Version 1.1.2.2 commit for Journal of Statistical Software publication.

Lauve NR, Nelson SJ, Young SS, Obenchain RL, Lambert CG. LocalControl:
An R Package for Comparative Safety and Effectiveness Research.
Journal of Statistical Software. 2020. p. 1–32.
Available from <doi:10.18637/jss.v096.i04>

DESCRIPTION

@@ -2,16 +2,16 @@ Package: LocalControl
 Type: Package
 Title: Nonparametric Methods for Generating High Quality Comparative
         Effectiveness Evidence
-Version: 1.1.2
-Date: 2019-02-22
+Version: 1.1.2.2
+Date: 2020-11-24
 Authors@R: c(
-  person(given = "Nicolas R.", family = "Lauve", role = "aut"),
-  person(given = "Stuart J.", family = "Nelson", role = "aut"),
-  person(given = "S. Stanley", family = "Young", role = "aut"),
-  person(given = "Robert L.", family = "Obenchain", role = "aut"),
+  person(given = "Nicolas R.", family = "Lauve", role = "aut", comment=c(ORCID="0000-0002-9348-0319")),
+  person(given = "Stuart J.", family = "Nelson", role = "aut", comment=c(ORCID="0000-0002-8756-0179")),
+  person(given = "S. Stanley", family = "Young", role = "aut", comment=c(ORCID="0000-0001-9449-5478")),
+  person(given = "Robert L.", family = "Obenchain", role = "aut", comment=c(ORCID="0000-0002-8395-1666")),
   person(given = "Melania", family = "Pintilie", role = "ctb"),
   person(given = "Martin", family = "Kutz", role = "ctb"),
-  person(given = "Christophe G.", family = "Lambert", role = c("aut","cre"), email = "[email protected]"))
+  person(given = "Christophe G.", family = "Lambert", role = c("aut","cre"), email = "[email protected]", comment=c(ORCID="0000-0003-1994-2893")))
 Description: Implements novel nonparametric approaches to address
     biases and confounding when comparing treatments or exposures in
     observational studies of outcomes. While designed and appropriate for use
@@ -22,15 +22,20 @@ Description: Implements novel nonparametric approaches to address
     analysis settings, where competing risks and/or censoring may be present.
     The approach extends to bias-corrected personalized predictions of treatment
     outcome differences, and analysis of heterogeneity of treatment effect-sizes
-    across patient subgroups.
+    across patient subgroups. For further details, please see: 
+    Lauve NR, Nelson SJ, Young SS, Obenchain RL, Lambert CG. LocalControl:
+    An R Package for Comparative Safety and Effectiveness Research.
+    Journal of Statistical Software. 2020. p. 1–32. Available from <doi:10.18637/jss.v096.i04>.
 License: Apache License 2.0 | file LICENSE
 SystemRequirements: C++11
 LazyData: TRUE
 LinkingTo: Rcpp
 Imports: Rcpp, gss, cluster, lattice, stats, graphics
-Suggests: colorspace, RColorBrewer, TeachingDemos, data.table, ggplot2, gridExtra, rpart, rpart.plot, xtable
-RoxygenNote: 6.1.1
+Suggests: colorspace, RColorBrewer, TeachingDemos, data.table, ggplot2,
+        gridExtra, rpart, rpart.plot, xtable
+RoxygenNote: 7.1.1
 Encoding: UTF-8
 NeedsCompilation: yes
 Depends: R (>= 3.0.0)
 Repository: CRAN
+Maintainer: Christophe G. Lambert <[email protected]>

