Repository files navigation

Describe and understand the world through data.

Data collection and data comparison are the foundations of scientific research.Mathematics provides the abstract framework to describe patterns we observe in nature andStatistics provides theframework to quantify the uncertainty of these patterns. In statistics, natural patternsare described in form of probability distributions which either follow a fixed pattern (parametric distributions) or more dynamic patterns (non-parametric distributions).

Thephilentropy package implements fundamental distance and similarity measures to quantify distances between probability density functions as well as traditional information theory measures. In this regard, it aims to provide a framework for comparingnatural patterns in a statistical notation.

This project is born out of my passion for statistics and I hope that it will be useful tothe people who share it with me.

# install philentropy version 0.9.0 from CRANinstall.packages("philentropy")

I am developingphilentropy in my spare time and would be very grateful if you would consider citing the following paper in casephilentropy was useful for your own research. I plan on maintaining and extending thephilentropy functionality and usability in the next years and require citations to back up these efforts. Many thanks in advance :)

HG Drost, (2018).Philentropy: Information Theory and Distance Quantification with R.Journal of Open Source Software, 3(26), 765.https://doi.org/10.21105/joss.00765

• Introduction to the philentropy package
• Distance and Similarity Measures implemented in philentropy
• Information Theory Metrics implemented in philentropy
• Comparing many probability density functions

library(philentropy)# retrieve available distance metricsphilentropy::getDistMethods()

 [1] "euclidean"         "manhattan"         "minkowski"         [4] "chebyshev"         "sorensen"          "gower"             [7] "soergel"           "kulczynski_d"      "canberra"         [10] "lorentzian"        "intersection"      "non-intersection" [13] "wavehedges"        "czekanowski"       "motyka"           [16] "kulczynski_s"      "tanimoto"          "ruzicka"          [19] "inner_product"     "harmonic_mean"     "cosine"           [22] "hassebrook"        "jaccard"           "dice"             [25] "fidelity"          "bhattacharyya"     "hellinger"        [28] "matusita"          "squared_chord"     "squared_euclidean"[31] "pearson"           "neyman"            "squared_chi"      [34] "prob_symm"         "divergence"        "clark"            [37] "additive_symm"     "kullback-leibler"  "jeffreys"         [40] "k_divergence"      "topsoe"            "jensen-shannon"   [43] "jensen_difference" "taneja"            "kumar-johnson"    [46] "avg"

# define a probability density function PP<-1:10/sum(1:10)# define a probability density function QQ<-20:29/sum(20:29)# combine P and Q as matrix objectx<- rbind(P,Q)# compute the jensen-shannon distance between# probability density functions P and Qphilentropy::distance(x,method="jensen-shannon")

jensen-shannon using unit 'log'.jensen-shannon     0.02628933

Alternatively, users can also retrieve values from all available distance/similarity metricsusingphilentropy::dist.diversity():

philentropy::dist.diversity(x,p=2,unit="log2")

        euclidean         manhattan        0.12807130        0.35250464         minkowski         chebyshev        0.12807130        0.06345083          sorensen             gower        0.17625232        0.03525046           soergel      kulczynski_d        0.29968454        0.42792793          canberra        lorentzian        2.09927095        0.49712136      intersection  non-intersection        0.82374768        0.17625232        wavehedges       czekanowski        3.16657887        0.17625232            motyka      kulczynski_s        0.58812616        2.33684211          tanimoto           ruzicka        0.29968454        0.70031546     inner_product     harmonic_mean        0.10612245        0.94948528            cosine        hassebrook        0.93427641        0.86613103           jaccard              dice        0.13386897        0.07173611          fidelity     bhattacharyya        0.97312397        0.03930448         hellinger          matusita        0.32787819        0.23184489     squared_chord squared_euclidean        0.05375205        0.01640226           pearson            neyman        0.16814418        0.36742465       squared_chi         prob_symm        0.10102943        0.20205886        divergence             clark        1.49843905        0.86557468     additive_symm  kullback-leibler        0.53556883        0.13926288          jeffreys      k_divergence        0.31761069        0.04216273            topsoe    jensen-shannon        0.07585498        0.03792749 jensen_difference            taneja        0.03792749        0.04147518     kumar-johnson               avg        0.62779644        0.20797774

# install.packages("devtools")# install the current version of philentropy on your systemlibrary(devtools)install_github("HajkD/philentropy",build_vignettes=TRUE,dependencies=TRUE)

The current status of the package as well as a detailed history of the functionality of each version ofphilentropy can be found in theNEWS section.

