tabscreen_gpt.tools: Title and abstract screening with GPT API models using...

In AIscreenR: AI Screening Tools in R for Systematic Reviewing

Title and abstract screening with GPT API models using function calls via the tools argument

Description

This function supports the conduct of title and abstract screening with GPT API models in R. Specifically, it allows the user to draw on GPT-3.5, GPT-4, GPT-4o, GPT-4o-mini, and fine-tuned models. The function allows to run title and abstract screening across multiple prompts and with repeated questions to check for consistency across answers. All of which can be done in parallel. The function draws on the newly developed function calling which is called via the tools argument in the request body. This is the main different between tabscreen_gpt.tools() and tabscreen_gpt.original(). Function calls ensure more reliable and consistent responses to ones requests. See Vembye et al. (2024) for guidance on how adequately to conduct title and abstract screening with GPT models.

Usage

tabscreen_gpt.tools(data, prompt, studyid, title, abstract,
   model = "gpt-4o-mini", role = "user", tools = NULL, tool_choice = NULL, top_p = 1,
   time_info = TRUE, token_info = TRUE, api_key = get_api_key(), max_tries = 16,
   max_seconds = NULL, is_transient = gpt_is_transient, backoff = NULL,
   after = NULL, rpm = 10000, reps = 1, seed_par = NULL, progress = TRUE,
   decision_description = FALSE, messages = TRUE, incl_cutoff_upper = NULL,
   incl_cutoff_lower = NULL, force = FALSE, fine_tuned = FALSE, ...)

tabscreen_gpt(data, prompt, studyid, title, abstract,
   model = "gpt-4o-mini", role = "user", tools = NULL, tool_choice = NULL, top_p = 1,
   time_info = TRUE, token_info = TRUE, api_key = get_api_key(), max_tries = 16,
   max_seconds = NULL, is_transient = gpt_is_transient, backoff = NULL,
   after = NULL, rpm = 10000, reps = 1, seed_par = NULL, progress = TRUE,
   decision_description = FALSE, messages = TRUE, incl_cutoff_upper = NULL,
   incl_cutoff_lower = NULL, force = FALSE, fine_tuned = FALSE, ...)

