check_arg_test_phevis

Function to check arguments passed to test_phevis()

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 Ferté et al. (2020) <doi:10.1101/2020.06.15.20131458>.

Thomas Ferte

PheVis

Automatic Phenotyping of Electronic Health Record at Visit
Resolution

Boris P. Hejblum

check_arg_test_phevis function

<dl><dt>train_param</dt>
<dd>Parameters for the model training (variables used, main ICD and CUIS, half_life, gold standard, omega). Usually obtained from train_phevis() function.</dd>
<dt>df_test</dt>
<dd>The dataframe on which to make the prediction.</dd>
<dt>surparam</dt>
<dd>The parameters used to compute the surrogate. Usually obtained by train_phevis() function.</dd>
<dt>model</dt>
<dd>The random intercept logistic regression. Usually obtained by train_phevis() function.</dd>
<dt>START_DATE</dt>
<dd>Column name of the time column. The time column should be numeric</dd>
<dt>PATIENT_NUM</dt>
<dd>Column name of the patient id column.</dd>
<dt>ENCOUNTER_NUM</dt>
<dd>Column name of the encounter id column.</dd></dl>

Arguments

check_arg_test_phevis — check_arg_test_phevis

<dl>

<dt>train_param</dt>
<dd>Parameters for the model training (variables used, main ICD and CUIS, half_life, gold standard, omega). Usually obtained from train_phevis() function.</dd>


<dt>df_test</dt>
<dd>The dataframe on which to make the prediction.</dd>


<dt>surparam</dt>
<dd>The parameters used to compute the surrogate. Usually obtained by train_phevis() function.</dd>


<dt>model</dt>
<dd>The random intercept logistic regression. Usually obtained by train_phevis() function.</dd>


<dt>START_DATE</dt>
<dd>Column name of the time column. The time column should be numeric</dd>


<dt>PATIENT_NUM</dt>
<dd>Column name of the patient id column.</dd>


<dt>ENCOUNTER_NUM</dt>
<dd>Column name of the encounter id column.</dd>

</dl>

check_arg_test_phevis: check_arg_test_phevis

Description

Usage

Value

Arguments