• distance() : Implements 46 fundamental probability distance (or similarity) measures
• getDistMethods() : Get available method names for 'distance'
• dist.diversity() : Distance Diversity between Probability Density Functions
• estimate.probability() : Estimate Probability Vectors From Count Vectors

• H() : Shannon's Entropy H(X)
• JE() : Joint-Entropy H(X,Y)
• CE() : Conditional-Entropy H(X | Y)
• MI() : Shannon's Mutual Information I(X,Y)
• KL() : Kullback–Leibler Divergence
• JSD() : Jensen-Shannon Divergence
• gJSD() : Generalized Jensen-Shannon Divergence

• A transcriptomic hourglass in brown algae JS Lotharukpong, M Zheng, R Luthringer et al. -Nature, 2024

• Annelid functional genomics reveal the origins of bilaterian life cycles FM Martín-Zamora, Y Liang, K Guynes et al.-Nature, 2023

• An atlas of gene regulatory elements in adult mouse cerebrum YE Li, S Preissl, X Hou, Z Zhang, K Zhang et al.-Nature, 2021

• Convergent somatic mutations in metabolism genes in chronic liver disease S Ng, F Rouhani, S Brunner, N Brzozowska et al.Nature, 2021

• Antigen dominance hierarchies shape TCF1+ progenitor CD8 T cell phenotypes in tumors ML Burger, AM Cruz, GE Crossland et al. -Cell, 2021

• High-content single-cell combinatorial indexing R Mulqueen et al. -Nature Biotechnology, 2021

• A comparative atlas of single-cell chromatin accessibility in the human brainYE Li, S Preissl, M Miller, ND Johnson, Z Wang et al. -Science, 2023

• Extinction at the end-Cretaceous and the origin of modern Neotropical rainforests MR Carvalho, C Jaramillo et al. -Science, 2021

• sciCSR infers B cell state transition and predicts class-switch recombination dynamics using single-cell transcriptomic dataJCF Ng, G Montamat Garcia, AT Stewart et al. -Nature Methods, 2024

• HERMES: a molecular-formula-oriented method to target the metabolomeR Giné, J Capellades, JM Badia et al. -Nature Methods, 2021

• Epithelial zonation along the mouse and human small intestine defines five discrete metabolic domainsRK Zwick, P Kasparek, B Palikuqi, et al. -Nature Cell Biology, 2024

• The genetic architecture of temperature adaptation is shaped by population ancestry and not by selection regime KA Otte, V Nolte, F Mallard et al. -Genome Biology, 2021

• The Tug1 lncRNA locus is essential for male fertility JP Lewandowski et al. -Genome Biology, 2020

• Decoding the gene regulatory network of endosperm differentiation in maizeY Yuan, Q Huo, Z Zhang, Q Wang, J Wang, et al. -Nature Communications, 2024

• A full-body transcription factor expression atlas with completely resolved cell identities in C. elegansY Li, S Chen, W Liu, D Zhao, Y Gao, S Hu, H Liu, Y Li… -Nature Communications, 2024

• Comprehensive mapping and modelling of the rice regulome landscape unveils the regulatory architecture underlying complex traits T Zhu, C Xia, R Yu, X Zhou, X Xu, L Wang et al. -Nature Communications, 2024

• Transcriptional vulnerabilities of striatal neurons in human and rodent models of Huntington's disease A Matsushima, SS Pineda, JR Crittenden et al. -Nature Communications, 2023

• Resolving the structure of phage–bacteria interactions in the context of natural diversity KM Kauffman, WK Chang, JM Brown et al. -Nature Communications, 2022

• Gut microbiome-mediated metabolism effects on immunity in rural and urban African populationsM Stražar, GS Temba, H Vlamakis et al. -Nature Communications, 2021

