Running examples in 'PheCAP-Ex.R' failed
The error most likely occurred in:

> ### Name: PheCAP-package
> ### Title: High-Throughput Phenotyping with EHR using a Common Automated
> ###   Pipeline
> ### Aliases: PheCAP-package PheCAP
> ### Keywords: package
> 
> ### ** Examples
> 
> # Simulate an EHR dataset
> size <- 2000
> latent <- rgamma(size, 0.3)
> latent2 <- rgamma(size, 0.3)
> ehr_data <- data.frame(
+   ICD1 = rpois(size, 7 * (rgamma(size, 0.2) + latent) / 0.5),
+   ICD2 = rpois(size, 6 * (rgamma(size, 0.8) + latent) / 1.1),
+   ICD3 = rpois(size, 1 * rgamma(size, 0.5 + latent2) / 0.5),
+   ICD4 = rpois(size, 2 * rgamma(size, 0.5) / 0.5),
+   NLP1 = rpois(size, 8 * (rgamma(size, 0.2) + latent) / 0.6),
+   NLP2 = rpois(size, 2 * (rgamma(size, 1.1) + latent) / 1.5),
+   NLP3 = rpois(size, 5 * (rgamma(size, 0.1) + latent) / 0.5),
+   NLP4 = rpois(size, 11 * rgamma(size, 1.9 + latent) / 1.9),
+   NLP5 = rpois(size, 3 * rgamma(size, 0.5 + latent2) / 0.5),
+   NLP6 = rpois(size, 2 * rgamma(size, 0.5) / 0.5),
+   NLP7 = rpois(size, 1 * rgamma(size, 0.5) / 0.5),
+   HU = rpois(size, 30 * rgamma(size, 0.1) / 0.1),
+   label = NA)
> ii <- sample.int(size, 400)
> ehr_data[ii, "label"] <- with(
+   ehr_data[ii, ], rbinom(400, 1, plogis(
+     -5 + 1.5 * log1p(ICD1) + log1p(NLP1) +
+       0.8 * log1p(NLP3) - 0.5 * log1p(HU))))
> 
> # Define features and labels used for phenotyping.
> data <- PhecapData(ehr_data, "HU", "label", validation = 0.4)
> data
PheCAP Data
Feature: 2000 observations of 12 variables
Label: 131 yes, 269 no, 1600 missing
Size of training samples: 240
Size of validation samples: 160
> 
> # Specify the surrogate used for
> # surrogate-assisted feature extraction (SAFE).
> # The typical way is to specify a main ICD code, a main NLP CUI,
> # as well as their combination.
> # The default lower_cutoff is 1, and the default upper_cutoff is 10.
> # In some cases one may want to define surrogate through lab test.
> # Feel free to change the cutoffs based on domain knowledge.
> surrogates <- list(
+   PhecapSurrogate(
+     variable_names = "ICD1",
+     lower_cutoff = 1, upper_cutoff = 10),
+   PhecapSurrogate(
+     variable_names = "NLP1",
+     lower_cutoff = 1, upper_cutoff = 10))
> 
> # Run surrogate-assisted feature extraction (SAFE)
> # and show result.
> feature_selected <- phecap_run_feature_extraction(
+   data, surrogates, num_subsamples = 50, subsample_size = 200)
Error in glmnet(x, y, weights = subject_weight, family = "binomial", thresh = 5e-07,  : 
  argument "subject_weight" is missing, with no default
Calls: phecap_run_feature_extraction ... t -> sapply -> lapply -> FUN -> fit_lasso_bic -> glmnet
Execution halted