Arguments

data	Dataset containing the titles and abstracts.
prompt	Prompt(s) to be added before the title and abstract.
studyid	Unique Study ID. If missing, this is generated automatically.
title	Name of the variable containing the title information.
abstract	Name of variable containing the abstract information.
model	Character string with the name of the completion model. Can take multiple models. Default is the latest "gpt-4o-mini". Find available model at https://platform.openai.com/docs/models/model-endpoint-compatibility.
role	Character string indicating the role of the user. Default is "user".
tools	This argument allows this user to apply customized functions. See https://platform.openai.com/docs/api-reference/chat/create#chat-create-tools. Default is NULL. If not specified the default function calls from AIscreenR are used.
tool_choice	If a customized function is provided this argument 'controls which (if any) tool is called by the model' (OpenAI). Default is NULL. If set to NULL when using a customized function, the default is "auto". See https://platform.openai.com/docs/api-reference/chat/create#chat-create-tool_choice.
top_p	'An alternative to sampling with temperature, called nucleus sampling, where the model considers the results of the tokens with top_p probability mass. So 0.1 means only the tokens comprising the top 10% probability mass are considered. We generally recommend altering this or temperature but not both.' (OpenAI). Default is 1. Find documentation at https://platform.openai.com/docs/api-reference/chat/create#chat/create-top_p.
time_info	Logical indicating whether the run time of each request/question should be included in the data. Default is TRUE.
token_info	Logical indicating whether token information should be included in the output data. Default is TRUE. When TRUE, the output object will include price information of the conducted screening.
api_key	Numerical value with your personal API key. Default setting draws on the get_api_key() to retrieve the API key from the R environment, so that the key is not compromised. The API key can be added to the R environment via set_api_key() or by using usethis::edit_r_environ(). In the .Renviron file, write CHATGPT_KEY=INSERT_YOUR_KEY_HERE. After entering the API key, close and save the .Renviron file and restart RStudio (ctrl + shift + F10). Alternatively, one can use httr2::secret_make_key(), httr2::secret_encrypt(), and httr2::secret_decrypt() to scramble and decrypt the API key.
max_tries, max_seconds	'Cap the maximum number of attempts with max_tries or the total elapsed time from the first request with max_seconds. If neither option is supplied (the default), httr2::req_perform() will not retry' (Wickham, 2023). The default of max_tries is 16.
is_transient	'A predicate function that takes a single argument (the response) and returns TRUE or FALSE specifying whether or not the response represents a transient error' (Wickham, 2023). This function runs automatically in the AIscreenR but can be customized by the user if necessary.
backoff	'A function that takes a single argument (the number of failed attempts so far) and returns the number of seconds to wait' (Wickham, 2023).
after	'A function that takes a single argument (the response) and returns either a number of seconds to wait or NULL, which indicates that a precise wait time is not available that the backoff strategy should be used instead' (Wickham, 2023).
rpm	Numerical value indicating the number of requests per minute (rpm) available for the specified model. Find more information at https://platform.openai.com/docs/guides/rate-limits/what-are-the-rate-limits-for-our-api. Alternatively, use rate_limits_per_minute().
reps	Numerical value indicating the number of times the same question should be send to the server. This can be useful to test consistency between answers, and/or can be used to make inclusion judgments based on how many times a study has been included across a the given number of screenings. Default is 1 but when using gpt-3.5-turbo models or gpt-4o-mini, we recommend setting this value to 10 to catch model uncertainty.
seed_par	Numerical value for a seed to ensure that proper, parallel-safe random numbers are produced.
progress	Logical indicating whether a progress line should be shown when running the title and abstract screening in parallel. Default is TRUE.
decision_description	Logical indicating whether a detailed description should follow the decision made by GPT. Default is FALSE. When conducting large-scale screening, we generally recommend not using this feature as it will substantially increase the cost of the screening. We generally recommend using it when encountering disagreements between GPT and human decisions.
messages	Logical indicating whether to print messages embedded in the function. Default is TRUE.
incl_cutoff_upper	Numerical value indicating the probability threshold for which a studies should be included. ONLY relevant when the same questions is requested multiple times (i.e., when any reps > 1). Default is 0.5, indicating that titles and abstracts should only be included if GPT has included the study more than 50 percent of the times.
incl_cutoff_lower	Numerical value indicating the probability threshold above which studies should be check by a human. ONLY relevant when the same questions is requested multiple times (i.e., when any reps > 1). Default is 0.4, meaning that if you ask GPT the same questions 10 times and it includes the title and abstract 4 times, we suggest that the study should be check by a human.
force	Logical argument indicating whether to force the function to use more than 10 iterations for gpt-3.5 models and more than 1 iteration for gpt-4 models other than gpt-4o-mini. This argument is developed to avoid the conduct of wrong and extreme sized screening. Default is FALSE.
fine_tuned	Logical indicating whether a fine-tuned model is used. Default is FALSE.
...	Further argument to pass to the request body. See https://platform.openai.com/docs/api-reference/chat/create.

Value

An object of class 'gpt'. The object is a list containing the following datasets and components:

answer_data	dataset of class 'gpt_tbl' with all individual answers.
price_dollar	numerical value indicating the total price (in USD) of the screening.
price_data	dataset with prices across all gpt models used for screening.
run_date	string indicating the date when the screening was ran. In some frameworks, time details are considered important to report (see e.g., Thomas et al., 2024).
...	some additional attributed values/components, including an attributed list with the arguments used in the function. These are used in screen_errors() to re-screen transient errors.

If the same question is requested multiple times, the object will also contain the following dataset with results aggregated across the iterated requests/questions.

answer_data_aggregated

dataset of class 'gpt_agg_tbl' with the summarized, probabilistic inclusion decision for each title and abstract across multiple repeated questions.

