Title and abstract screening with Gemini API models using function calls

This function supports title and abstract screening using API models in R. Specifically, it allows users to draw on Gemini's API completion models, including fine-tuned versions. The function enables title and abstract screening across multiple prompts, with repeated questions to assess consistency across responses. All of this can be performed in parallel. The function utilizes function calling, which is invoked via the tools argument in the request body. See Vembye, Christensen, Mølgaard, and Schytt. (2025) for guidance on how adequately to conduct title and abstract screening with GPT models.

Usage

tabscreen_gemini(data, prompt, studyid, title, abstract,
  api_url = "https://generativelanguage.googleapis.com", model = "gemini-3.1-flash-lite",
  role = "user", tools = NULL, tool_choice = NULL, top_p = 1,
  time_info = TRUE, token_info = TRUE, api_key = get_api_key_gemini(), 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, custom_model = FALSE,
  reasoning_effort = "medium", overinclusive = TRUE, ...)

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.
api_url: Character string with the Gemini API base URL. Default is "https://generativelanguage.googleapis.com". The v1beta path and model endpoint will be appended automatically.
model: Character string with the name of the Gemini completion model. Can take multiple models. Default is "gemini-3.1-flash-lite". Find available models at https://ai.google.dev/gemini-api/docs/models.
role: Character string indicating the role of the user. Default is "user" (required for Gemini API).
tools: This argument allows users to apply customized function declarations. See https://ai.google.dev/gemini-api/docs/function-calling. Default is NULL. If not specified, the default function calls from AIscreenR (Gemini format) are used.
tool_choice: If a customized function is provided, this argument controls which mode Gemini uses for function calling ("auto", "any", "none"). Default is NULL. If set to NULL when using a customized function, the default is "auto". See https://ai.google.dev/gemini-api/docs/function-calling.
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. Default is 1.
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. Rate limits are not available through the Gemini API and must be manually checked via your Google AI Studio dashboard at https://aistudio.google.com/app/apikey under the rate limits section. Default is 10000 rpm, but adjust this based on your actual quota.
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.
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 0.1, indicating that titles and abstracts should only be included if GPT has included the study more than 10 percent of the times (e.g., 1 out of 10 screenings). This has been shown by Vembye et al. (2025) to work well with cheaper models.
incl_cutoff_lower: Numerical value indicating the probability threshold above which studies should be checked by a human. ONLY relevant when the same questions is requested multiple times (i.e., when any reps > 1) and incl_cutoff_upper > 0.1. Records with inclusion probabilities between incl_cutoff_lower and incl_cutoff_upper will be flagged for human checking. Default is NULL, which means that no studies will be flagged for human checking.
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.
custom_model: Logical indicating whether a fine-tuned or custom model is used. Default is FALSE.
reasoning_effort: Character string indicating the level of reasoning effort required for the task. Default is "low". Can take the values "minimal", "low", "medium", and "high". For Gemini 3.1 Pro, "minimal" is not supported. Be aware that 2.5 models don't support thinkingLevel/reasoning_effort, but use thinkingBudget instead. Therefore, reasoning_effort is mapped to budget values when using 2.5 models. See https://ai.google.dev/gemini-api/docs/thinking#rest for more information.
overinclusive: Logical indicating whether uncertain decisions ("1.1") should be allowed in the default function calling setup. Default is TRUE, which means that the default function calling setup will allow for uncertain decisions. If FALSE, the default function calling setup will not allow for uncertain decisions and will only return binary decisions (i.e., "1" or "0"). This argument only affects the default function calling setup.
...: Further argument to pass to the request body. See https://ai.google.dev/gemini-api/docs/text-generation#rest.

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 Gemini model used.
iterations	`numeric`	indicating the number of times the same question has been sent to Gemini API.
question	`character`	indicating the final question sent to Gemini API.
top_p	`numeric`	indicating the applied top_p.
decision_gpt	`character`	indicating the raw Gemini decision - either `"1", "0", "1.1"` for inclusion, exclusion, or uncertainty, respectively.
detailed_description	`character`	indicating detailed description of the decision made by Gemini. ONLY included if the detailed function calling is used.
decision_binary	`integer`	indicating the binary decision (1 = include, 0 = exclude).
prompt_tokens	`integer`	indicating the number of prompt tokens used.
completion_tokens	`integer`	indicating the number of completion tokens used.
submodel	`character`	indicating the exact model version used for screening.
run_time	`numeric`	indicating the time it took to obtain a response from the server.
run_date	`character`	indicating the date the response was received.
n	`integer`	indicating iteration ID (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 Gemini's 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 Gemini's 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://ai.google.dev/gemini-api/docs/pricing or model_prizes.

References

Vembye, M. H., Christensen, J., Mølgaard, A. B., & Schytt, F. L. W. (2025). Generative Pretrained Transformer Models Can Function as Highly Reliable Second Screeners of Titles and Abstracts in Systematic Reviews: A Proof of Concept and Common Guidelines. Psychological Methods. doi:10.1037/met0000769

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

if (FALSE) { # \dontrun{

library(future)

set_api_key()

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

plan(multisession)

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

plan(sequential)

} # }