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aggrecat

Methods for mathematically aggregating expert judgements

https://github.com/metamelb-replicats/aggrecat

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aggregation elicitation expert
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Methods for mathematically aggregating expert judgements

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aggregation elicitation expert
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README.md

README

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aggreCAT: methods for mathematically aggregating expert judgements

Problem Context

The use of structured elicitation to inform decision making has grown dramatically across fields like ecology and environmental science over the last decade, as researchers and managers are faced with the need to act rapidly in the face of uncertainty and absent, uninformative data. However, judgements from multiple experts must be aggregated into a single estimate or distribution, and empirical evidence suggests that mathematical aggregation provides more reliable estimates than behavioural consensus models.

Unfortunately, there is a dearth of accessible tools for implementing more complex aggregation methods other than linear averages, which are arguably the most commonly used aggregation method, but may not be the best approach for yielding robust estimates. The lack of readily available aggregation methods severely limits users who may want to utilise alternative aggregation methods more suitable for the task at hand, but who do not have the time or technical capacity to implement.

The availability of methods implemented in R is even more limited, with the most fully-fledged package expert being archived from CRAN in 2022, the SHELF package implementing only a single aggregation method (weighted linear pool / arithmetic mean), and the opera package aggregating non-point-estimate judgements only (time-series predictions).

An archived version of expert is still available, however, the package provides only three aggregation methods, and stipulates a structured elicitation protocol that ‘calibrates’ experts through the use of seed questions, which are required as additional input data to the aggregation functions.

The aggreCAT Package

The aggreCAT package aims to fill this void, implementing 22 unique state-of-the-art and readily deployable methods for mathematically aggregating expert judgements, described in Hanea et al. (2021).

Aggregation methods comprise unweighted linear combinations of judgements, weighted linear combinations of judgements where weights are proxies of forecasting performance constructed from characteristics of participants and/or their judgements, and, and Bayesian methods that use expert judgement to update uninformative and informative priors.

Aside from prescribing elicited judgements be derived from any structured elicitation method that does not force behavioural consensus, the aggreCAT package does not force users into adhering to one particular approach to structured expert elicitation. However, some methods are more prescriptive about input data types and the elicitation method used to derive them than others. At minimum, a single point-estimate is required for aggregation, and for some methods, repliCATS IDEA protocol, is required to generate the necessary data as inputs to the aggregation function. The IDEA (Investigate, Discuss, Estimate, Aggregate) protocol generates robust estimates by leveraging the wisdom-of-the-crowd, and is more onerous than collecting only single point-estimates, but generates more robust and reliable estimates.

Installation

You can install:

  • the latest development version of aggreCAT package:

r install.packages("devtools") devtools::install_github("metamelb-repliCATS/aggreCAT")

  • the most recent official version of aggreCAT from CRAN:

    • TBC! We will upload to CRAN once our manuscript (Gould et al. in prep.) has been submitted.

Then load the package:

r library(aggreCAT)

Getting Started with aggreCAT

Below we provide a brief summary of the package, for a detailed overview, please consult the manuscript (Gould et al. in prep.).

Core Functionality and Design

Aggregation Functions

Aggregation methods are grouped based on their mathematical properties into eight ‘wrapper’ functions, denoted by the suffix WAgg, the abbreviation of “weighted aggregation”: LinearWAgg(), AverageWAgg(), BayesianWAgg(), IntervalWAgg(), ShiftingWAgg(), ReasoningWAgg(), DistributionWAgg(), and ExtremisationWAgg().

All wrapper functions adhere to the following basic argument structure:

``` r args(AverageWAgg)

> function (expert_judgements, type = "ArMean", name = NULL, placeholder = FALSE,

> percenttoggle = FALSE, round2_filter = TRUE)

> NULL

```

  • expert judgements are contained a dataframe parsed to expert_judgements,
  • the type argument specifies the specific flavour of the wrapper aggregation function to be executed on the expert_judgements data, with the available aggregation methods detailed in each wrapper function’s help page, e.g. ?AverageWAgg,
  • name allows a user-specified name with which to label the method in the results,
  • toggling the placeholder argument to TRUE returns ‘placeholder’ values, set to $0.65$,
  • toggling percent_toggle to TRUE facilitates aggregating quantities rather than probabilities.

