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‎DESCRIPTION

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Package: pcalg
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Version: 2.7-11
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Date: 2024-02-12
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Version: 2.7-12
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Date: 2024-09-12
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Title: Methods for Graphical Models and Causal Inference
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Description: Functions for causal structure
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learning and causal inference using graphical models. The main algorithms
@@ -34,7 +34,7 @@ NeedsCompilation: yes
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Encoding: UTF-8
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License: GPL (>= 2)
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URL: https://pcalg.r-forge.r-project.org/
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Packaged: 2024-02-12 10:30:09 UTC; kalischm
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Packaged: 2024-09-12 08:25:27 UTC; kalischm
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Author: Markus Kalisch [aut, cre],
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Alain Hauser [aut],
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Martin Maechler [aut],
@@ -53,4 +53,4 @@ Author: Markus Kalisch [aut, cre],
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Leonard Henckel [ctb],
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Joris Mooij [ctb]
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Repository: CRAN
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Date/Publication: 2024-02-12 12:00:05 UTC
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Date/Publication: 2024-09-12 17:40:27 UTC

‎MD5

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1c213fc1c5a5ec68e7a5ba9293440dc3 *ChangeLog
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440a9d31b6239ad5dcca646c3094c714 *DESCRIPTION
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df21900a61d14d6ed06eb49da18d0da3 *DESCRIPTION
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79fd4acb4bfb63ec9e5f128b83d9b519 *NAMESPACE
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1ff3899574f2834d3ccd16abecf9bb1a *R/Aaux.R
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b93a5be8eca41fda6c169327121fbf98 *R/AllClasses.R
@@ -27,8 +27,8 @@ be8549091476fb77e357c1eb091126dd *R/searchAM.R
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87a281b79088f0d9ab6974755915e0d4 *R/udag2pag.R
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0db1ba6d57801a4d8fc6cdf996384a4d *R/zzz.R
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d599e23940bca0203504c0fa6b09e01c *TODO
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7080893e02c49cd296d4424b9be55069 *build/partial.rdb
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d758c7bd1bc4de0d72601af7f33f28d7 *build/vignette.rds
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e23903adc990d9515ba1ebd23e3bff59 *build/partial.rdb
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7294bcfa49420edc123dbca6ade01655 *build/vignette.rds
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f832779eae511757a99906c7670fc0ad *cleanup
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7cbe431a233e6c454e24f7b92d63fe75 *data/datalist
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1d8d4c43b9cbb9dc9dd57acd59f565bf *data/gmB.rda
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4e33425acbef8bf36705d8a75622baa8 *inst/doc/mkVignettes.R
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415ef587902bfe185df240f1fd7a983f *inst/doc/vignette2018.R
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e3ccf4421514bf7e337aa67d75bde656 *inst/doc/vignette2018.Rnw
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2969d85808d0f6373b26d73301641825 *inst/doc/vignette2018.pdf
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1d30b28e985c54ef030ab82ee66239e3 *inst/doc/vignette2018.pdf
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cee0b4475c720bf58c466e1495451b22 *inst/external/N_6_1000.rds
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0d84fdc119d76d992b72f9bdbd0e613d *inst/external/gac-pags.rds
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e7a2a9117d97986b2ab6afc6b4f77478 *inst/external/test_conservative_pc_data1.rda
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146b7ce241783ddaa4627949ae1f370a *man/GaussL0penIntScore-class.Rd
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7a13c14340cd1794323ce09720787218 *man/GaussL0penObsScore-class.Rd
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84f4260988cdcfafadee14e0bbe56cc9 *man/GaussParDAG-class.Rd
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4c1a2c4b81350916099f7952358f9550 *man/LINGAM.Rd
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f66e9e4dfe482c8eaa28f06812ffa66f *man/LINGAM.Rd
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4733da421bc6790c136557833a08b0dc *man/ParDAG-class.Rd
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84fcdb8aca0888d4a312f23d1c9ca46c *man/Score-class.Rd
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377940596c67e1dd0c304d17f0dd8c89 *man/addBgKnowledge.Rd
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10598435a2f4beaab82a426fd62e4c55 *man/adjustment.Rd
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dab3cfa8aee7b15acfce954f4d63a030 *man/ages.Rd
