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jeremyrcoylejeremyrcoyle
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Merge pull request #433 from tlverse/fix-impute
don't attempt to impute covariates if there is no missingness
2 parents b794bb1 + d9ab177 commit c87f76c

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5 files changed

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‎.github/workflows/R-CMD-check.yml‎

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steps:
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- name: Checkout repo
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uses: actions/checkout@v3
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uses: actions/checkout@v4
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- name: Setup R
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uses: r-lib/actions/setup-r@v2
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- name: Install package dependencies
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run: |
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install.packages(c("remotes", "devtools", "rcmdcheck", "covr", "sessioninfo"))
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install.packages(c("remotes", "rcmdcheck", "covr", "sessioninfo"))
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remotes::install_deps(dependencies = TRUE)
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shell: Rscript {0}
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‎DESCRIPTION‎

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@@ -33,7 +33,7 @@ Depends: R (>= 3.6.0)
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Imports:
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data.table,
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assertthat,
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origami (>= 1.0.3),
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origami (>= 1.0.7),
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R6,
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uuid,
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BBmisc,
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glmnet,
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grf,
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gbm,
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hal9001 (>= 0.4.4),
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hal9001 (>= 0.4.6),
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h2o,
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keras,
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nloptr,
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xgboost,
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lightgbm,
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dbarts,
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gam (>= 1.15.0),
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haldensify (>= 0.2.3),
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gam,
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haldensify (>= 0.2.7),
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mgcv,
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hts,
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GA,
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SIS,
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partykit
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Remotes:
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github::tlverse/origami,
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github::tlverse/hal9001@devel,
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github::nhejazi/haldensify
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License: GPL-3
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Language: en-US

‎R/process_data.R‎

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@@ -132,13 +132,15 @@ process_data <- function(data, nodes, column_names, flag = TRUE,
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# add inidicators to column map and covariate list
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column_names[missing_indicator_vars] <- missing_indicator_cols
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nodes$covariates <- c(nodes$covariates, missing_indicator_vars)
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# impute covariates
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data_missing_covars <- data[, missing_covar_cols, with = FALSE]
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imputed <- impute(data.frame(data_missing_covars))
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# update data
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set(data, , missing_covar_cols, imputed)
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}
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# impute covariates
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data_missing_covars <- data[, missing_covar_cols, with = FALSE]
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imputed <- impute(data.frame(data_missing_covars))
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# update data
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set(data, , missing_covar_cols, imputed)
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}
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na_Y <- (!is.null(nodes$outcome) && any(is.na(data[, outcome_columns, with = F])))

