R version 4.0.4 (2021-02-15) -- "Lost Library Book"
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> 
> 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’

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    combine


Attaching package: ‘reshape2’

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    smiths

Loading required package: Matrix

Attaching package: ‘Matrix’

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    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’

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    dcast, melt

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Loading required package: viridisLite

Attaching package: ‘maps’

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Attaching package: ‘assertthat’

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Loading required package: nlme

Attaching package: ‘nlme’

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This is mgcv 1.8-31. For overview type 'help("mgcv-package")'.

Attaching package: ‘lazyeval’

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    is_atomic, is_formula


Attaching package: ‘scales’

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Attaching package: ‘foreach’

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Loading required package: iterators
Loading required package: parallel
Loading required package: survival

Attaching package: ‘survey’

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Loading required package: bit

Attaching package: ‘bit’

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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’

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Attaching package: ‘zoo’

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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