MD5

@@ -1,75 +1,74 @@
-cb18157c041037a5d9a22123c5158ada  ./DESCRIPTION
-77118432fa8e2ad7debd7e39b1b57d2e  ./LICENSE
-f52396691ab8a05ae076ce5b06d37ede  ./LocalControl.Rproj
-75038098522f7cb67e4fbb280bf72117  ./NAMESPACE
-ba5a7746d34b6c7956fefb500a705e61  ./NEWS.md
-6de53e744f009c412b979c38919d934b  ./R/RcppExports.R
-5145981cf0ece2f67e93b6cc0db189ab  ./R/clusteringLC.R
-194bb8daf4520b5508044b58d5f24203  ./R/dataDesc.R
-ced7aa6cec69d6d9936f9c4b8b45f775  ./R/deprecatedLC.R
-13214f479bd27b18b97e3ac1a79cb731  ./R/localControl.R
-752879b6b8f4c9d01464043455f7443c  ./README.md
-ea6adf66c362ccbf1de2e9134d02c496  ./data/cardSim.rda
-f7110346e04183da00306fc743ba57a5  ./data/framingham.rda
-07cd71710ee7b05dd13c3b3b58684a16  ./data/lindner.rda
-b8a8878e97fe71cffea7175e4b8453cf  ./deploy.sh
-afb9aa056cb21659e533f11c7a87f303  ./extras/LocalControl.pdf
-7f3bbfb69885cd4f3b393b674a49c392  ./extras/PackageMaintenance.R
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-b0d9ae20bd99a73b510e6593d3b75121  ./man/SPSloess.Rd
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-647b9db7bd6e92a52adf6465969454aa  ./man/SPSoutco.Rd
-1399040b84e756dad6a4a4397be0617f  ./man/UPSLTDdist.Rd
-5a35e1d193537bae05c088432ea1c6e4  ./man/UPSaccum.Rd
-d43e7e826bfa31983ebea4afa3dfb02a  ./man/UPSaltdd.Rd
-c85b8130c012b185b31090ed20c56718  ./man/UPSboxplot.Rd
-d8e4837932765a9df8dc2a5e7b63a41d  ./man/UPSgraph.Rd
-8a7e5d6786b4dcc3042fc08eada35f99  ./man/UPShclus.Rd
-ac3bdb9b6ea367a8c72f17ac4b721606  ./man/UPSivadj.Rd
-2d2ef37505cf83ec692988007beeeaf7  ./man/UPSnnltd.Rd
-9d7c925eb0ed329d90fb289ccaf0313d  ./man/cardSim.Rd
-490b91e410e54cd8f416d0dc8c7c4405  ./man/framingham.Rd
-2047ffe603ffb653d80020f2897754c6  ./man/lindner.Rd
-17fa8557dbab442f13f10f5524281d77  ./man/plot.LocalControlCR.Rd
-04fce757a79e2fd57e980136b83a253c  ./man/plot.LocalControlCS.Rd
-f6381b85480b41289ae3cdafa1e8ad50  ./src/LocalControl.cpp
-31cd9438cca2f7b2b3c9edca8ac770ea  ./src/Makevars
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-5848982f1b736b260ab626fbe24bc00e  ./src/seb/Subspan.h
-35e1203b6a6efa0d5b05002d64d92a79  ./vignettes/LocalControl-jss-2018.Rnw
-88563ce3bd5aad139a61eead69eaa0e9  ./vignettes/LocalControl.bib
-b706b1780ad924da7c73483e26809210  ./vignettes/calcs/FHSPlotLines.rds
-2500db3661861177d703d99b1e91c3b2  ./vignettes/calcs/FHSSummary.rds
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-8b6cb191a45d205e3ec7c0df23a72857  ./vignettes/calcs/ccc.rds
-007e1d79ba7412d5be45b17eeeafa264  ./vignettes/calcs/ffltdf.rds
-ae8bd1cc56b239a7e30d37bc5c9d4d9b  ./vignettes/calcs/ffltdv.rds
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-7a673bd32d12c0e46cd0e008301cb520  ./vignettes/calcs/linCI.rds
-12d1e4682b1b481714e45ee93e7c6287  ./vignettes/calcs/linRad33.rds
-993f0e13b9d6835afb0d5e10522464f7  ./vignettes/calcs/linRes.rds
-9ffdce8e86de5b49afb452db6acd5d2d  ./vignettes/calcs/linSummary.rds
-658ed9ac77a3646fef16a78bbbe3761c  ./vignettes/calcs/lindnerResults.rds
-012c026c94bb6e247aebaa411e9e87ac  ./vignettes/calcs/localoutcomes.rds
-525ebd2e2b83d95ddc34971def598fcf  ./vignettes/calcs/resultSummary.rds
-a9a40db760d73754c694f4958ad4af55  ./vignettes/calcs/sSimFTs.rds
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-abc1d10a59eb0501705f051f07ac09ab  ./vignettes/calcs/sSimT1R1.rds
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-e9270191bb15c9084e2e72c4185fd368  ./vignettes/calcs/xSultsT1.rds
-f2603762fa769650ca0ba17bc63ca519  ./vignettes/LocalControl-jss-2018.pdf