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8a41e2a67114f073aef8388fdf316531 *man/amatType.Rd
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240c028d0bf23ae2f17e1071c9e26f9c *man/ages.Rd
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df2763427d81575578463e6a2a19c343 *man/amatType.Rd
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ae81d09d32bc121b2b84c1a2138dd9fb *man/backdoor.Rd
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6feb25e396846cbb7c1fc4de8d7e2eaa *man/beta.special.Rd
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e5e54569fa1222405f18ee7c189b68cd *man/beta.special.pcObj.Rd
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25029c568795bdac3d6f3b8e9e05326a *man/binCItest.Rd
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966d0b8af075b8f40c5f1021abb41f67 *man/checkTriple.Rd
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4b0dfb506510f7cf16ebc7e3e6fb6339 *man/compareGraphs.Rd
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297092d27f80a859b5d89a49a54926d1 *man/condIndFisherZ.Rd
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b2ded6b2c0cd2cf0c30b845d07646736 *man/corGraph.Rd
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48a29470740bc47e434343007e798ce3 *man/corGraph.Rd
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14cc497daabf3441d1c1db24ef338244 *man/dag2cpdag.Rd
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4cb38ff25dcd9cdf5c983da476409c8b *man/dag2essgraph.Rd
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ad4fcb4e1f73ffd1483862b88eb950d2 *man/dag2essgraph.Rd
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9825306a115fb2370a8bf8d481284983 *man/dag2pag.Rd
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4e804b480585e6a4d57b1ac0f6100760 *man/disCItest.Rd
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3d880e7f58fe68731e9ed4ecb4c13bf4 *man/dreach.Rd
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bca518ac995023186ff2945b62486043 *man/dsepTest.Rd
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18e3f7854dd0af498e231296825f64cc *man/fci.Rd
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4210c617d4929290e295ced5e0eeeb43 *man/fciAlgo-class.Rd
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adce79a344a395951d251d5fbb63b1d9 *man/fciPlus.Rd
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94407964a7b930180e35672a2ac86aa2 *man/fciPlus.Rd
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44127d2a6a6234ed84cf650a3273e504 *man/find.unsh.triple.Rd
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efed404b8bbbd6700520e6587d65d4ac *man/gAlgo-class.Rd
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b7b554b6006cf4a67024618db013e5ed *man/gac.Rd
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cb526c1eceaf53b0239c888ecbbdbbaf *man/gds.Rd
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318fbf7901347ed604e65d13ccfe9e88 *man/ges.Rd
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fdc0ad5d17fff5f2c8734504041af969 *man/getGraph.Rd
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932c079ecf9b2d271ee279647376deae *man/ges.Rd
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54662d98d24003eef72b1193565d4dd6 *man/getGraph.Rd
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f7e5c22255b62a23431b08c2d3080b66 *man/getNextSet.Rd
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6d8175892f5ba9aa3ac75187bbfa5c89 *man/gies.Rd
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cbb33c4976caf365b69cb9c76a7a493e *man/gmB.Rd
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5d6bd5e0a6ddce6b8b4dae1dc02bd26c *man/gmD.Rd
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44fc91f89bacfcf44cc596240aa5895f *man/gmG.Rd
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66a7855809f1fd6e9a0ced7dbd612af6 *man/gmI.Rd
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6e0e58a3ea2ba21d0e3df60b6f8d77c0 *man/gmG.Rd
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7299a9b977703f1155b39fc5eacef145 *man/gmI.Rd
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6a624691a6a19dd55526a9e9585ce0b3 *man/gmInt.Rd
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0fc0725cd27113dfa0505deb9504b3ec *man/gmL.Rd
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09869c2316e23e93cb53a2863f74cbfb *man/ida.Rd
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240d9c697a86a1aad34a623a487d3f5e *man/legal.path.Rd
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7c28e6a542763fa65c25784a96d32e1f *man/mat2targets.Rd
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cd8a6e38249822fc7c54c66b96a6a967 *man/mcor.Rd
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1c7ed5406ee7aed47987da8900ab144e *man/opt.target.Rd
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088eee045f4ee07c7fd39971203f4c18 *man/optAdjSet.Rd
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03b85555134c828b6d3eb61d30f08754 *man/opt.target.Rd
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93b991d491eb1246af2ccc3483c4efa6 *man/optAdjSet.Rd
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b19638bed84ac520eef81968bf75eec7 *man/pag2anc.Rd
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4d3e89b74016644821e676808d9ac720 *man/pag2conf.Rd
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a05d67efd1b2ecef92b144176a7e4802 *man/pag2edge.Rd
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67426f4203b1334a56a8715423083745 *man/pag2mag.Rd
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999058226d5b92a97826254353da24b9 *man/pc.Rd
