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0-prep_tmle_analysis.Rout
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0-prep_tmle_analysis.Rout
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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