• Aging, inflammation and DNA damage in the somatic testicular niche with idiopathic germ cell aplasia M Alfano, AS Tascini, F Pederzoli et al. -Nature Communications, 2021

• Single cell census of human kidney organoids shows reproducibility and diminished off-target cells after transplantation A Subramanian et al. -Nature Communications, 2019

• A single-cell multi-omic atlas spanning the adult rhesus macaque brainKL Chiou, X Huang, MO Bohlen et al. -Science Advances, 2023

• Different languages, similar encoding efficiency: Comparable information rates across the human communicative nicheC Coupé, YM Oh, D Dediu, F Pellegrino -Science Advances, 2019

• Single-cell deletion analyses show control of pro–T cell developmental speed and pathways by Tcf7, Spi1, Gata3, Bcl11a, Erg, and Bcl11b W Zhou, F Gao, M Romero-Wolf, S Jo, EV Rothenberg -Science Immunology, 2022

• Large-scale iterated singing experiments reveal oral transmission mechanisms underlying music evolutionM Anglada-Tort, PMC Harrison, H Lee, N Jacoby -Current Biology, 2023

• Detecting and diagnosing prior and likelihood sensitivity with power-scalingN Kallioinen, T Paananen, PC Bürkner, A Vehtari -Statistics and Computing, 2024

• SLAPSHOT reveals rapid dynamics of extracellularly exposed proteome in response to calcium-activated plasma membrane phospholipid scrambling ST Tuomivaara, CF Teo, YN Jan, AP Wiita et al. -Communications Biology, 2024

• TAS-Seq is a robust and sensitive amplification method for bead-based scRNA-seq S Shichino, S Ueha, S Hashimoto, T Ogawa et al. -Communications biology, 2022

• Mapping hormone-regulated cell-cell interaction networks in the human breast at single-cell resolutionLM Murrow, RJ Weber, JA Caruso et al. -Cell Systems, 2022

• Gene module reconstruction identifies cellular differentiation processes and the regulatory logic of specialized secretion in zebrafish Y Wang, J Liu, LY Du, JL Wyss, JA Farrell, AF Schier -Developmental Cell, 2024

• The temporal progression of lung immune remodeling during breast cancer metastasis CS McGinnis, Z Miao, D Superville, W Yao, et al. -Cancer Cell, 2024

• Large-scale chromatin reorganization reactivates placenta-specific genes that drive cellular aging Z Liu, Q Ji, J Ren, P Yan, Z Wu, S Wang, L Sun, Z Wang et al. -Developmental Cell, 2022

• Direct epitranscriptomic regulation of mammalian translation initiation through N4-acetylcytidine D Arango, D Sturgill, R Yang, T Kanai, P Bauer et al. -Molecular Cell, 2022

• Spotless, a reproducible pipeline for benchmarking cell type deconvolution in spatial transcriptomics C Sang-Aram, R Browaeys, R Seurinck, Y Saeys -eLife, 2024

• Loss of adaptive capacity in asthmatic patients revealed by biomarker fluctuation dynamics after rhinovirus challenge A Sinha et al. -eLife, 2019

• Sex and hatching order modulate the association between MHC‐II diversity and fitness in early‐life stages of a wild seabirdM Pineaux et al -Molecular Ecology, 2020

• BELMM: Bayesian model selection and random walk smoothing in time-series clusteringO Sarala, T Pyhäjärvi, MJ Sillanpää -Bioinformatics, 2023

• Cellsig plug-in enhances CIBERSORTx signature selection for multi-dataset transcriptomes with sparse multilevel modellingMA Al Kamran Khan, J Wu, S Yuhan et al. -Bioinformatics, 2023

• Neutrality in plant–herbivore interactions VS Pan, WC Wetzel -Proceedings of the Royal Society B, 2024

• How the Choice of Distance Measure Influences the Detection of Prior-Data ConflictK Lek, R Van De Schoot -Entropy, 2019

• Differential variation analysis enables detection of tumor heterogeneity using single-cell RNA-sequencing dataEF Davis-Marcisak, TD Sherman et al. -Cancer research, 2019

• Multi-Omics Investigation of Innate Navitoclax Resistance in Triple-Negative Breast Cancer Cells M Marczyk et al. -Cancers, 2020