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01d980deb40fe93c7e3c2f5039882f9d *man/pc.cons.intern.Rd
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342566226ce52d9795a928ef44a7ca3c *man/pcAlgo-class.Rd
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b85ec6d5f9f8caf5aa6a458e1a155eeb *man/pcAlgo-class.Rd
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143110b2d6797b5ef727a5c05d2790f8 *man/pcAlgo.Rd
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9ac47786c259e034f8884a317471413c *man/pcSelect.Rd
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ef7c030654d7a92a9664076d2a0eac5f *man/pcSelect.presel.Rd
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7b6d586d1487a8147af049ddff205984 *man/pcalg-internal.Rd
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85c443f6cceb717c08a7405a693759ba *man/pcalg2dagitty.Rd
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69e62cafe0cebc0d0d4faac5ad06408e *man/pcorOrder.Rd
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800c3348670b4ca01c406d5e5d67839c *man/pdag2allDags.Rd
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4d4299e5a352bec011257e53bfd3634f *man/pdag2allDags.Rd
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208807c0c6b5ead3e89f414adc9136c1 *man/pdag2dag.Rd
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23be39839c6b197c4e4d4b795434c897 *man/pdsep.Rd
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89b20dd90d54188d453dde9d8ca13d07 *man/plotAG.Rd
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a68ad0b469bf17525891e7670bfee92a *man/plotSG.Rd
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a0959170421383962a6da152d50a7533 *man/possAn.Rd
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f25aca5cbb7a581b13d96fb52b520ff7 *man/possDe.Rd
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54df65eb3082bb6c3d71d25a5015aced *man/possAn.Rd
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c79ecb227810b093283ddc9008e3d0ce *man/possDe.Rd
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7f5b7ce6779ae9d3536ed8d2f4c61ddc *man/possibleDe.Rd
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5782fc04b6408ebfc706d4d43d232fb1 *man/qreach.Rd
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d0196c418afe2af7c6bf89cd2a5d18e5 *man/r.gauss.pardag.Rd
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a2b64baab3e522ab16fb7eabcf6d4b0e *man/randDAG.Rd
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d28b8fbb54c9bdd378363a74325fcb8a *man/randomDAG.Rd
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cd0bb4991af0eb3495d50b38d7a5c824 *man/randDAG.Rd
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1c99d0898bf5b63f24c4049edeb17f70 *man/randomDAG.Rd
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7d17d98b4d76d4ae6ee5646d94b7d18d *man/rfci.Rd
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d6eb86a8b2f04f416a59792f35cdaa2c *man/rmvDAG.Rd
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35da0b2746092325096fa471446e465e *src/greedy.cpp
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c5e0eb959f4162f8655ea795eec34c50 *src/init.c
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bc5cab68e323949bed42d3d87b68e5a2 *src/score.cpp
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2a3703c998cfee5643aba359c366c621 *tests/Rplots.pdf
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7e9becd2ef6f689c10618dd96b69a7c8 *tests/Rplots.pdf
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83187ba1f22cdb1b239e07027ddf489a *tests/discr100k.rda
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4d3ceefb0a5c86642b5ccc887758358e *tests/filesToFix_Tests.txt
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d41d8cd98f00b204e9800998ecf8427e *tests/nohup.out
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e55f723241bfbf463ec914b2bcc694d0 *tests/test_LINGAM.R
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daeeb27e6aae053f7b69fa562716582f *tests/test_addBgKnowledge.R
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2d43ff479d17e1f0371108624fa71f9a *tests/test_addBgKnowledge.R
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94d9a6136b5d720bfa53e96616e459ca *tests/test_adjustment.R
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d90e667e134646f47bb8e06972d7601d *tests/test_ages.R
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ecaacf0c68bf72d9d96eeeeffd824357 *tests/test_pcorOrder.R
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67fbdda0dd8ab5f4fbd185ee85916d12 *tests/test_pdag2allDags.R
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6e781edbdbfa26fbff95bac51ebac9bc *tests/test_possDeAn.R
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507c58ed9fd5d94df32413b3293b4618 *tests/test_randDAG.R
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df10c14587ea074ed0f3b95f3211f81a *tests/test_randDAG.Rout.save
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dbdcee5fd6b2be716c6bdff785441167 *tests/test_randDAG.R
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aee8ad2108a151b25666eaf0ed1b4205 *tests/test_randomDAG.R
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e265f1b5aa31a977b1d25841ceebf3dd *tests/test_rfci.R
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37b491b0af1332bd0713579bd0a16da7 *tests/test_rfci.R
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aca0d1fb3b38a6f54fb2d84040aa009d *tests/test_rmvDAG.R
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d795c92a5d7f9fa10296170c950bd5f1 *tests/test_searchAM.R
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‎man/LINGAM.Rd