Each aggregation wrapper function returns a dataframe / tibble of results, with one row or observation per unique judgement task.

Elicitation Data

aggreCAT includes datasets with judgements about the likely replicability of research claims, collected by the repliCATS project team as a pilot study for the DARPA SCORE program. Data were elicited using a modified version of the IDEA protocol (Hemming et al. 2017, Figure 1), whereby participants Investigate, Discuss, Estimate, and finally Aggregate their judgements using methods from the aggreCAT package (Fraser et al. 2021). Following the IDEA protocol, best estimates, and upper and lower bounds are elicited from each participant, over two rounds. The judgement data is contained in the object data_ratings, described at ?data_ratings.

Figure 1: the repliCATS IDEA protocol was used to elicit judgements about the likely replicability of research claims, a pilot version of this dataset is included in the aggreCAT package

A minimal working example with AverageWAgg()

Figure 2: Mathematically aggregating a small subset of expert judgements for the claim 28, using the unweighted arithmetic mean. The aggreCAT wrapper function AverageWAgg() is used on this dataset, with the type argument set to the default ArMean.

Below we demonstrate how to use the most simple commonly implemented aggregation method ArMean, which takes the arithmetic mean of participant Best Estimates. We first use a small subset of 5 participants for a single claim, 28, which is represented visually in Figure 1.

``` r library(dplyr) data(data_ratings) set.seed(1234)

participantsubset <- dataratings %>% distinct(username) %>% samplen(5) %>% mutate(participant_name = paste("participant", rep(1:n())))

singleclaim <- dataratings %>% filter(paperid == "28") %>% rightjoin(participantsubset, by = "username")

AverageWAgg(expertjudgements = singleclaim, type = "ArMean")

>

> ── AverageWAgg: ArMean ─────────────────────────────────────────────────────────

>

> ── Pre-Processing Options ──

>

> ℹ Round Filter: TRUE

> ℹ Three Point Filter: TRUE

> ℹ Percent Toggle: FALSE

> # A tibble: 1 × 4

> method paperid cs nexperts

>

> 1 ArMean 28 70.8 5

```

Often times during expert elicitation multiple quantities or measures are put to experts to provide judgements for, and so we might want to batch aggregation over more than a single judgement at a time (this time called without explicitly specifying arguments):

``` r data_ratings %>% AverageWAgg()

>

> ── AverageWAgg: ArMean ─────────────────────────────────────────────────────────

>

> ── Pre-Processing Options ──

>

> ℹ Round Filter: TRUE

> ℹ Three Point Filter: TRUE

> ℹ Percent Toggle: FALSE

> # A tibble: 25 × 4

> method paperid cs nexperts

>

> 1 ArMean 100 70.6 25

> 2 ArMean 102 30.8 25

> 3 ArMean 103 62.5 25

> 4 ArMean 104 47.1 25

> 5 ArMean 106 36.5 25

> 6 ArMean 108 71.8 25

> 7 ArMean 109 72.5 25

> 8 ArMean 116 62.6 25

> 9 ArMean 118 54.8 25

> 10 ArMean 133 59.9 25

> # … with 15 more rows

```

And other times, we might want to trial different aggregation methods over those judgements, examining how their mathematical properties might change the results, for example:

r purrr::map_dfr(.x = list(AverageWAgg, IntervalWAgg, ShiftingWAgg), .f = ~ .x(data_ratings))

Attribution

This research was conducted as a part of the repliCATS project, funded by the DARPA SCORE programme

