Description: Data on overall fate of all 80 studies for Figure 1 of paper. Figure 1 was made with Adobe Illustrator using the following data.
Coder name(s): Althea ArchMiller
Load libraries
library(ezknitr)
library(knitr)
library(devtools)
library(Hmisc)
Clear environment and set seed
remove(list=ls())
set.seed(8675)
load(file = "data/processed_data/averages_of_reviewed_studies.Rdata")
load(file = "data/processed_data/reviewed_studies_data.Rdata")
load(file = "data/processed_data/all_studies_data.Rdata")
table(new_data$Why.not.reviewed)
##
## Author Declined: Data saved for future article
## 1
## Author Declined: No reason given
## 2
## Author Declined: Not enough time
## 3
## Author Declined: Proprietary/confidential data
## 5
## Author wanted to participate, but did not send data
## 2
## NA: Study was reviewed
## 38
## No correspondence
## 42
## Unsuitable for review
## 6
Status by Journal: JWM
table(new_data$Why.not.reviewed[new_data$journal=="JWM"])
##
## Author Declined: Data saved for future article
## 1
## Author Declined: No reason given
## 2
## Author Declined: Not enough time
## 2
## Author Declined: Proprietary/confidential data
## 1
## NA: Study was reviewed
## 14
## No correspondence
## 26
## Unsuitable for review
## 1
Status by Journal: WSB
table(new_data$Why.not.reviewed[new_data$journal=="WSB"])
##
## Author Declined: Not enough time
## 1
## Author Declined: Proprietary/confidential data
## 4
## Author wanted to participate, but did not send data
## 2
## NA: Study was reviewed
## 24
## No correspondence
## 16
## Unsuitable for review
## 5
sort(averages$conclusionsReproduced)
## [1] 1.0 1.0 1.0 1.5 2.0 2.5 3.0 4.0 4.0 4.5 4.5 5.0 5.0 5.0 5.0 5.0 5.0
## [18] 5.0 5.0
hist(averages$conclusionsReproduced)
By journal: JWM
sort(averages$conclusionsReproduced[averages$journal=="JWM"])
## [1] 1.0 2.0 3.0 4.0 4.5 5.0 5.0
hist(averages$conclusionsReproduced[averages$journal=="JWM"])
By jounral: WSB
sort(averages$conclusionsReproduced[averages$journal=="WSB"])
## [1] 1.0 1.0 1.5 2.5 4.0 4.5 5.0 5.0 5.0 5.0 5.0 5.0
hist(averages$conclusionsReproduced[averages$journal=="WSB"])
Non-reproducible number
Hmisc::binconf(x = 6, n = 19, method = "wilson")
## PointEst Lower Upper
## 0.3157895 0.1536438 0.5398959
Reproducible number
Hmisc::binconf(x = 13, n = 19, method = "wilson")
## PointEst Lower Upper
## 0.6842105 0.4601041 0.8463562
Number reviewed
Hmisc::binconf(x = 19, n = 74, method = "wilson")
## PointEst Lower Upper
## 0.2567568 0.1709771 0.3665444
devtools::session_info()
