An R package for chat completion and text annotation with both local LLMs and OpenAI models. Key features include:
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Versatile Model Access: Interact with either local LLMs (via Python/reticulate) or OpenAI models through a straightforward function.
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Multiple Annotator Support: Facilitate text annotation workflows with support for multiple annotators, including ensembling and majority voting methods.
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Batch and Parallel Processing: Handle multiple inputs simultaneously, leveraging local LLMs or speeding up tasks by utilizing multiple cores when working with OpenAI models.
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Consistent Output: Ensure uniform data frame outputs across model types.
Get the development version from GitHub with:
remotes::install_github("jaytimm/hollr")pmids <- puremoe::search_pubmed('("political ideology"[TiAb])',
use_pub_years = F) |>
puremoe::get_records(endpoint = 'pubmed_abstracts',
cores = 3,
sleep = 1) | pmid | year | articletitle | ab |
|---|---|---|---|
| 39374517 | 2024 | Racial Minorities Face Discrimination From Across the Political Spectrum When Seeking to Form Ties on Social Media: Evidence From a Field Experiment. | We conducted a preregistered field experiment examining racial discrimination in tie formation on social media. We randomly assigned research accounts … |
| 39340096 | 2024 | Messaging to Reduce Booster Hesitancy among the Fully Vaccinated. | Vaccine hesitancy was a serious problem in the United States throughout the COVID-19 pandemic, due in part to the reduction … |
| 39320049 | 2024 | Rural reticence to inform physicians of cannabis use. | Over 75% of Americans have legal access to medical cannabis, though physical access is not uniform and can be difficult … |
| 39222956 | 2024 | The prototypical UK blood donor, homophily and blood donation: Blood donors are like you, not me. | Homophily represents the extent to which people feel others are like them and encourages the uptake of activities they feel … |
| 39194099 | 2024 | The impact of conspiracy theories and vaccine knowledge on vaccination intention: a longitudinal study. | In this study, we analyzed associations between vaccination knowledge, vaccination intention, political ideology, and belief in conspiracy theories before and … |
| 39148747 | 2024 | Formative reasons for state-to-state influences on firearm acquisition in the U.S. | Firearm-related crimes and self-inflicted harms pose a significant threat to the safety and well-being of Americans. Investigation of firearm prevalence … |
## For the PubMed abstract provided below, provide a
## single sentence summary of the research findings
## in 30 words. Ensure that the summary is concise,
## starts with "Study results demonstrate," and
## highlights the key outcomes. Also, identify the
## country or countries where the study was
## conducted.
##
## Expected Output:
## {
## "country": "Country or countries where the study
## was conducted.",
## "summary": "Study results demonstrate ...
## (summary of the research findings in 30 words)."
## }
##
## Abstract:
prompt <- paste(p1, pmids$abstract, sep = '\n\n')class_task1 <- hollr::hollr(
model = 'gpt-4o-mini',
id = pmids$pmid[1:6],
user_message = prompt[1:6],
cores = 1,
annotators = 1,
max_attempts = 7,
force_json = T,
flatten_json = T
)| id | country | summary |
|---|---|---|
| 39374517 | United States | Study results demonstrate racial discrimination in social media tie formation, with individuals less likely to reciprocate ties with Black accounts compared to White ones, regardless of political orientation. |
| 39340096 | United States | Study results demonstrate that providing scientific explanations about mRNA booster safety and effectiveness significantly improved willingness to get boosted, trust in scientists, and perceptions across political ideology groups. |
| 39320049 | United States | Study results demonstrate that rural Pennsylvanians are less likely to disclose marijuana use to healthcare providers due to stigma, potentially impacting their health outcomes and care quality. |
| 39222956 | United Kingdom | Study results demonstrate current blood donors and MSM show higher homophily with the prototypical UK donor, while ethnic minorities and recipients exhibit lower homophily, influencing donation likelihood. |
| 39194099 | Brazil | Study results demonstrate that increased belief in vaccine conspiracy theories correlates with decreased vaccination intention and knowledge, highlighting the need for targeted health education in Brazil. |
| 39148747 | United States | Study results demonstrate that U.S. states’ firearm acquisition patterns co-evolve with crime rates and laws, indicating that stricter laws and lower homicides can reduce inter-state acquisition influences. |
class_task2 <- hollr::hollr(
model = 'gpt-4o-mini',
id = pmids$pmid[1:10],
user_message = prompt[1:10],
cores = 7,
annotators = 3,
max_attempts = 7,
force_json = T,
flatten_json = T
)# Create and activate a new conda environment with Python 3.9
conda create -n llm_base python=3.9 -y
conda activate llm_base
# Update all packages in the environment
conda update --all -y
# Install required packages with conda
conda install nmslib pandas numpy spacy -c conda-forge -y
conda install pytorch torchvision torchaudio pytorch-cuda=12.1 -c pytorch -c nvidia -y
# Install additional packages with pip
pip install transformers packaging ninja flash-attn --no-build-isolation accelerate protobuf auto-gptq \
"git+https://github.com/PanQiWei/[email protected]" optimum tiktoken sentencepiece# Set environment variables and use conda environment
Sys.setenv(RETICULATE_PYTHON = file.path(miniconda_path, "envs", env_name, "bin/python"))
reticulate::use_condaenv(condaenv = env_name, conda = file.path(miniconda_path, "bin/conda"))llm = 'meta-llama/Meta-Llama-3.1-8B-Instruct'batch_seq <- hollr::hollr(
model = llm,
id = pmids$pmid[1:10],
user_message = prompt[1:10],
annotators = 3,
#max_attempts = 7,
force_json = F,
flatten_json = F,
max_new_tokens = 75,
batch_size = 5
)