R version 4.0.4 (2021-02-15) -- "Lost Library Book" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > > rm(list=ls()) > source(paste0(here::here(), "/0-config.R")) ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.0 ── ✔ ggplot2 3.3.2 ✔ purrr 0.3.4 ✔ tibble 3.1.0 ✔ dplyr 1.0.5 ✔ tidyr 1.1.1 ✔ stringr 1.4.0 ✔ readr 1.3.1 ✔ forcats 0.5.0 ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ── ✖ dplyr::filter() masks stats::filter() ✖ dplyr::lag() masks stats::lag() here() starts at /home/andrew.mertens/ki-synthetic Attaching package: ‘gridExtra’ The following object is masked from ‘package:dplyr’: combine Attaching package: ‘reshape2’ The following object is masked from ‘package:tidyr’: smiths Loading required package: Matrix Attaching package: ‘Matrix’ The following objects are masked from ‘package:tidyr’: expand, pack, unpack Loading 'metafor' package (version 2.4-0). For an overview and introduction to the package please type: help(metafor). Attaching package: ‘data.table’ The following objects are masked from ‘package:reshape2’: dcast, melt The following objects are masked from ‘package:dplyr’: between, first, last The following object is masked from ‘package:purrr’: transpose Loading required package: viridisLite Attaching package: ‘maps’ The following object is masked from ‘package:purrr’: map Attaching package: ‘assertthat’ The following object is masked from ‘package:tibble’: has_name Loading required package: nlme Attaching package: ‘nlme’ The following object is masked from ‘package:dplyr’: collapse This is mgcv 1.8-31. For overview type 'help("mgcv-package")'. Attaching package: ‘lazyeval’ The following objects are masked from ‘package:purrr’: is_atomic, is_formula Attaching package: ‘scales’ The following object is masked from ‘package:viridis’: viridis_pal The following object is masked from ‘package:purrr’: discard The following object is masked from ‘package:readr’: col_factor Attaching package: ‘foreach’ The following objects are masked from ‘package:purrr’: accumulate, when Loading required package: iterators Loading required package: parallel Loading required package: survival Attaching package: ‘survey’ The following object is masked from ‘package:graphics’: dotchart Loading required package: bit Attaching package: ‘bit’ The following object is masked from ‘package:data.table’: setattr The following object is masked from ‘package:base’: xor Attaching package bit64 package:bit64 (c) 2011-2017 Jens Oehlschlaegel creators: integer64 runif64 seq : coercion: as.integer64 as.vector as.logical as.integer as.double as.character as.bitstring logical operator: ! & | xor != == < <= >= > arithmetic operator: + - * / %/% %% ^ math: sign abs sqrt log log2 log10 math: floor ceiling trunc round querying: is.integer64 is.vector [is.atomic} [length] format print str values: is.na is.nan is.finite is.infinite aggregation: any all min max range sum prod cumulation: diff cummin cummax cumsum cumprod access: length<- [ [<- [[ [[<- combine: c rep cbind rbind as.data.frame WARNING don't use as subscripts WARNING semantics differ from integer for more help type ?bit64 Attaching package: ‘bit64’ The following objects are masked from ‘package:base’: :, %in%, is.double, match, order, rank Attaching package: ‘zoo’ The following objects are masked from ‘package:base’: as.Date, as.Date.numeric Warning message: package ‘tidyverse’ was built under R version 4.0.5 > > source(here("3-prep-tmle-analysis/02_calc_wast_rf_outcome.R")) `summarise()` has grouped output by 'syntype', 'studyid', 'country', 'subjid'. You can override using the `.groups` argument. Adding missing grouping variables: `syntype` Adding missing grouping variables: `syntype` > source(here("3-prep-tmle-analysis/03_calc_wlz-stunt_rf_outcomes.R")) Error in eval(substitute(select), nl, parent.frame()) : object 'syntype' not found Calls: source ... rename -> subset -> subset.data.table -> eval -> eval Execution halted