• Impact of Gut Microbiome on Hypertensive Patients with Low-Salt Intake: Shika Study Results S Nagase et al. -Frontiers in Medicine, 2020

• Tumor-associated neutrophils upregulate PANoptosis to foster an immunosuppressive microenvironment of non-small cell lung cancerQ Hu, R Wang, J Zhang, Q Xue, B Ding -Cancer Immunology, Immunotherapy, 2023

• Spatial and Temporal Relationships Between Atrophy and Hypometabolism in Behavioral-Variant Frontotemporal Dementia J Stocks, E Gibson, K Popuri, MF Beg et al. -Alzheimer Disease & Associated Disorders, 2024

• Unveiling Dynamic Changes and Regulatory Mechanisms of T Cell Subsets in Sepsis Pathogenesis C Jiang, J Chen, T Sun, J Xu, H Zhu, J Chen -ImmunoTargets and Therapy, 2024

• Integrated analysis reveals NLRC4 as a potential biomarker in sepsis pathogenesis C Jiang, J Chen, J Xu, C Chen, H Zhu, Y Xu, H Zhao et al. -Genes & Immunity, 2024

• Temporal composition of the cervicovaginal microbiome associates with hrHPV infection outcomes in a longitudinal study MA Molina, WPJ Leenders, MA Huynen, WJG Melchers et al. -BMC Infectious Diseases, 2024

• PlantFUNCO: Integrative functional genomics database reveals clues into duplicates divergence evolution V Roces, S Guerrero, A Álvarez, J Pascual, M Meijón -Molecular Biology and Evolution, 2024

• Cross-tissue human fibroblast atlas reveals myofibroblast subtypes with distinct roles in immune modulation Y Gao, J Li, W Cheng, T Diao, H Liu, Y Bo, C Liu et al. -Cancer Cell, 2024

• Enhancing Immunotherapy Response Prediction in Metastatic Lung Adenocarcinoma: Leveraging Shallow and Deep Learning with CT-Based Radiomics C Masson-Grehaigne, M Lafon, J Palussière, L Leroy et al. -Cancers, 2024

• A general framework for implementing distances for categorical variables M van de Velden, AI D'Enza, A Markos, C Cavicchia -Pattern Recognition, 2024

• Early transcriptional similarities between two distinct neural lineages during ascidian embryogenesis RR Copley, J Buttin, MJ Arguel, G Williaume et al. -Developmental Biology, 2024

• The power of visualizing distributional differences: formal graphical n-sample tests K Konstantinou, T Mrkvička, M Myllymäki -Computational Statistics, 2024

• cisDynet: An integrated platform for modeling gene‐regulatory dynamics and networksT Zhu, X Zhou, Y You, L Wang, Z He, D Chen -iMeta, 2023

• Children's social networks in developmental psychology: A network approach to capture and describe early social environmentsN Burke, N Brezack, A Woodward -Frontiers in psychology, 2022

• Whole Genome Sequencing and Morphological Trait-Based Evaluation of UPOV Option 2 for DUS Testing in RiceH Liu, D Rao, T Guo, SS Gangurde, Y Hong, et al. -Frontiers in Genetics, 2022

• Combined TCR Repertoire Profiles and Blood Cell Phenotypes Predict Melanoma Patient Response to Personalized Neoantigen Therapy plus Anti-PD-1 A Poran et al. -Cell Reports Medicine, 2020

• Identification of a glioma functional network from gene fitness data using machine learning C Xiang, X Liu, D Zhou, Y Zhou, X Wang, F Chen -Journal of Cellular and Molecular Medicine, 2022

• Whole genome assemblies of Zophobas morio and Tenebrio molitorS Kaur, SA Stinson, GC diCenzo -G3: Genes, Genomes, Genetics, 2023

• Prediction of New Risk Genes and Potential Drugs for Rheumatoid Arthritis from Multiomics Data AM Birga, L Ren, H Luo, Y Zhang, J Huang -Computational and Mathematical Methods in Medicine, 2022

