From 29316935ae82a7c4a8516bf662a67ab605c369e4 Mon Sep 17 00:00:00 2001 From: Nima Hejazi Date: Sat, 21 Sep 2024 14:33:10 -0400 Subject: [PATCH] fix dagitty --- 04-roadmap.Rmd | 19 ++-- renv.lock | 296 +++++++++++++++++++++++++++++++++++++------------ 2 files changed, 233 insertions(+), 82 deletions(-) diff --git a/04-roadmap.Rmd b/04-roadmap.Rmd index c9fd629..c2e7741 100644 --- a/04-roadmap.Rmd +++ b/04-roadmap.Rmd @@ -417,16 +417,15 @@ library(dagitty) library(ggdag) # make DAG by specifying dependence structure -dag <- dagitty( - "dag { - W -> A - W -> Y - A -> Y - W -> A -> Y - }" -) -exposures(dag) <- c("A") -outcomes(dag) <- c("Y") +dag <- dagitty("dag{ + W -> A ; + W -> Y ; + A -> Y ; + W -> A -> Y ; + W [confounders] + A [exposure] + Y [outcome] + }") tidy_dag <- tidy_dagitty(dag) # visualize DAG diff --git a/renv.lock b/renv.lock index ae58be7..df6f921 100644 --- a/renv.lock +++ b/renv.lock @@ -58,9 +58,15 @@ }, "MASS": { "Package": "MASS", - "Version": "7.3-60", + "Version": "7.3-61", "Source": "Repository", "Repository": "CRAN", + "RemoteType": "standard", + "RemotePkgRef": "MASS", + "RemoteRef": "MASS", + "RemoteRepos": "https://cran.rstudio.com", + "RemotePkgPlatform": "aarch64-apple-darwin20", + "RemoteSha": "7.3-61", "Requirements": [ "R", "grDevices", @@ -69,7 +75,7 @@ "stats", "utils" ], - "Hash": "a56a6365b3fa73293ea8d084be0d9bb0" + "Hash": "0cafd6f0500e5deba33be22c46bf6055" }, "Matrix": { "Package": "Matrix", @@ -155,14 +161,20 @@ }, "Rcpp": { "Package": "Rcpp", - "Version": "1.0.8.3", + "Version": "1.0.13", "Source": "Repository", - "Repository": "CRAN", + "Repository": "RSPM", + "RemoteType": "standard", + "RemotePkgRef": "Rcpp", + "RemoteRef": "Rcpp", + "RemoteRepos": "https://cran.rstudio.com", + "RemotePkgPlatform": "aarch64-apple-darwin20", + "RemoteSha": "1.0.13", "Requirements": [ "methods", "utils" ], - "Hash": "32e79b908fda56ee57fe518a8d37b864" + "Hash": "f27411eb6d9c3dada5edd444b8416675" }, "RcppArmadillo": { "Package": "RcppArmadillo", @@ -271,16 +283,22 @@ }, "V8": { "Package": "V8", - "Version": "5.0.0", + "Version": "5.0.1", "Source": "Repository", "Repository": "CRAN", + "RemoteType": "standard", + "RemotePkgRef": "V8", + "RemoteRef": "V8", + "RemoteRepos": "https://cran.rstudio.com", + "RemotePkgPlatform": "aarch64-apple-darwin20", + "RemoteSha": "5.0.1", "Requirements": [ "Rcpp", "curl", "jsonlite", "utils" ], - "Hash": "9eb7b2df315593e726b029200fc0276c" + "Hash": "7f3867df00a91c63089beb85b9ef0208" }, "abind": { "Package": "abind", @@ -471,15 +489,21 @@ }, "boot": { "Package": "boot", - "Version": "1.3-28", + "Version": "1.3-31", "Source": "Repository", "Repository": "CRAN", + "RemoteType": "standard", + "RemotePkgRef": "boot", + "RemoteRef": "boot", + "RemoteRepos": "https://cran.rstudio.com", + "RemotePkgPlatform": "aarch64-apple-darwin20", + "RemoteSha": "1.3-31", "Requirements": [ "R", "graphics", "stats" ], - "Hash": "0baa960e3b49c6176a4f42addcbacc59" + "Hash": "de2a4646c18661d6a0a08ec67f40b7ed" }, "brew": { "Package": "brew", @@ -717,9 +741,15 @@ }, "colorspace": { "Package": "colorspace", - "Version": "2.0-3", + "Version": "2.1-1", "Source": "Repository", "Repository": "CRAN", + "RemoteType": "standard", + "RemotePkgRef": "colorspace", + "RemoteRef": "colorspace", + "RemoteRepos": "https://cran.rstudio.com", + "RemotePkgPlatform": "aarch64-apple-darwin20", + "RemoteSha": "2.1-1", "Requirements": [ "R", "grDevices", @@ -727,7 +757,7 @@ "methods", "stats" ], - "Hash": "bb4341986bc8b914f0f0acf2e4a3f2f7" + "Hash": "d954cb1c57e8d8b756165d7ba18aa55a" }, "commonmark": { "Package": "commonmark", @@ -813,9 +843,15 @@ }, "dagitty": { "Package": "dagitty", - "Version": "0.3-1", + "Version": "0.3-4", "Source": "Repository", "Repository": "CRAN", + "RemoteType": "standard", + "RemotePkgRef": "dagitty", + "RemoteRef": "dagitty", + "RemoteRepos": "https://cran.rstudio.com", + "RemotePkgPlatform": "aarch64-apple-darwin20", + "RemoteSha": "0.3-4", "Requirements": [ "MASS", "R", @@ -828,7 +864,7 @@ "stats", "utils" ], - "Hash": "22d2afac8432f195aabdf417ce42fdf4" + "Hash": "dfbd13468fb3d6747b4d9541a648df9d" }, "data.table": { "Package": "data.table", @@ -997,12 +1033,19 @@ }, "dplyr": { "Package": "dplyr", - "Version": "1.0.9", + "Version": "1.1.4", "Source": "Repository", "Repository": "CRAN", + "RemoteType": "standard", + "RemotePkgRef": "dplyr", + "RemoteRef": "dplyr", + "RemoteRepos": "https://cran.rstudio.com", + "RemotePkgPlatform": "aarch64-apple-darwin20", + "RemoteSha": "1.1.4", "Requirements": [ "R", "R6", + "cli", "generics", "glue", "lifecycle", @@ -1015,7 +1058,7 @@ "utils", "vctrs" ], - "Hash": "f0bda1627a7f5d3f9a0b5add931596ac" + "Hash": "fedd9d00c2944ff00a0e2696ccf048ec" }, "dtplyr": { "Package": "dtplyr", @@ -1100,22 +1143,34 @@ }, "fansi": { "Package": "fansi", - "Version": "1.0.3", + "Version": "1.0.6", "Source": "Repository", "Repository": "CRAN", + "RemoteType": "standard", + "RemotePkgRef": "fansi", + "RemoteRef": "fansi", + "RemoteRepos": "https://cran.rstudio.com", + "RemotePkgPlatform": "aarch64-apple-darwin20", + "RemoteSha": "1.0.6", "Requirements": [ "R", "grDevices", "utils" ], - "Hash": "83a8afdbe71839506baa9f90eebad7ec" + "Hash": "962174cf2aeb5b9eea581522286a911f" }, "farver": { "Package": "farver", - "Version": "2.1.0", + "Version": "2.1.2", "Source": "Repository", "Repository": "CRAN", - "Hash": "c98eb5133d9cb9e1622b8691487f11bb" + "RemoteType": "standard", + "RemotePkgRef": "farver", + "RemoteRef": "farver", + "RemoteRepos": "https://cran.rstudio.com", + "RemotePkgPlatform": "aarch64-apple-darwin20", + "RemoteSha": "2.1.2", + "Hash": "680887028577f3fa2a81e410ed0d6e42" }, "fastmap": { "Package": "fastmap", @@ -1150,17 +1205,25 @@ }, "forcats": { "Package": "forcats", - "Version": "0.5.1", + "Version": "1.0.0", "Source": "Repository", "Repository": "CRAN", + "RemoteType": "standard", + "RemotePkgRef": "forcats", + "RemoteRef": "forcats", + "RemoteRepos": "https://cran.rstudio.com", + "RemotePkgPlatform": "aarch64-apple-darwin20", + "RemoteSha": "1.0.0", "Requirements": [ "R", - "ellipsis", + "cli", + "glue", + "lifecycle", "magrittr", "rlang", "tibble" ], - "Hash": "81c3244cab67468aac4c60550832655d" + "Hash": "1a0a9a3d5083d0d573c4214576f1e690" }, "foreach": { "Package": "foreach", @@ -1296,14 +1359,20 @@ }, "generics": { "Package": "generics", - "Version": "0.1.2", + "Version": "0.1.3", "Source": "Repository", "Repository": "CRAN", + "RemoteType": "standard", + "RemotePkgRef": "generics", + "RemoteRef": "generics", + "RemoteRepos": "https://cran.rstudio.com", + "RemotePkgPlatform": "aarch64-apple-darwin20", + "RemoteSha": "0.1.3", "Requirements": [ "R", "methods" ], - "Hash": "177475892cf4a55865868527654a7741" + "Hash": "15e9634c0fcd294799e9b2e929ed1b86" }, "gert": { "Package": "gert", @@ -1639,14 +1708,24 @@ }, "gtable": { "Package": "gtable", - "Version": "0.3.0", + "Version": "0.3.5", "Source": "Repository", "Repository": "CRAN", + "RemoteType": "standard", + "RemotePkgRef": "gtable", + "RemoteRef": "gtable", + "RemoteRepos": "https://cran.rstudio.com", + "RemotePkgPlatform": "aarch64-apple-darwin20", + "RemoteSha": "0.3.5", "Requirements": [ "R", - "grid" + "cli", + "glue", + "grid", + "lifecycle", + "rlang" ], - "Hash": "ac5c6baf7822ce8732b343f14c072c4d" + "Hash": "e18861963cbc65a27736e02b3cd3c4a0" }, "gtools": { "Package": "gtools", @@ -2083,14 +2162,20 @@ }, "labeling": { "Package": "labeling", - "Version": "0.4.2", + "Version": "0.4.3", "Source": "Repository", "Repository": "CRAN", + "RemoteType": "standard", + "RemotePkgRef": "labeling", + "RemoteRef": "labeling", + "RemoteRepos": "https://cran.rstudio.com", + "RemotePkgPlatform": "aarch64-apple-darwin20", + "RemoteSha": "0.4.3", "Requirements": [ "graphics", "stats" ], - "Hash": "3d5108641f47470611a32d0bdf357a72" + "Hash": "b64ec208ac5bc1852b285f665d6368b3" }, "later": { "Package": "later", @@ -2343,22 +2428,20 @@ }, "munsell": { "Package": "munsell", - "Version": "0.5.0", + "Version": "0.5.1", "Source": "Repository", "Repository": "CRAN", - "RemotePkgRef": "munsell@0.5.0", "RemoteType": "standard", - "RemoteEtag": "\"2c97d-56e6a4ec0bce6\"", - "RemotePackaged": "TRUE", + "RemotePkgRef": "munsell", "RemoteRef": "munsell", - "RemoteRepos": "https://cloud.r-project.org", - "RemotePkgPlatform": "source", - "RemoteSha": "0.5.0", + "RemoteRepos": "https://cran.rstudio.com", + "RemotePkgPlatform": "aarch64-apple-darwin20", + "RemoteSha": "0.5.1", "Requirements": [ "colorspace", "methods" ], - "Hash": "6dfe8bf774944bd5595785e3229d8771" + "Hash": "4fd8900853b746af55b81fda99da7695" }, "mvtnorm": { "Package": "mvtnorm", @@ -2502,13 +2585,17 @@ }, "pillar": { "Package": "pillar", - "Version": "1.7.0", + "Version": "1.9.0", "Source": "Repository", "Repository": "CRAN", + "RemoteType": "standard", + "RemotePkgRef": "pillar", + "RemoteRef": "pillar", + "RemoteRepos": "https://cran.rstudio.com", + "RemotePkgPlatform": "aarch64-apple-darwin20", + "RemoteSha": "1.9.0", "Requirements": [ "cli", - "crayon", - "ellipsis", "fansi", "glue", "lifecycle", @@ -2517,7 +2604,7 @@ "utils", "vctrs" ], - "Hash": "51dfc97e1b7069e9f7e6f83f3589c22e" + "Hash": "15da5a8412f317beeee6175fbc76f4bb" }, "pkgbuild": { "Package": "pkgbuild", @@ -2656,13 +2743,19 @@ }, "polyclip": { "Package": "polyclip", - "Version": "1.10-0", + "Version": "1.10-7", "Source": "Repository", "Repository": "CRAN", + "RemoteType": "standard", + "RemotePkgRef": "polyclip", + "RemoteRef": "polyclip", + "RemoteRepos": "https://cran.rstudio.com", + "RemotePkgPlatform": "aarch64-apple-darwin20", + "RemoteSha": "1.10-7", "Requirements": [ "R" ], - "Hash": "cb167f328b3ada4ec5cf67a7df4c900a" + "Hash": "5879bf5aae702ffef0a315c44328f984" }, "praise": { "Package": "praise", @@ -3474,16 +3567,26 @@ }, "stringr": { "Package": "stringr", - "Version": "1.4.0", + "Version": "1.5.1", "Source": "Repository", "Repository": "CRAN", + "RemoteType": "standard", + "RemotePkgRef": "stringr", + "RemoteRef": "stringr", + "RemoteRepos": "https://cran.rstudio.com", + "RemotePkgPlatform": "aarch64-apple-darwin20", + "RemoteSha": "1.5.1", "Requirements": [ "R", + "cli", "glue", + "lifecycle", "magrittr", - "stringi" + "rlang", + "stringi", + "vctrs" ], - "Hash": "0759e6b6c0957edb1311028a49a35e76" + "Hash": "960e2ae9e09656611e0b8214ad543207" }, "survival": { "Package": "survival", @@ -3589,12 +3692,17 @@ }, "tibble": { "Package": "tibble", - "Version": "3.1.7", + "Version": "3.2.1", "Source": "Repository", "Repository": "CRAN", + "RemoteType": "standard", + "RemotePkgRef": "tibble", + "RemoteRef": "tibble", + "RemoteRepos": "https://cran.rstudio.com", + "RemotePkgPlatform": "aarch64-apple-darwin20", + "RemoteSha": "3.2.1", "Requirements": [ "R", - "ellipsis", "fansi", "lifecycle", "magrittr", @@ -3605,19 +3713,26 @@ "utils", "vctrs" ], - "Hash": "08415af406e3dd75049afef9552e7355" + "Hash": "a84e2cc86d07289b3b6f5069df7a004c" }, "tidygraph": { "Package": "tidygraph", - "Version": "1.2.1", + "Version": "1.3.1", "Source": "Repository", "Repository": "CRAN", + "RemoteType": "standard", + "RemotePkgRef": "tidygraph", + "RemoteRef": "tidygraph", + "RemoteRepos": "https://cran.rstudio.com", + "RemotePkgPlatform": "aarch64-apple-darwin20", + "RemoteSha": "1.3.1", "Requirements": [ "R6", "cli", "cpp11", "dplyr", "igraph", + "lifecycle", "magrittr", "pillar", "rlang", @@ -3627,44 +3742,58 @@ "tools", "utils" ], - "Hash": "19f5f240d255ff0bf91e76d062fdc176" + "Hash": "2149824d406f233b57b087be72c5f163" }, "tidyr": { "Package": "tidyr", - "Version": "1.2.0", + "Version": "1.3.1", "Source": "Repository", "Repository": "CRAN", + "RemoteType": "standard", + "RemotePkgRef": "tidyr", + "RemoteRef": "tidyr", + "RemoteRepos": "https://cran.rstudio.com", + "RemotePkgPlatform": "aarch64-apple-darwin20", + "RemoteSha": "1.3.1", "Requirements": [ "R", + "cli", "cpp11", "dplyr", - "ellipsis", "glue", "lifecycle", "magrittr", "purrr", "rlang", + "stringr", "tibble", "tidyselect", "utils", "vctrs" ], - "Hash": "d8b95b7fee945d7da6888cf7eb71a49c" + "Hash": "915fb7ce036c22a6a33b5a8adb712eb1" }, "tidyselect": { "Package": "tidyselect", - "Version": "1.1.2", + "Version": "1.2.1", "Source": "Repository", "Repository": "CRAN", + "RemoteType": "standard", + "RemotePkgRef": "tidyselect", + "RemoteRef": "tidyselect", + "RemoteRepos": "https://cran.rstudio.com", + "RemotePkgPlatform": "aarch64-apple-darwin20", + "RemoteSha": "1.2.1", "Requirements": [ "R", - "ellipsis", + "cli", "glue", - "purrr", + "lifecycle", "rlang", - "vctrs" + "vctrs", + "withr" ], - "Hash": "17f6da8cfd7002760a859915ce7eef8f" + "Hash": "829f27b9c4919c16b593794a6344d6c0" }, "tidyverse": { "Package": "tidyverse", @@ -3872,18 +4001,24 @@ }, "tweenr": { "Package": "tweenr", - "Version": "1.0.2", + "Version": "2.0.3", "Source": "Repository", "Repository": "CRAN", + "RemoteType": "standard", + "RemotePkgRef": "tweenr", + "RemoteRef": "tweenr", + "RemoteRepos": "https://cran.rstudio.com", + "RemotePkgPlatform": "aarch64-apple-darwin20", + "RemoteSha": "2.0.3", "Requirements": [ "R", - "Rcpp", + "cpp11", "farver", - "grDevices", "magrittr", - "rlang" + "rlang", + "vctrs" ], - "Hash": "6cc663f970a529dbf776f11d5bcd1a2e" + "Hash": "82fac2b73e6a1f3874fc000aaf96d8bc" }, "tzdb": { "Package": "tzdb", @@ -3957,13 +4092,19 @@ }, "utf8": { "Package": "utf8", - "Version": "1.2.2", + "Version": "1.2.4", "Source": "Repository", "Repository": "CRAN", + "RemoteType": "standard", + "RemotePkgRef": "utf8", + "RemoteRef": "utf8", + "RemoteRepos": "https://cran.rstudio.com", + "RemotePkgPlatform": "aarch64-apple-darwin20", + "RemoteSha": "1.2.4", "Requirements": [ "R" ], - "Hash": "c9c462b759a5cc844ae25b5942654d13" + "Hash": "62b65c52671e6665f803ff02954446e9" }, "uuid": { "Package": "uuid", @@ -4004,13 +4145,19 @@ }, "viridisLite": { "Package": "viridisLite", - "Version": "0.4.0", + "Version": "0.4.2", "Source": "Repository", "Repository": "CRAN", + "RemoteType": "standard", + "RemotePkgRef": "viridisLite", + "RemoteRef": "viridisLite", + "RemoteRepos": "https://cran.rstudio.com", + "RemotePkgPlatform": "aarch64-apple-darwin20", + "RemoteSha": "0.4.2", "Requirements": [ "R" ], - "Hash": "55e157e2aa88161bdb0754218470d204" + "Hash": "c826c7c4241b6fc89ff55aaea3fa7491" }, "visNetwork": { "Package": "visNetwork", @@ -4105,16 +4252,21 @@ }, "withr": { "Package": "withr", - "Version": "2.5.0", + "Version": "3.0.1", "Source": "Repository", "Repository": "CRAN", + "RemoteType": "standard", + "RemotePkgRef": "withr", + "RemoteRef": "withr", + "RemoteRepos": "https://cran.rstudio.com", + "RemotePkgPlatform": "aarch64-apple-darwin20", + "RemoteSha": "3.0.1", "Requirements": [ "R", "grDevices", - "graphics", - "stats" + "graphics" ], - "Hash": "c0e49a9760983e81e55cdd9be92e7182" + "Hash": "07909200e8bbe90426fbfeb73e1e27aa" }, "xfun": { "Package": "xfun",