+ee199e55d1db1e1abcafa40e55ca4fe9 *DESCRIPTION
+77118432fa8e2ad7debd7e39b1b57d2e *LICENSE
+75038098522f7cb67e4fbb280bf72117 *NAMESPACE
+41bb537be3641c6a9e8148200ad2f353 *NEWS.md
+6de53e744f009c412b979c38919d934b *R/RcppExports.R
+5145981cf0ece2f67e93b6cc0db189ab *R/clusteringLC.R
+194bb8daf4520b5508044b58d5f24203 *R/dataDesc.R
+ced7aa6cec69d6d9936f9c4b8b45f775 *R/deprecatedLC.R
+477e04e6cbdc68dacbe82eedd61369f6 *R/localControl.R
+a54f8c6cf9a1c0ec47a25f62c727cfd8 *README.md
+b0f98d780cb15c70d2b88efad2d691e9 *build/vignette.rds
+fd19ca1346503d27c091c2a324241f34 *data/cardSim.rda
+6757b06f5310e1108977b98697734be4 *data/framingham.rda
+3a82d0af7b61f49c233243230739f47e *data/lindner.rda
+286c6c1e5b337edd5a3ba2b255208ead *inst/doc/LocalControl-jss-2018.R
+dc7fac64ef5e41c0bc322e282da58881 *inst/doc/LocalControl-jss-2018.Rnw
+6f4d7560440ed5cc55d66cbc2994d333 *inst/doc/LocalControl-jss-2018.pdf
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+9934159cbe47244d1d42e716f6147cfe *man/LocalControl.Rd
+d853dae1e6e741021fa3f2574ffb8c78 *man/LocalControlClassic.Rd
+d1365060ae667d81fab93bf93a18e84b *man/LocalControlCompetingRisksConfidence.Rd
+e9736a169f0759009b4ceba95256de04 *man/LocalControlNearestNeighborsConfidence.Rd
+4f864a977e3c82451b11021e1cf39d5e *man/SPSbalan.Rd
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+d43e7e826bfa31983ebea4afa3dfb02a *man/UPSaltdd.Rd
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+d8e4837932765a9df8dc2a5e7b63a41d *man/UPSgraph.Rd
+8a7e5d6786b4dcc3042fc08eada35f99 *man/UPShclus.Rd
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+90473088d19aee94367b5398b3152c76 *man/plot.LocalControlCR.Rd
+72f0642db1638398750b4c06cbf9c19e *man/plot.LocalControlCS.Rd
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+31cd9438cca2f7b2b3c9edca8ac770ea *src/Makevars
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+5608d379fd170d25274235c73d91eb07 *src/init.c
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+dc7fac64ef5e41c0bc322e282da58881 *vignettes/LocalControl-jss-2018.Rnw
+88563ce3bd5aad139a61eead69eaa0e9 *vignettes/LocalControl.bib
+fd7d06a20238ccd5f2b3316a07615500 *vignettes/calcs/FHSPlotLines.rds
+3bf44b57145ec4394095ea26e59dc510 *vignettes/calcs/FHSSummary.rds
+de7203975158f4844302b8a1e7b80884 *vignettes/calcs/allRands.rds
+6455c6e5ccadd86145e9bd07d555d8d0 *vignettes/calcs/ccc.rds
+726f3b561e5614a9d294cb725045394f *vignettes/calcs/ffltdf.rds
+5bac5e0e47f59ec3e0f9468f00c713f7 *vignettes/calcs/ffltdv.rds
+d95490363dbd93af8d253fad5bfb796f *vignettes/calcs/ffvc.rds
+220e73b9a7091c8254b0a83f8c83d9c7 *vignettes/calcs/linCI.rds
+4f2ec261d20a5c2749726a6c72a8554c *vignettes/calcs/linRad33.rds
+0a71b00f288d9cd90e65d91269c26c53 *vignettes/calcs/linRes.rds
+a61453966113624add238d537044ec8f *vignettes/calcs/linSummary.rds
+74d72fef8507f9d5b05a23cef9f1b0fa *vignettes/calcs/lindnerResults.rds
+16fcb18fee1756ed9c812da28d87dcf1 *vignettes/calcs/localoutcomes.rds
+d24ab04f02d5b3cf4f01cf4dd765f7f8 *vignettes/calcs/resultSummary.rds
+b713e631e875fe52506acd0695badb03 *vignettes/calcs/sSimFTs.rds
+6bfddbd120a66689810048cbb6412d08 *vignettes/calcs/sSimT0R1.rds
+d6681de7676d7dfd88e51b2ffe4a8085 *vignettes/calcs/sSimT0R21.rds
+22e745f438f3e291c76a1009473a7893 *vignettes/calcs/sSimT1R1.rds
+1114229d0bf31f0602e759d9e525b307 *vignettes/calcs/sSimT1R21.rds
+8ac60ebc81820389770a863a5fad0053 *vignettes/calcs/xSultsT0.rds
+dff7f409755dc5ee0bf71ee307a4c6f4 *vignettes/calcs/xSultsT1.rds