‎testresults.txt‎

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[2024-04-29 20:20:53] ══ Documenting ═════════════════════════════════════════════════════════════════
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[2024-04-29 20:20:53] ℹ Updating sl3 documentation
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[2024-04-29 20:20:54] ℹ Loading sl3
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[2024-04-29 20:20:57]
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[2024-04-29 20:20:57] ══ Building ════════════════════════════════════════════════════════════════════
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[2024-04-29 20:20:57] Setting env vars:
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[2024-04-29 20:20:57] • CFLAGS : -Wall -pedantic
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[2024-04-29 20:20:57] • CXXFLAGS : -Wall -pedantic
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[2024-04-29 20:20:57] • CXX11FLAGS: -Wall -pedantic
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[2024-04-29 20:20:57] • CXX14FLAGS: -Wall -pedantic
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[2024-04-29 20:20:57] • CXX17FLAGS: -Wall -pedantic
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[2024-04-29 20:20:57] • CXX20FLAGS: -Wall -pedantic
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[2024-04-29 20:20:57] ── R CMD build ─────────────────────────────────────────────────────────────────
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[2024-04-29 20:20:57] * checking for file ‘/home/jrcoyle/Dropbox/tlverse/sl3/DESCRIPTION’ ... OK
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[2024-04-29 20:20:57] * preparing ‘sl3’:
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[2024-04-29 20:20:57] * checking DESCRIPTION meta-information ... OK
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[2024-04-29 20:20:57] * installing the package to process help pages
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[2024-04-29 20:21:14] Loading required namespace: sl3
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[2024-04-29 20:21:15] * saving partial Rd database
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[2024-04-29 20:21:19] * creating vignettes ... OK
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[2024-04-29 20:21:19] * checking for LF line-endings in source and make files and shell scripts
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[2024-04-29 20:21:19] * checking for empty or unneeded directories
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[2024-04-29 20:21:19] Removed empty directory ‘sl3/tests/testthat/_snaps’
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[2024-04-29 20:21:19] * building ‘sl3_1.4.5.tar.gz’
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[2024-04-29 20:21:19]
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[2024-04-29 20:21:19] ══ Checking ════════════════════════════════════════════════════════════════════
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[2024-04-29 20:21:19] Setting env vars:
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[2024-04-29 20:21:19] • _R_CHECK_CRAN_INCOMING_USE_ASPELL_ : TRUE
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[2024-04-29 20:21:19] • _R_CHECK_CRAN_INCOMING_REMOTE_ : FALSE
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[2024-04-29 20:21:19] • _R_CHECK_CRAN_INCOMING_ : FALSE
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[2024-04-29 20:21:19] • _R_CHECK_FORCE_SUGGESTS_ : FALSE
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[2024-04-29 20:21:19] • _R_CHECK_PACKAGES_USED_IGNORE_UNUSED_IMPORTS_: FALSE
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[2024-04-29 20:21:19] • NOT_CRAN : false
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[2024-04-29 20:21:19] ── R CMD check ─────────────────────────────────────────────────────────────────
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[2024-04-29 20:21:19] * using log directory ‘/tmp/RtmpZW35EK/file1237e20c4dd84/sl3.Rcheck’
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[2024-04-29 20:21:19] * using R version 4.3.3 (2024-02-29)
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[2024-04-29 20:21:19] * using platform: x86_64-pc-linux-gnu (64-bit)
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[2024-04-29 20:21:19] * R was compiled by
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[2024-04-29 20:21:19] gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
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[2024-04-29 20:21:19] GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
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[2024-04-29 20:21:19] * running under: Pop!_OS 20.04 LTS
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[2024-04-29 20:21:19] * using session charset: UTF-8
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[2024-04-29 20:21:20] * using options ‘--no-manual --as-cran’
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[2024-04-29 20:21:20] * checking for file ‘sl3/DESCRIPTION’ ... OK
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[2024-04-29 20:21:20] * this is package ‘sl3’ version ‘1.4.5’
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[2024-04-29 20:21:20] * package encoding: UTF-8
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[2024-04-29 20:21:20] * checking package namespace information ... OK
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[2024-04-29 20:21:20] * checking package dependencies ... OK
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[2024-04-29 20:21:20] * checking if this is a source package ... OK
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[2024-04-29 20:21:20] * checking if there is a namespace ... OK
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[2024-04-29 20:21:21] * checking for executable files ... OK
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[2024-04-29 20:21:21] * checking for hidden files and directories ... OK
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[2024-04-29 20:21:21] * checking for portable file names ... OK
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[2024-04-29 20:21:21] * checking for sufficient/correct file permissions ... OK
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[2024-04-29 20:21:37] * checking whether package ‘sl3’ can be installed ... [16s/16s] OK
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[2024-04-29 20:21:37] * checking installed package size ... OK
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[2024-04-29 20:21:37] * checking package directory ... OK
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[2024-04-29 20:21:37] * checking for future file timestamps ... OK
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[2024-04-29 20:21:37] * checking ‘build’ directory ... OK
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[2024-04-29 20:21:37] * checking DESCRIPTION meta-information ... OK
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[2024-04-29 20:21:37] * checking top-level files ... OK
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[2024-04-29 20:21:37] * checking for left-over files ... OK
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[2024-04-29 20:21:37] * checking index information ... OK
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[2024-04-29 20:21:38] * checking package subdirectories ... OK
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[2024-04-29 20:21:38] * checking R files for non-ASCII characters ... OK