## Warning in as.POSIXlt.POSIXct(Sys.time()): unknown timezone 'zone/tz/2019c.
## 1.0/zoneinfo/America/Chicago'
## Session info -------------------------------------------------------------
## setting value
## version R version 3.3.2 (2016-10-31)
## system x86_64, darwin13.4.0
## ui RStudio (1.0.143)
## language (EN)
## collate en_US.UTF-8
## tz <NA>
## date 2019-12-14
## Packages -----------------------------------------------------------------
## package * version date source
## acepack 1.4.1 2016-10-29 CRAN (R 3.3.0)
## backports 1.1.1 2017-09-25 CRAN (R 3.3.2)
## base * 3.3.2 2016-10-31 local
## base64enc 0.1-3 2015-07-28 CRAN (R 3.3.0)
## checkmate 1.8.4 2017-09-25 CRAN (R 3.3.2)
## cluster 2.0.6 2017-03-16 CRAN (R 3.3.2)
## colorspace 1.3-2 2016-12-14 CRAN (R 3.3.2)
## data.table 1.10.4-2 2017-10-12 CRAN (R 3.3.2)
## datasets * 3.3.2 2016-10-31 local
## devtools * 1.13.3 2017-08-02 CRAN (R 3.3.2)
## digest 0.6.12 2017-01-27 CRAN (R 3.3.2)
## evaluate 0.10.1 2017-06-24 CRAN (R 3.3.2)
## ezknitr * 0.6 2016-09-16 CRAN (R 3.3.0)
## foreign 0.8-69 2017-06-21 CRAN (R 3.3.2)
## Formula * 1.2-2 2017-07-10 CRAN (R 3.3.2)
## ggplot2 * 2.2.1 2016-12-30 CRAN (R 3.3.2)
## graphics * 3.3.2 2016-10-31 local
## grDevices * 3.3.2 2016-10-31 local
## grid 3.3.2 2016-10-31 local
## gridExtra 2.3 2017-09-09 CRAN (R 3.3.2)
## gtable 0.2.0 2016-02-26 CRAN (R 3.3.0)
## highr 0.6 2016-05-09 CRAN (R 3.3.0)
## Hmisc * 4.0-3 2017-05-02 CRAN (R 3.3.2)
## htmlTable 1.9 2017-01-26 CRAN (R 3.3.2)
## htmltools 0.3.6 2017-04-28 CRAN (R 3.3.2)
## htmlwidgets 0.9 2017-07-10 CRAN (R 3.3.2)
## knitr * 1.17 2017-08-10 CRAN (R 3.3.2)
## lattice * 0.20-35 2017-03-25 CRAN (R 3.3.2)
## latticeExtra 0.6-28 2016-02-09 CRAN (R 3.3.0)
## lazyeval 0.2.0 2016-06-12 CRAN (R 3.3.0)
## magrittr 1.5 2014-11-22 CRAN (R 3.3.0)
## Matrix 1.2-11 2017-08-16 CRAN (R 3.3.2)
## memoise 1.1.0 2017-04-21 CRAN (R 3.3.2)
## methods * 3.3.2 2016-10-31 local
## munsell 0.4.3 2016-02-13 CRAN (R 3.3.0)
## nnet 7.3-12 2016-02-02 CRAN (R 3.3.2)
## plyr 1.8.4 2016-06-08 CRAN (R 3.3.0)
## R.methodsS3 1.7.1 2016-02-16 CRAN (R 3.3.0)
## R.oo 1.21.0 2016-11-01 CRAN (R 3.3.0)
## R.utils 2.5.0 2016-11-07 CRAN (R 3.3.0)
## RColorBrewer 1.1-2 2014-12-07 CRAN (R 3.3.0)
## Rcpp 0.12.13 2017-09-28 CRAN (R 3.3.2)
## rlang 0.1.2 2017-08-09 CRAN (R 3.3.2)
## rpart 4.1-11 2017-04-21 CRAN (R 3.3.2)
## scales 0.5.0 2017-08-24 CRAN (R 3.3.2)
## splines 3.3.2 2016-10-31 local
## stats * 3.3.2 2016-10-31 local
## stringi 1.1.5 2017-04-07 CRAN (R 3.3.2)
## stringr 1.2.0 2017-02-18 CRAN (R 3.3.2)
## survival * 2.41-3 2017-04-04 CRAN (R 3.3.2)
## tibble 1.3.4 2017-08-22 CRAN (R 3.3.2)
## tools 3.3.2 2016-10-31 local
## utils * 3.3.2 2016-10-31 local
## withr 2.0.0 2017-07-28 CRAN (R 3.3.2)
spun with: ezknitr::ezspin(file = “programs/02_study_overview_figure.R”, keep_md = FALSE, out_dir = “html_reports”, fig_dir = “figures”)