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PheVis
View on CRAN: Click
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Download and install PheVis package within the R console
Install from CRAN:
install.packages("PheVis")
Install from Github:
library("remotes")
install_github("cran/PheVis") Install by package version:
library("remotes")
install_version("PheVis", "1.0.4") Attach the package and use:
library("PheVis")
Maintained by
Thomas Ferte
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[Scholar Profile | Author Map]
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First Published: 2021-02-16
Latest Update: 2023-10-20
Description:
Using Electronic Health Record (EHR) is difficult because most of the time the true characteristic of the patient is not available. Instead we can retrieve the International Classification of Disease code related to the disease of interest or we can count the occurrence of the Unified Medical Language System. None of them is the true phenotype which needs chart review to identify. However chart review is time consuming and costly. 'PheVis' is an algorithm which is phenotyping (i.e identify a characteristic) at the visit level in an unsupervised fashion. It can be used for chronic or acute diseases. An example of how to use 'PheVis' is available in the vignette. Basically there are two functions that are to be used: `train_phevis()` which trains the algorithm and `test_phevis()` which get the predicted probabilities. The detailed method is described in preprint by Fert
How to cite:
Thomas Ferte (2021). PheVis: Automatic Phenotyping of Electronic Health Record at Visit Resolution. R package version 1.0.4, https://cran.r-project.org/web/packages/PheVis. Accessed 26 Jun. 2026.
Previous versions and publish date:
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imports, suggests or enhances
Complete documentation for PheVis
Functions, R codes and Examples using
the PheVis R package
Some associated functions: PheVis . boot_df . build_qantsur . build_quali . check_arg_test_phevis . check_arg_train_phevis . cum_lag . data_perf . data_phevis . expcorrectC . fct_surrogate_quanti . ggindividual_plot . matrix_exp_smooth . noising . norm_var . phenorm_longit_fit . phenorm_longit_simpl . pred_lme4model . pretty_cv.glmnet . roll_time_sum . rolling_var . safe_selection . sur_exp_smooth . test_phevis . train_phevis .
Some associated R codes: PheVis.R . RcppExports.R . boot_df.R . build_qantsur.R . build_quali.R . check_arg_test_phevis.R . check_arg_train_phevis.R . cum_lag.R . data_perf.R . data_phevis.R . fct_surrogate_quanti.R . ggindividual_plot.R . matrix_exp_smooth.R . noising.R . norm_var.R . phenorm_longit_fit.R . phenorm_longit_simpl.R . pred_lme4model.R . pretty_cv.glmnet.R . roll_time_sum.R . rolling_var.R . safe_selection.R . sur_exp_smooth.R . test_phevis.R . train_phevis.R . Full PheVis package functions and examples
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