The aggreCAT package is the culmination of the hard work and persistence of a small team of researchers. Use of this package shall be appropriately attributed and cited accordingly:

``` r citation("aggreCAT")

>

> To cite package 'aggreCAT' in publications use:

>

> Willcox A, Gray C, Gould E, Wilkinson D, Hanea A, Wintle B, E. O'Dea

> R (????). aggreCAT: Mathematically Aggregating Expert Judgments. R

> package version 0.0.0.9002,

> https://replicats.research.unimelb.edu.au/.

>

> A BibTeX entry for LaTeX users is

>

> @Manual{,

> title = {aggreCAT: Mathematically Aggregating Expert Judgments},

> author = {Aaron Willcox and Charles T. Gray and Elliot Gould and David Wilkinson and Anca Hanea and Bonnie Wintle and Rose {E. O'Dea}},

> note = {R package version 0.0.0.9002},

> url = {https://replicats.research.unimelb.edu.au/},

> }

```

References

Fraser, Hannah, Martin Bush, Bonnie Wintle, Fallon Mody, Eden T Smith, Anca Hanea, Elliot Gould, et al. 2021. “Predicting Reliability Through Structured Expert Elicitation with repliCATS (Collaborative Assessments for Trustworthy Science).” MetaArXiv. .
Gould, Elliot, Charles T Gray, Aaron Willcox, Rose E O’Dea, Rebecca Groenewegen, and David P Wilkinson. in prep. “aggreCAT: An r Package for Mathematically Aggregating Expert Judgments.” MetaArXiv. .
Hanea, Anca, David P Wilkinson, Marissa McBride, Aidan Lyon, Don van Ravenzwaaij, Felix Singleton Thorn, Charles T Gray, et al. 2021. “Mathematically Aggregating Experts’ Predictions of Possible Futures.” *PLoS ONE* 16 (9). https://doi.org/.
Hemming, Victoria, Mark A. Burgman, Anca M. Hanea, Marissa F. McBride, and Bonnie C. Wintle. 2017. “A Practical Guide to Structured Expert Elicitation Using the IDEA Protocol.” Edited by Barbara Anderson. *Methods in Ecology and Evolution* 9 (1): 169–80. .

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  "codeRepository": "https://github.com/metamelb-repliCATS/aggreCAT",
  "readme": "https://github.com/metamelb-repliCATS/aggreCAT/blob/master/README.md",
  "fileSize": "203638.969KB",
  "contIntegration": "https://travis-ci.com/softloud/aggreCAT"
}

GitHub Events

Total
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  • Push event: 13
  • Pull request event: 7
  • Create event: 6
Last Year
  • Watch event: 1
  • Delete event: 3
  • Push event: 13
  • Pull request event: 7
  • Create event: 6

Dependencies

DESCRIPTION cran
  • R >= 2.10 depends
  • GoFKernel * imports
  • R2jags * imports
  • VGAM * imports
  • cli * imports
  • coda * imports
  • crayon * imports
  • dplyr * imports
  • ggplot2 * imports
  • insight * imports
  • magrittr * imports
  • mathjaxr * imports
  • precrec * imports
  • purrr * imports
  • rfUtilities * imports
  • stringr * imports
  • tibble * imports
  • tidyr * imports
  • BiocStyle * suggests
  • DescTools * suggests
  • R.rsp * suggests
  • covr * suggests
  • forcats * suggests
  • ggforce * suggests
  • ggpubr * suggests
  • ggridges * suggests
  • gt * suggests
  • gtExtras * suggests
  • here * suggests
  • janitor * suggests
  • knitr * suggests
  • lubridate * suggests
  • nlme * suggests
  • pointblank * suggests
  • qualtRics * suggests
  • readr * suggests
  • readxl * suggests
  • rjags * suggests
  • rmarkdown * suggests
  • stats * suggests
  • testthat >= 2.1.0 suggests
  • tidybayes * suggests
  • tidyverse * suggests
  • usethis * suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v3 composite
.github/workflows/render-quarto-README.yml actions
  • actions/checkout v3 composite
  • quarto-dev/quarto-actions/render v2 composite
  • quarto-dev/quarto-actions/setup v2 composite
.github/workflows/update-citation-cff.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite