for interval-censored data yet). Thanks to Eugenie Hunsicker for picking up deficiencies in the code. o In multinomial.Rd, it was stated that setting parallel = TRUE did not make the intercepts the same. It does make them the same. Thanks to Stuart Coles for picking this up. o binomialff(multiple.responses = TRUE) returned an incorrect deviance. o bilogistic() uses SFS rather than BFGS as its algorithm. o Deprecated: lrp(), normal1() [use uninormal() instead]. @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.1 2018/01/22 19:22:44 minskim Exp $ d3 4 a6 4 SHA1 (R/VGAM_1.0-5.tar.gz) = 61108ebc40739fb1753680ea822d31e620df33bd RMD160 (R/VGAM_1.0-5.tar.gz) = b9ffee8f357ab81723b71e7a4c79d21fc7241e21 SHA512 (R/VGAM_1.0-5.tar.gz) = 3e2096535153069e200ede3f4c073ab6f753b3a2c38d5ffd102bcfd94c5505f403f22275d03fde892332ad0c0eb217be61de2022fdbf5f4b394813635aa06d2e Size (R/VGAM_1.0-5.tar.gz) = 2552397 bytes @ 1.1 log @math/R-VGAM: Import version 1.0-4 from pkgsrc-wip Vector generalized linear and additive models, and associated models (Reduced-Rank VGLMs, Quadratic RR-VGLMs, Reduced-Rank VGAMs). This package fits many models and distribution by maximum likelihood estimation (MLE) or penalized MLE. Also fits constrained ordination models in ecology. Packaged by Mike M. Volokhov, and updated by Kamil Rytarowski and me. @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.3 2013/06/12 17:37:31 bubuchka Exp $ d3 4 a6 4 SHA1 (R/VGAM_1.0-4.tar.gz) = f52f70a01e37042f82a7272d8198e1a80fecb88d RMD160 (R/VGAM_1.0-4.tar.gz) = b5448508408504b8fed0d1763cfe102b5c7e6a24 SHA512 (R/VGAM_1.0-4.tar.gz) = ccbcb9273de4ff4150577d4ab5eff751ccc350dd1e6d109fed4b37d3f55c641aee6b4e5fda1b0e6df41d94fadf50a886cca7f67daab6b49d919f666b408cf74e Size (R/VGAM_1.0-4.tar.gz) = 1374748 bytes @