• Phenotyping of acute and persistent COVID-19 features in the outpatient setting: exploratory analysis of an international cross-sectional online survey S Sahanic, P Tymoszuk, D Ausserhofer et al. -medRxiv, 2021

• A two-part evaluation approach for measuring the usability and user experience of an Augmented Reality-based assistance system to support the temporal coordination of spatially dispersed teams L Thomaschewski, B Weyers, A Kluge -Cognitive Systems Research, 2021

• SEDE-GPS: socio-economic data enrichment based on GPS informationT Sperlea, S Füser, J Boenigk, D Heider -BMC bioinformatics, 2018

• Longitudinal analysis on the ecological dynamics of the cervicovaginal microbiome in hrHPV infectionMA Molina, WJG Melchers, et al. -Computational and structural biotechnology, 2023

• Spatial and molecular anatomy of germ layers in the gastrulating primate embryo G Cui, S Feng, Y Yan, L Wang, X He, X Li, et al. -bioRxiv, 2022

• Evacuees and Migrants Exhibit Different Migration Systems after the Great East Japan Earthquake and TsunamiM Hauer, S Holloway, T Oda – 2019

• Robust comparison of similarity measures in analogy based software effort estimationP Phannachitta -11th International Conference on Software, 2017

• RUNIMC - An R-based package for imaging mass cytometry data analysis and pipeline validation L Dolcetti, PR Barber, G Weitsman, S Thavarajet al. -bioRxiv, 2021

• Expression variation analysis for tumor heterogeneity in single-cell RNA-sequencing dataEF Davis-Marcisak, P Orugunta et al. -BioRxiv, 2018

• Concept acquisition and improved in-database similarity analysis for medical dataI Wiese, N Sarna, L Wiese, A Tashkandi, U Sax -Distributed and Parallel Databases, 2019

• Dynamics of Vaginal and Rectal Microbiota over Several Menstrual Cycles in Female Cynomolgus MacaquesMT Nugeyre, N Tchitchek, C Adapen et al. -Frontiers in Cellular and Infection Microbiology, 2019

• Inferring the quasipotential landscape of microbial ecosystems with topological data analysisWK Chang, L Kelly -BioRxiv, 2019

• Shifts in the nasal microbiota of swine in response to different dosing regimens of oxytetracycline administrationKT Mou, HK Allen, DP Alt, J Trachsel et al. -Veterinary microbiology, 2019

• The Patchy Distribution of Restriction–Modification System Genes and the Conservation of Orphan Methyltransferases in HalobacteriaMS Fullmer, M Ouellette, AS Louyakis et al. -Genes, 2019

• Genetic differentiation and intrinsic genomic features explain variation in recombination hotspots among cocoa tree populationsEJ Schwarzkopf, JC Motamayor, OE Cornejo -BioRxiv, 2019

• Metastable regimes and tipping points of biochemical networks with potential applications in precision medicineSS Samal, J Krishnan, AH Esfahani et al. -Reasoning for Systems Biology and Medicine, 2019

• Genome‐wide characterization and developmental expression profiling of long non‐coding RNAs in Sogatella furciferaZX Chang, OE Ajayi, DY Guo, QF Wu -Insect science, 2019

• Development of a simulation system for modeling the stock market to study its characteristicsP Mariya – 2018

• The Tug1 Locus is Essential for Male FertilityJP Lewandowski, G Dumbović, AR Watson, T Hwang et al. -BioRxiv, 2019

• Microbiotyping the sinonasal microbiomeA Bassiouni, S Paramasivan, A Shiffer et al. -BioRxiv, 2019

• Critical search: A procedure for guided reading in large-scale textual corporaJ Guldi -Journal of Cultural Analytics, 2018

• A Bibliography of Publications about the R, S, and S-Plus Statistics Programming LanguagesNHF Beebe – 2019

• Improved state change estimation in dynamic functional connectivity using hidden semi-Markov modelsH Shappell, BS Caffo, JJ Pekar, MA Lindquist -NeuroImage, 2019

• A Smart Recommender Based on Hybrid Learning Methods for Personal Well-Being ServicesRM Nouh, HH Lee, WJ Lee, JD Lee -Sensors, 2019

