CVS commit: pkgsrc/math/R-survey

["Makoto Fujiwara" <mef%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   mef
Date:           Mon Sep 20 00:49:49 UTC 2021

Modified Files:
        pkgsrc/math/R-survey: Makefile distinfo

Log Message:
(math/R-survey) Updated 3.36 to 4.1.1

4.1-1   CRAN

4.1     svyquantile() has been COMPLETELY REWRITTEN. The old version is available
        as oldsvyquantile() (for David Eduardo Jorquera Petersen)

        svycontrast()'s improvements for statistics with replicates are now also there with
        svyby(), for domain comparisons (Robert Baskin)

        svyttest() now gives an error message if the binary group variable isn't binary
        (for StackOverflow 60930323)

        confint.svyglm Wald-type intervals now correctly label the columns (eg 2.5%, 97.5%)
        (for Molly Petersen)

        svyolr() using linearisation had the wrong standard errors for intercepts
        other than the first, if extracted using vcov (it was correct in summary() output)

        svyglm() gave deffs that were too large by a factor of nrow(design). (Adrianne Bradford)

        svycoxph() now warns if you try to use frailty or other penalised terms, because they
        just come from calling coxph and I have no reason to believe they work correctly
        in complex samples (for Claudia Rivera)

        coef.svyglm() now has a complete= argument to match coef.default(). (for Thomas Leeper)

        summary.svyglm() now gives NA p-values and a warning, rather than Inf standard errors,
        when the residual df are zero or negative (for Dan Simpson and Lauren Kennedy)

        In the multigroup case, svyranktest() now documents which elements of the 'htest'
        object have which parts of the result, because it's a bit weird (for Justin Allen)

        svycontrast() gets a new argument add=TRUE to keep the old coefficients as well

        twophase() can now take strata= arguments that are character, not just factor
        or numeric. (for Pam Shaw)

        add reference to Chen & Lumley on tail probabilities for quadratic forms.

        add reference to Breslow et al for calibrate()

        add svyqqplot and svyqqmath for quantile-quantile plots

        SE.svyby would grab confidence interval limits instead of SEs if vartype=c("ci","se").

        svylogrank(method="small") was wrong (though method="score" and method="large" are ok),
        because of problems in obtaining the at-risk matrix from coxph.detail. (for Zhiwen Yao)

        added as.svrepdesign.svyimputationList and withReplicates.svyimputationList
        (for Ángel Rodríguez Laso)

        logLik.svyglm used to return the deviance and now divides it by -2

        svybys() to make multiple tables by separate variables rather than a joint table
        (for Hannah Evans)

        added predictat= option to svypredmeans for Steven Johnston.

        Fixed bug in postStratify.svyrep.design, was reweighting all reps the same (Steven Johnston)

        Fix date for Thomas & Rao (1987) (Neil Diamond)

        Add svygofchisq() for one-sample chisquared goodness of fit (for Natalie Gallagher)

        confint.svyglm(method="Wald") now uses t distribution with design df by default.
        (for Ehsan Karim)

        confint.svyglm() checks for zero/negative degrees of freedom

        confint.svyglm() checks for zero/negative degrees of freedom

        mrb bootstrap now doesn't throw an error when there's a single PSU in a stratum
        (Steve White)

        oldsvyquantile() bug with producing replicate-weight confidence intervals for
        multiple quantiles (Ben Schneider)

        regTermTest(,method="LRT") didn't work if the survey design object and model were
        defined in a function (for Keiran Shao)

        svyglm() has clearer error message when the subset= argument contains NAs (for Pam Shaw)
        and when the weights contain NAs (for Paige Johnson)

        regTermTest was dropping the first term for coxph() models (Adam Elder)

        svydesign() is much faster for very large datasets with character ids or strata.

        svyglm() now works with na.action=na.exclude (for Terry Therneau)

        extractAIC.svylm does the design-based AIC for the two-parameter Gaussian model, so
        estimating the variance parameter as well as the regression parameters.
        (for Benmei Liu and Barry Graubard)

        svydesign(, pps=poisson_sampling()) for Poisson sampling, and ppscov() for
        specifying PPS design with weighted or unweighted covariance of sampling indicators
        (for Claudia Rivera Rodriguez)

4.0     Some (and eventually nearly all) functions now return influence functions when
        called with a survey.design2 object and the influence=TRUE option.  These allow
        svyby() to estimate covariances between domains, which could previously only be
        done for replicate-weight designs, and so allow svycontrast() to do domain contrasts
         - svymean, svytotal, svyratio, svymle, svyglm, svykappa

        Nonlinear least squares with svynls() now available

        Document that predict.svyglm() doesn't use a rescaled residual mean square
        to estimate standard errors, and so disagrees with some textbooks. (for Trent Buskirk)

3.38    When given a statistic including replicates, svycontrast() now transforms the replicates
        and calculates the variance, rather than calculating the variance then using the
        delta method.  Allows geometric means to exactly match SAS/SUDAAN (for Robert Baskin)

        vcov.svyrep.design to simplify computing variances from replicates (for William Pelham)

        svykm() no longer throws an error with single-observation domains (for Guy Cafri)

        Documentation for svyglm() specifies that it has always returned
        model-robust standard errors. (for various people wanting to fit relative risk
        regression models).