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[2024-04-29 20:21:38] * checking R files for syntax errors ... OK
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[2024-04-29 20:21:39] * checking whether the package can be loaded ... OK
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[2024-04-29 20:21:40] * checking whether the package can be loaded with stated dependencies ... OK
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[2024-04-29 20:21:41] * checking whether the package can be unloaded cleanly ... OK
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[2024-04-29 20:21:42] * checking whether the namespace can be loaded with stated dependencies ... OK
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[2024-04-29 20:21:44] * checking whether the namespace can be unloaded cleanly ... OK
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[2024-04-29 20:21:45] * checking loading without being on the library search path ... OK
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[2024-04-29 20:21:48] * checking startup messages can be suppressed ... OK
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[2024-04-29 20:21:49] * checking dependencies in R code ... OK
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[2024-04-29 20:21:50] * checking S3 generic/method consistency ... OK
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[2024-04-29 20:21:52] * checking replacement functions ... OK
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[2024-04-29 20:21:53] * checking foreign function calls ... OK
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[2024-04-29 20:22:00] * checking R code for possible problems ... OK
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[2024-04-29 20:22:02] * checking Rd files ... OK
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[2024-04-29 20:22:02] * checking Rd metadata ... OK
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[2024-04-29 20:22:02] * checking Rd line widths ... OK
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[2024-04-29 20:22:03] * checking Rd cross-references ... OK
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[2024-04-29 20:22:04] * checking for missing documentation entries ... OK
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[2024-04-29 20:22:08] * checking for code/documentation mismatches ... OK
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[2024-04-29 20:22:09] * checking Rd \usage sections ... OK
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[2024-04-29 20:22:09] * checking Rd contents ... OK
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[2024-04-29 20:22:10] * checking for unstated dependencies in examples ... OK
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[2024-04-29 20:22:10] * checking contents of ‘data’ directory ... OK
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[2024-04-29 20:22:10] * checking data for non-ASCII characters ... OK
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[2024-04-29 20:22:10] * checking LazyData ... OK
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[2024-04-29 20:22:10] * checking data for ASCII and uncompressed saves ... OK
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[2024-04-29 20:22:10] * checking installed files from ‘inst/doc’ ... OK
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[2024-04-29 20:22:10] * checking files in ‘vignettes’ ... OK
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[2024-04-29 20:22:41] * checking examples ... [30s/31s] OK
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[2024-04-29 20:22:44] * checking for unstated dependencies in ‘tests’ ... OK
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[2024-04-29 20:22:44] * checking tests ...
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[2024-04-29 20:28:05] Running ‘testthat.R’ [401s/321s]
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[2024-04-29 20:28:05] [401s/321s] OK
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[2024-04-29 20:28:05] * checking for unstated dependencies in vignettes ... OK
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[2024-04-29 20:28:05] * checking package vignettes in ‘inst/doc’ ... OK
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[2024-04-29 20:28:10] * checking re-building of vignette outputs ... OK
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[2024-04-29 20:28:10] * checking for non-standard things in the check directory ... OK
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[2024-04-29 20:28:10] * checking for detritus in the temp directory ... OK
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[2024-04-29 20:28:10] * DONE
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[2024-04-29 20:28:10]
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[2024-04-29 20:28:10] Status: OK
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[2024-04-29 20:28:10]
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[2024-04-29 20:28:11] ── R CMD check results ────────────────────────────────────────── sl3 1.4.5 ────
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[2024-04-29 20:28:11] Duration: 6m 51.5s
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[2024-04-29 20:28:11]
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[2024-04-29 20:28:11] 0 errors ✔ | 0 warnings ✔ | 0 notes ✔

‎tests/testthat/test-missing_outcome.R‎

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context("Incorporating corrections for missingness in covariates")
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library(data.table)
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library(assertthat)
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library(uuid)
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library(sl3)
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library(tmle3)
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set.seed(34831)
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# setup data for test
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data(cpp)
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data <- as.data.table(cpp)
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data[, parity01 := as.numeric(data$parity > 0)]
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data[, parity01_fac := factor(data$parity01)]
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data[, haz01 := as.numeric(data$haz > 0)]
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node_list <- list(
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W = c(
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"apgar1", "apgar5", "gagebrth", "mage",
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"meducyrs", "sexn"
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),
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A = "waz",
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Y = "haz01"
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)
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# drop missing A for now, might add back to test later
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missing_W <- apply(is.na(data[, c(node_list$W, node_list$A),
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with = FALSE
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]), 1, any)
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data <- data[!missing_W]
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task <- sl3_Task$new(data, outcome=node_list$Y, covariates = node_list$W)

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