NEWS.md

@@ -1,3 +1,9 @@
+LocalControl 1.1.2.2
+================
+
+### Minor changes
+* Added citation file and doi for vignette's JSS publication.
+
 LocalControl 1.1.2
 ================
 

R/localControl.R

@@ -94,6 +94,7 @@
 #' }
 #' @references
 #' \itemize{
+#'    \item Lauve NR, Nelson SJ, Young SS, Obenchain RL, Lambert CG. LocalControl: An R Package for Comparative Safety and Effectiveness Research. Journal of Statistical Software. 2020. p. 1–32. Available from: http://dx.doi.org/10.18637/jss.v096.i04
 #'    \item Fischer K, Gartner B, Kutz M. Fast Smallest-Enclosing-Ball Computation in High Dimensions. In: Algorithms - ESA 2003. Springer, Berlin, Heidelberg; 2003:630-641.
 #'    \item Martin Kutz, Kaspar Fischer, Bernd Gartner. miniball-1.0.3. \url{https://github.com/hbf/miniball}.
 #' }
@@ -345,6 +346,10 @@ data.frame("radius" = lccs$rads,
 #' @param main The main plot title. Default is empty.
 #' @param group1 The name of the primary group (Treatment 1).
 #' @param group0 The name of the secondary group (Treatment 0).
+#' @references
+#' \itemize{
+#'    \item Lauve NR, Nelson SJ, Young SS, Obenchain RL, Lambert CG. LocalControl: An R Package for Comparative Safety and Effectiveness Research. Journal of Statistical Software. 2020. p. 1–32. Available from: http://dx.doi.org/10.18637/jss.v096.i04
+#' }
 #' @examples
 #' data("cardSim")
 #' results = LocalControl(data = cardSim,
@@ -409,6 +414,11 @@ plot.LocalControlCR = function(x, ..., rad2plot, xlim, ylim = c(0,1),
 #' @param xlab The x axis label. Defaults to "Fraction of maximum radius".
 #' @param main The main plot title. Default is empty.
 #'
+#' @references
+#' \itemize{
+#'    \item Lauve NR, Nelson SJ, Young SS, Obenchain RL, Lambert CG. LocalControl: An R Package for Comparative Safety and Effectiveness Research. Journal of Statistical Software. 2020. p. 1–32. Available from: http://dx.doi.org/10.18637/jss.v096.i04
+#' }
+#' 
 #' @examples
 #' data(lindner)
 #' # Specify clustering variables.
@@ -529,8 +539,11 @@ plot.LocalControlCS = function(x, ..., nnConfidence, ylim,
 #'   "log" and "linear" are also implemented.
 #'
 #' @references
-#' Choudhury JB (2002) Non-parametric confidence interval estimation for competing risks analysis: application to contraceptive data.
-#' Stat Med 21:1129-1144. doi: 10.1002/sim.1070
+#' \itemize{
+#'    \item Lauve NR, Nelson SJ, Young SS, Obenchain RL, Lambert CG. LocalControl: An R Package for Comparative Safety and Effectiveness Research. Journal of Statistical Software. 2020. p. 1–32. Available from: http://dx.doi.org/10.18637/jss.v096.i04
+#'    \item Choudhury JB (2002) Non-parametric confidence interval estimation for competing risks analysis: application to contraceptive data. Stat Med 21:1129-1144. doi: 10.1002/sim.1070
+#' }
+#'
 #' @examples
 #'  data(cardSim)
 #'  results = LocalControl(data = cardSim,
@@ -650,6 +663,12 @@ LocalControlCompetingRisksConfidence <- function(LCCompRisk, confLevel = "95%",
 #'
 #' @param nBootstrap The number of times to resample and run LocalControl for the confidence intervals.
 #' @param randSeed The seed used to set random number generator state prior to resampling. No default value, provide one for reproducible results.
+#' @references
+#' \itemize{
+#'    \item Lauve NR, Nelson SJ, Young SS, Obenchain RL, Lambert CG. LocalControl: An R Package for Comparative Safety and Effectiveness Research. Journal of Statistical Software. 2020. p. 1–32. Available from: http://dx.doi.org/10.18637/jss.v096.i04
+#'    \item Kereiakes DJ, Obenchain RL, Barber BL, Smith A, McDonald M, Broderick TM, Runyon JP, Shimshak TM, Schneider JF, Hattemer CR, Roth EM, Whang DD, Cocks D, Abbottsmith CW. Abciximab provides cost-effective survival advantage in high-volume interventional practice. Am Heart J. 2000 Oct;140(4):603–610. PMID: 11011333
+#' }
+#' 
 #' @examples
 #' \dontrun{
 #' #input the abciximab study data of Kereiakes et al. (2000).

README.md

@@ -10,9 +10,9 @@ See R help pages for examples on how to run each of the package functions.
 
 Getting Involved
 ================
-* Package manual: [LocalControl manual](https://raw.githubusercontent.com/OHDSI/LocalControl/master/extras/LocalControl.pdf) 
+* Package manual: [LocalControl manual](https://cran.r-project.org/package=LocalControl/LocalControl.pdf) 
 * Developer questions/comments/feedback: <a href="http://forums.ohdsi.org/c/developers">OHDSI Forum</a>
-* We use the <a href="../../issues">GitHub issue tracker</a> for all bugs/issues/enhancements
+* We use the <a href="https://github.com/OHDSI/LocalControl/issues">GitHub issue tracker</a> for all bugs/issues/enhancements
 
 License
 =======