Note

The answer_data data contains the following mandatory variables:

studyid	integer	indicating the study ID of the reference.
title	character	indicating the title of the reference.
abstract	character	indicating the abstract of the reference.
promptid	integer	indicating the prompt ID.
prompt	character	indicating the prompt.
model	character	indicating the specific gpt-model used.
iterations	numeric	indicating the number of times the same question has been sent to OpenAI's GPT API models.
question	character	indicating the final question sent to OpenAI's GPT API models.
top_p	numeric	indicating the applied top_p.
decision_gpt	character	indicating the raw gpt decision - either "1", "0", "1.1" for inclusion, exclusion, or uncertainty, respectively.
detailed_description	character	indicating detailed description of the given decision made by OpenAI's GPT API models. ONLY included if the detailed function calling function is used. See 'Examples' below for how to use this function.
decision_binary	integer	indicating the binary gpt decision, that is 1 for inclusion and 0 for exclusion. 1.1 decision are coded equal to 1 in this case.
prompt_tokens	integer	indicating the number of prompt tokens sent to the server for the given request.
completion_tokens	integer	indicating the number of completion tokens sent to the server for the given request.
submodel	character	indicating the exact (sub)model used for screening.
run_time	numeric	indicating the time it took to obtain a response from the server for the given request.
run_date	character	indicating the date the given response was received.
n	integer	indicating iteration ID. Is only different from 1, when reps > 1.

If any requests failed, the gpt object contains an error dataset (error_data) containing the same variables as answer_data but with failed request references only.

When the same question is requested multiple times, the answer_data_aggregated data contains the following mandatory variables:

studyid	integer	indicating the study ID of the reference.
title	character	indicating the title of the reference.
abstract	character	indicating the abstract of the reference.
promptid	integer	indicating the prompt ID.
prompt	character	indicating the prompt.
model	character	indicating the specific gpt-model used.
question	character	indicating the final question sent to OpenAI's GPT API models.
top_p	numeric	indicating the applied top_p.
incl_p	numeric	indicating the probability of inclusion calculated across multiple repeated responses on the same title and abstract.
final_decision_gpt	character	indicating the final decision reached by gpt - either 'Include', 'Exclude', or 'Check'.
final_decision_gpt_num	integer	indicating the final numeric decision reached by gpt - either 1 or 0.
longest_answer	character	indicating the longest gpt response obtained across multiple repeated responses on the same title and abstract. Only included when decision_description = TRUE. See 'Examples' below for how to use this function.
reps	integer	indicating the number of times the same question has been sent to OpenAI's GPT API models.
n_mis_answers	integer	indicating the number of missing responses.
submodel	character	indicating the exact (sub)model used for screening.

The price_data data contains the following variables:

prompt	character	if multiple prompts are used this variable indicates the given prompt-id.
model	character	the specific gpt model used.
iterations	integer	indicating the number of times the same question was requested.
input_price_dollar	integer	price for all prompt/input tokens for the correspondent gpt-model.
output_price_dollar	integer	price for all completion/output tokens for the correspondent gpt-model.
total_price_dollar	integer	total price for all tokens for the correspondent gpt-model.

Find current token pricing at https://openai.com/pricing or model_prizes.

References

Vembye, M. H., Christensen, J., Mølgaard, A. B., & Schytt, F. L. W. (2024) GPT API Models Can Function as Highly Reliable Second Screeners of Titles and Abstracts in Systematic Reviews: A Proof of Concept and Common Guidelines https://osf.io/preprints/osf/yrhzm

Thomas, J. et al. (2024). Responsible AI in Evidence SynthEsis (RAISE): guidance and recommendations. https://osf.io/cn7x4

Wickham H (2023). httr2: Perform HTTP Requests and Process the Responses. https://httr2.r-lib.org, https://github.com/r-lib/httr2.

Examples

## Not run: 

library(future)

set_api_key()

prompt <- "Is this study about a Functional Family Therapy (FFT) intervention?"

plan(multisession)

tabscreen_gpt(
  data = filges2015_dat[1:2,],
  prompt = prompt,
  studyid = studyid,
  title = title,
  abstract = abstract
  )

plan(sequential)

 # Get detailed descriptions of the gpt decisions.

 plan(multisession)

 tabscreen_gpt(
   data = filges2015_dat[1:2,],
   prompt = prompt,
   studyid = studyid,
   title = title,
   abstract = abstract,
   decision_description = TRUE
 )

plan(sequential)


## End(Not run)

AIscreenR documentation built on April 3, 2025, 7:11 p.m.