In CognitionOpenDataProject/CODreports: Build reproducibility reports for the Cognition Open Data (COD) project

Article ID: [Insert article ID number]

Pilot: [Insert name of pilot]

Co-pilot: Tom Hardwicke

Start date: [Insert start date - use US format]

End date: [Insert end date - use US format]

---

Methods summary:

[Write a brief summary of the methods underlying the target outcomes written in your own words]

---

Target outcomes:

[Insert the target outcomes identified in targetOutcomes.md]

---

[The chunk below sets up some formatting options for the R Markdown document]

knitr::opts_chunk$set(echo=TRUE, warning=FALSE, message=FALSE)

# prepare an empty report object, we will update this each time we run compareValues2()
reportObject <- data.frame("Article_ID" = NA, "valuesChecked" = 0, "eyeballs" = 0, "Total_df" = 0, "Total_p" = 0, "Total_mean" = 0, "Total_sd" = 0, "Total_se" = 0, "Total_ci" = 0, "Total_bf" = 0, "Total_t" = 0, "Total_F" = 0, "Total_es" = 0, "Total_median" = 0, "Total_irr" = 0, "Total_r" = 0, "Total_z" = 0, "Total_coeff" = 0, "Total_n" = 0, "Total_x2" = 0, "Total_other" = 0, "Insufficient_Information_Errors" = 0, "Decision_Errors" = 0, "Major_Numerical_Errors" = 0, "Minor_Numerical_Errors" = 0, "Major_df" = 0, "Major_p" = 0, "Major_mean" = 0, "Major_sd" = 0, "Major_se" = 0, "Major_ci" = 0, "Major_bf" = 0, "Major_t" = 0, "Major_F" = 0, "Major_es" = 0, "Major_median" = 0, "Major_irr" = 0, "Major_r" = 0, "Major_z" = 0, "Major_coeff" = 0, "Major_n" = 0, "Major_x2" = 0, "Major_other" = 0, "affectsConclusion" = NA, "error_typo" = 0, "error_specification" = 0, "error_analysis" = 0, "error_data" = 0, "error_unidentified" = 0, "Author_Assistance" = NA, "resolved_typo" = 0, "resolved_specification" = 0, "resolved_analysis" = 0, "resolved_data" = 0, "correctionSuggested" = NA, "correctionPublished" = NA)

Step 1: Load packages

[Some useful packages are being loaded below. You can add any additional ones you might need too.]

library(tidyverse) # for data munging
library(knitr) # for kable table formating
library(haven) # import and export 'SPSS', 'Stata' and 'SAS' Files
library(readxl) # import excel files
library(CODreports) # custom report functions

Step 2: Load data

Step 3: Tidy data

Step 4: Run analysis

Pre-processing

[you can remove this section if no pre-processing is required]

Descriptive statistics

Inferential statistics

Step 5: Conclusion

reportObject$Article_ID <- "articleID"
reportObject$affectsConclusion <- "yes, no, or unclear"
reportObject$error_typo <- 0
reportObject$error_specification <- 0
reportObject$error_analysis <- 0
reportObject$error_data <- 0
reportObject$error_unidentified <- 0
reportObject$Author_Assistance <- T or F
reportObject$resolved_typo <- 0
reportObject$resolved_specification <- 0
reportObject$resolved_analysis <- 0
reportObject$resolved_data <- 0
reportObject$correctionSuggested <- NA
reportObject$correctionPublished <- NA

# decide on final outcome
if(reportObject$Decision_Errors > 0 | reportObject$Major_Numerical_Errors > 0 | reportObject$Insufficient_Information_Errors > 0){
  reportObject$finalOutcome <- "Failure"
  if(reportObject$Author_Assistance == T){
    reportObject$finalOutcome <- "Failure despite author assistance"
  }
}else{
  reportObject$finalOutcome <- "Success"
  if(reportObject$Author_Assistance == T){
    reportObject$finalOutcome <- "Success with author assistance"
  }
}

# save the report object
filename <- paste0("reportObject_", reportObject$Article_ID,".csv")
write_csv(reportObject, filename)

[Please also include a brief text summary describing your findings. If this reproducibility check was a failure, you should note any suggestions as to what you think the likely cause(s) might be.]

[This function will output information about the package versions used in this report:]

devtools::session_info()

CognitionOpenDataProject/CODreports documentation built on May 6, 2019, 12:21 p.m.