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and Jonas Peters <[email protected]>.
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}
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\seealso{
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\code{\link{fastICA}} from package \pkg{fastICA} is used.
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\code{\link[fastICA]{fastICA}} from package \pkg{fastICA} is used.
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\examples{
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##################################################

‎man/ages.Rd

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## Plots
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## Example 2: ages adds correct orientations: Author --> Goal and Author --> V5
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## Example 3: ges and ages return the same graph
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}
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% Add one or more standard keywords, see file 'KEYWORDS' in the
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‎man/amatType.Rd

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adjacency matrix as input; \code{\linkS4class{fciAlgo}} for a class
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\code{\link{getGraph}(x)} extracts the \code{\link[graph]{graph-class}}
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‎man/corGraph.Rd

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\value{
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Undirected correlation graph, a \code{\linkS4class{graph}} object
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Undirected correlation graph, a \code{\link[graph]{graph-class}} object
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‎man/dag2essgraph.Rd

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\arguments{
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object of \code{\link[graph]{graphNEL}} (package \pkg{graph}) or
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\item{an instance of \code{\link[graph]{graphNEL}}, if \code{dag} is an
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‎man/fciPlus.Rd

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summary(m.fci)
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## require("Rgraphviz")
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sfsmisc::mult.fig(2, main="True DAG // fciPlus(.) \"oracle\" estimate")
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if (require(Rgraphviz)) {
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par(mfrow=c(1,2))
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}
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## Joint Causal Inference Example

‎man/ges.Rd

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## alternative:
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‎man/getGraph.Rd

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\alias{getGraph,pcAlgo-method}
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\title{Get the "graph" Part or Aspect of R Object}
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\description{
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Get the \code{\link[graph]{graph-class}} part or \dQuote{aspect} of an \R
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\value{
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a \code{\linkS4class{graph}} object, i.e., one inheriting from (the
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a \code{\link[graph]{graph-class}} object, i.e., one inheriting from (the
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virtual) class \code{"graph"}, package \pkg{graph}.
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}
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\section{Methods}{
@@ -31,7 +31,7 @@ getGraph(x)
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\item{\code{signature(x = "fciAlgo")}}{extract the graph part
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explicitly.}
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\item{\code{signature(x = "matrix")}}{interpret \code{x} as adjacency
34-
matrix and return the corresponding \code{"\linkS4class{graphAM}"}
34+
matrix and return the corresponding \code{"\link[graph]{graphAM}"}
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object.}
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}
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For sparseMatrix methods, see the \sQuote{Note}.
@@ -47,7 +47,7 @@ getGraph(x)
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\author{Martin Maechler}
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\seealso{
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\code{\link{fci}}, etc.
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The \code{\linkS4class{graph}} class description in package \pkg{graph}.
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The \code{\link[graph]{graph-class}} class description in package \pkg{graph}.
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}
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\examples{
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A <- rbind(c(0,1,0,0,1),

