Custom Reports

Andreas Brandmaier

2025-07-23

Here, I demonstrate how custom reports about the success of reproduction of a document can be generated within a markdown document. To illustrate, we first create three chunks using the code chunk type reproducibleR of which the first two reproduce just fine while not all variables of the third chunk reproduce. Finally, we generate custom reports.

Styling of chunk-level reports

The following code defines a new format for the chunk-level reports based on HTML/CSS. We draw a thin dashed line as border and fill the box with a light gray color. Last, we change the title.

options(reproducibleRchunks.templates = list(
html="<div style='border: 1px dashed gray;
padding: 15px 15px 5px 15px;
background-color: #F7F7F7;'>
<small><b>Reproducibility Checks</b><br>

${content}</small></div><br><br>"))

Next, we define some reproducibleR chunks of which some contain reproducible and some non-reproducible parts.

Cereals

In this first example we work with the UScereal data set from the MASS package. The chunk loads the data, runs an analysis of variance on calorie content by manufacturer and prints the summary of the model.

cereal_data <- MASS::UScereal
model <- anova(lm(calories~mfr, cereal_data))
summary(model)
#>        Df           Sum Sq          Mean Sq        F value         Pr(>F)      
#>  Min.   : 5.0   Min.   : 25769   Min.   :3789   Min.   :1.36   Min.   :0.2523  
#>  1st Qu.:18.5   1st Qu.: 75208   1st Qu.:4130   1st Qu.:1.36   1st Qu.:0.2523  
#>  Median :32.0   Median :124648   Median :4471   Median :1.36   Median :0.2523  
#>  Mean   :32.0   Mean   :124648   Mean   :4471   Mean   :1.36   Mean   :0.2523  
#>  3rd Qu.:45.5   3rd Qu.:174087   3rd Qu.:4812   3rd Qu.:1.36   3rd Qu.:0.2523  
#>  Max.   :59.0   Max.   :223527   Max.   :5154   Max.   :1.36   Max.   :0.2523  
#>                                                 NA's   :1      NA's   :1

Reproducibility Checks

  • ✅cereal_data: REPRODUCTION SUCCESSFUL

  • ✅model: REPRODUCTION SUCCESSFUL



Linear Model

The next chunk demonstrates a simple linear regression. We use the Animals data from MASS to predict brain weight from body weight and print the model summary.

animals <- MASS::Animals
model2 <- lm(brain~body, animals)
summary(model2)
#> 
#> Call:
#> lm(formula = brain ~ body, data = animals)
#> 
#> Residuals:
#>    Min     1Q Median     3Q    Max 
#> -576.0 -554.1 -438.1 -156.3 5138.5 
#> 
#> Coefficients:
#>               Estimate Std. Error t value Pr(>|t|)  
#> (Intercept)  5.764e+02  2.659e+02   2.168   0.0395 *
#> body        -4.326e-04  1.589e-02  -0.027   0.9785  
#> ---
#> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
#> 
#> Residual standard error: 1360 on 26 degrees of freedom
#> Multiple R-squared:  2.853e-05,  Adjusted R-squared:  -0.03843 
#> F-statistic: 0.0007417 on 1 and 26 DF,  p-value: 0.9785

Reproducibility Checks

  • ✅animals: REPRODUCTION SUCCESSFUL

  • ✅model2: REPRODUCTION SUCCESSFUL



Random Numbers

The following chunk contains some fixed numbers and numbers that are randomly drawn without setting a seed. Because the random numbers change from run to run, the chunk mixes reproducible and non-reproducible behaviour and serves as an example of how such situations are reported.

fixed_numbers <- 1:10
numbers <- rnorm(10, mean = 0, sd = 1)

Reproducibility Checks

  • ❌.Random.seed: REPRODUCTION FAILED Fingerprints are not identical.

  • ✅fixed_numbers: REPRODUCTION SUCCESSFUL

  • ❌numbers: REPRODUCTION FAILED Fingerprints are not identical.



Report

After the chunks above have been executed, reproducibleRchunks stores metadata about all created variables. The following code demonstrates how to extract and summarise this information. We start by counting the total number of variables that did not reproduce correctly:

num_errors <- reproducibleRchunks::get_num_reproducibility_errors()
 ifelse(num_errors > 0,"There were some results that did not reproduce!","The entire document reproduced succesfully")
#> [1] "There were some results that did not reproduce!"

The second function get_reproducibility_summary() generates a table that can either be used to inspect details about the reproduction status of each variable in each chunk, or to compute further summaries from. First, we obtain the table:

repro_table <- reproducibleRchunks::get_reproducibility_summary()
knitr::kable(repro_table)
Chunk Variable Success
cereal cereal_data TRUE
cereal model TRUE
lm animals TRUE
lm model2 TRUE
random .Random.seed FALSE
random fixed_numbers TRUE
random numbers FALSE

Next, we summarise the table by chunk and create a bar plot that visualises the proportion of successful reproductions.

if (nrow(repro_table) > 0) {
  prop_success <- aggregate(Success ~ Chunk, data = repro_table, FUN = mean)
  
  barplot(prop_success$Success,
          names.arg = prop_success$Chunk,
          ylim = c(0, 1),
          ylab = "Relative Proportion",
          xlab = "Chunk",
          main = "Proportion of Successful Reproductions per Chunk")
} else {
  print("No reproducibility information available yet.")
}