• Cognitive Structural AccuracyV Frenz – 2019

• Kidney organoid reproducibility across multiple human iPSC lines and diminished off target cells after transplantation revealed by single cell transcriptomicsA Subramanian, EH Sidhom, M Emani et al. -BioRxiv, 2019

• Multi-classifier majority voting analyses in provenance studies on iron artefactsG Żabiński et al. -Journal of Archaeological Science, 2020

• Identifying inhibitors of epithelial–mesenchymal plasticity using a network topology-based approachK Hari et al. -NPJ systems biology and applications, 2020

• Genetic differentiation and intrinsic genomic features explain variation in recombination hotspots among cocoa tree populationsEJ Schwarzkopf et al. -BMC Genomics, 2020

• Enhancing Card Sorting Dendrograms through the Holistic Analysis of Distance Methods and Linkage Criteria. JA Macías -Journal of Usability Studies, 2021

• Pattern-based identification and mapping of landscape types using multi-thematic data J Nowosad, TF Stepinski -International Journal of Geographical Information, 2021

• Motif Analysis in k-mer Networks: An Approach towards Understanding SARS-CoV-2 Geographical ShiftsS Biswas, S Saha, S Bandyopadhyay, M Bhattacharyya -bioRxiv, 2020

• Motif: an open-source R tool for pattern-based spatial analysis J Nowosad -Landscape Ecology, 2021

• New effective spectral matching measures for hyperspectral data analysis C Kumar, S Chatterjee, T Oommen, A Guha -International Journal of Remote Sensing, 2021

• Innovative activity of Polish enterprises–a strategic aspect. The similarity of NACE divisions E Bielińska-Dusza, M Hamerska -Journal of Entrepreneurship, Management and innovation, 2021

• Multi-classifier majority voting analyses in provenance studies on iron artefacts G Żabiński, J Gramacki et al.-Journal of Archaeological Science, 2020

• Unraveling the record of a tropical continental Cretaceous-Paleogene boundary in northern Colombia, South America F de la Parra, C Jaramillo, P Kaskes et al. -Journal of South American Earth Sciences, 2022

• A roadmap to reconstructing muscle architecture from CT dataJ Katzke, P Puchenkov, H Stark, EP Economo -Integrative Organismal Biology, 2022

• Pandemonium: a clustering tool to partition parameter space—application to the B anomalies U Laa, G Valencia -The European Physical Journal Plus, 2022

• Identification of a glioma functional network from gene fitness data using machine learning C Xiang, X Liu, D Zhou, Y Zhou, X Wang, F Chen -Journal of Cellular and Molecular Medicine, 2022

• Cross compatibility in intraspecific and interspecific hybridization in yam (Dioscorea spp.) JM Mondo, PA Agre, A Edemodu et al. -Scientific reports, 2022

• A Modular and Expandable Ecosystem for Metabolomics Data Annotation in R J Rainer, A Vicini, L Salzer, J Stanstrup et al. -Metabolites, 2022

• Single-Cell Transcriptome Integration Analysis Reveals the Correlation Between Mesenchymal Stromal Cells and Fibroblasts C Fan, M Liao, L Xie, L Huang, S Lv, S Cai et al. -Frontiers in genetics, 2022

• Phenotypic regionalization of the vertebral column in the thorny skate Amblyraja radiata: Stability and variation F Berio, Y Bayle, C Riley, O Larouche, R Cloutier -Journal of Anatomy, 2022

• Community assembly during vegetation succession after metal mining is driven by multiple processes with temporal variation T Li, H Yang, X Yang, Z Guo, D Fu, C Liu, S Li et al. -Ecology and evolution, 2022

• Integrative Organismal Biology J Katzke, P Puchenkov, H Stark,EP Economo - 2022

• Optimizing use of US Ex-PVP inbred lines for enhancing agronomic performance of tropical Striga resistant maize inbred lines ARS Maazou, M Gedil, VO Adetimirin et al. -BMC Plant Biology, 2022

I would be very happy to learn more about potential improvements of the concepts and functionsprovided in this package.

Furthermore, in case you find some bugs or need additional (more flexible) functionality of partsof this package, please let me know:

https://github.com/drostlab/philentropy/issues

or find me ontwitter: HajkDrost