‎man/gmG.Rd

+1-1
Original file line numberDiff line numberDiff line change
@@ -48,7 +48,7 @@ str(gmG, max=3)
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stopifnot(identical(gmG $ g, gmG8 $ g))
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if(dev.interactive()) { ## to save time in tests
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round(as(gmG $ g, "Matrix"), 2) # weight ("adjacency") matrix
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plot(gmG $ g)
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if (require(Rgraphviz)) plot(gmG$g)
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pairs(gmG$x, gap = 0,
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panel=function(...) smoothScatter(..., add=TRUE))
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}

‎man/gmI.Rd

+1-1
Original file line numberDiff line numberDiff line change
@@ -37,7 +37,7 @@ str(gmI, max=3)
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stopifnot(identical(gmI $ g, gmI7 $ g))
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if(dev.interactive()) { ## to save time in tests
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round(as(gmI $ g, "Matrix"), 2) # weight ("adjacency") matrix
40-
plot(gmI $ g)
40+
if (require(Rgraphviz)) plot(gmI $ g)
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pairs(gmI$x, gap = 0,
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panel=function(...) smoothScatter(..., add=TRUE))
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}

‎man/opt.target.Rd

+1-1
Original file line numberDiff line numberDiff line change
@@ -13,7 +13,7 @@
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\usage{opt.target(essgraph, max.size, use.node.names = TRUE)}
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\arguments{
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\item{essgraph}{An \code{\linkS4class{EssGraph}} or
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\code{\linkS4class{graphNEL}} object representing a (observational or
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\code{\link[graph]{graphNEL}} object representing a (observational or
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interventional) essential graph (or "CPDAG").}
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\item{max.size}{Maximum size of the intervention target. Only 1 and the
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number of vertices of \code{essgraph} are allowed; the latter means no size

‎man/optAdjSet.Rd

+2
Original file line numberDiff line numberDiff line change
@@ -49,10 +49,12 @@ myDAG <- randomDAG(p, prob = 0.3)
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myCPDAG <- dag2cpdag(myDAG)
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## true PDAG with added background knowledge 5 -> 6
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myPDAG <- addBgKnowledge(myCPDAG,5,6)
52+
if (require(Rgraphviz)) {
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par(mfrow = c(1,3))
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plot(myDAG)
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plot(myPDAG)
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plot(myCPDAG) ## plot of the graphs
57+
}
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## if the CPDAG C is amenable relative to (X,Y),
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## the optimal set will be the same for all DAGs

‎man/pcAlgo-class.Rd

+1-1
Original file line numberDiff line numberDiff line change
@@ -49,7 +49,7 @@
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In addition, \code{"pcAlgo"} has slots
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\describe{
52-
\item{\code{graph}:}{Object of class \code{"\linkS4class{graph}"}:
52+
\item{\code{graph}:}{Object of class \code{"\link[graph]{graph-class}"}:
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the undirected or partially directed graph that was estimated.}
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\item{\code{zMin}:}{Deprecated.}

‎man/pdag2allDags.Rd

+2
Original file line numberDiff line numberDiff line change
@@ -63,6 +63,7 @@ amat3 <- matrix(res3$dags[1,],5,5, byrow = TRUE)
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colnames(amat3) <- rownames(amat3) <- res3$nodeNms
6464
amat3
6565

66+
if (require(Rgraphviz)) {
6667
## for convenience a simple plotting function
6768
## for the function output
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plotAllDags <- function(res) {
@@ -83,3 +84,4 @@ amat2 ## adj.matrix corresponding to the first plot for expl 2
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plotAllDags(res3)
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amat3 ## adj.matrix corresponding to the first plot for expl 3
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}
87+
}

‎man/possAn.Rd

+1-1
Original file line numberDiff line numberDiff line change
@@ -49,7 +49,7 @@ type = c("cpdag", "pdag", "dag", "mag", "pag"))
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## a -- b -> c
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amat <- matrix(c(0,1,0, 1,0,1, 0,0,0), 3,3)
5151
colnames(amat) <- rownames(amat) <- letters[1:3]
52-
plot(as(t(amat), "graphNEL"))
52+
if (require(Rgraphviz)) plot(as(t(amat), "graphNEL"))
5353

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possAn(m = amat, x = 3, possible = TRUE, ds = FALSE, type = "pdag") ## all nodes
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possAn(m = amat, x = 3, y = 2, possible = TRUE, ds = FALSE, type = "pdag") ## only node 1

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