3.37    RODBC database connections are no longer supported.
        Use the DBI-compatible 'odbc' package

        set scale<-1 if it is still NULL after processing, inside svrepdesign()
        [https://stats.stackexchange.com/questions/409463]

        Added withPV for replicate-weight designs [for Tomasz Żółtak]

        svyquantile for replicate-weight designs now uses a supplied alpha to get
        confidence intervals and estimates SE by dividing confidence interval length
        by twice abs(qnorm(alpha/2)). [For Klaus Ignacio Lehmann Melendez]

        All the svyquantile methods now take account of design degrees of freedom and
        use t distributions for confidence intervals. Specify df=Inf to get a Normal.
        [For Klaus Ignacio Lehmann Melendez]

        svyivreg() for 2-stage least-squares (requires the AER package)

        warn when rho= is used with type="BRR" in svrepdesign [for Tomasz Żółtak]

        Add "ACS" and "successive-difference" to type= in svrepdesign(),
        for the American Community Survey weights

        Add "JK2" to type= in svrepdesign

        Warn when scale, rscales are supplied unnecessarily to svyrepdesign

        More explanation of 'symbolically nested' in anova.svyglm

        Link to blog post about design df with replicate weights.

        Chase 'Encyclopedia of Design Theory' link again.


To generate a diff of this commit:
cvs rdiff -u -r1.2 -r1.3 pkgsrc/math/R-survey/Makefile
cvs rdiff -u -r1.1 -r1.2 pkgsrc/math/R-survey/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/math/R-survey/Makefile
diff -u pkgsrc/math/R-survey/Makefile:1.2 pkgsrc/math/R-survey/Makefile:1.3
--- pkgsrc/math/R-survey/Makefile:1.2   Thu Aug  8 19:53:54 2019
+++ pkgsrc/math/R-survey/Makefile       Mon Sep 20 00:49:49 2021
@@ -1,8 +1,7 @@
-# $NetBSD: Makefile,v 1.2 2019/08/08 19:53:54 brook Exp $
+# $NetBSD: Makefile,v 1.3 2021/09/20 00:49:49 mef Exp $
 
 R_PKGNAME=     survey
-R_PKGVER=      3.36
-CATEGORIES=    math
+R_PKGVER=      4.1-1
 
 MAINTAINER=    pkgsrc-users%NetBSD.org@localhost
 COMMENT=       Analysis of complex survey samples
@@ -12,6 +11,11 @@ DEPENDS+=    R-minqa>=1.2.4:../../math/R-mi
 DEPENDS+=      R-mitools>=2.4:../../math/R-mitools
 DEPENDS+=      R-numDeriv>=2016.8.1.1:../../math/R-numDeriv
 
+# Packages suggested but not available: 'CompQuadForm', 'AER'
+TEST_DEPENDS+= R-hexbin-[0-9]*:../../math/R-hexbin
+TEST_DEPENDS+= R-RSQLite-[0-9]*:../../databases/R-RSQLite
+TEST_DEPENDS+= R-quantreg-[0-9]*:../../math/R-quantreg
+
 USE_LANGUAGES= # none
 
 .include "../../math/R/Makefile.extension"

Index: pkgsrc/math/R-survey/distinfo
diff -u pkgsrc/math/R-survey/distinfo:1.1 pkgsrc/math/R-survey/distinfo:1.2
--- pkgsrc/math/R-survey/distinfo:1.1   Wed Jul 31 13:30:20 2019
+++ pkgsrc/math/R-survey/distinfo       Mon Sep 20 00:49:49 2021
@@ -1,6 +1,6 @@
-$NetBSD: distinfo,v 1.1 2019/07/31 13:30:20 brook Exp $
+$NetBSD: distinfo,v 1.2 2021/09/20 00:49:49 mef Exp $
 
-SHA1 (R/survey_3.36.tar.gz) = 9505042993c610a311b6b26f9b56bbd004e358c3
-RMD160 (R/survey_3.36.tar.gz) = f5268b49a748f2a379130d938468d68174d52b20
-SHA512 (R/survey_3.36.tar.gz) = c383068281004b855638eb0835969b35d7fad2bd4bace0f75f4bedf1925121231e5373662f2d26cdbd4c4543564109b3de37e7a6edde9a560bdc241e5314c008
-Size (R/survey_3.36.tar.gz) = 1550706 bytes
+SHA1 (R/survey_4.1-1.tar.gz) = 99ff92ff4e0711bf9fea79d356dd63f75df474aa
+RMD160 (R/survey_4.1-1.tar.gz) = 57e81198c8637e65046004052c28ef4d84c3ae1e
+SHA512 (R/survey_4.1-1.tar.gz) = 54264ef11b075f3a22e3ff1818879f57ab3be4df80d17d3a5810c552a2fbcb7a7de98f13429c4dc7200e9f58dfb3071f197276c21e462594e46c121933c5776b
+Size (R/survey_4.1-1.tar.gz) = 1736232 bytes