Nothing
## ----knitrsetup, include = FALSE, eval=TRUE-----------------------------------
# Set environment variables to limit thread usage while building the vignette
Sys.setenv(
OMP_NUM_THREADS = "1",
MKL_NUM_THREADS = "1",
OPENBLAS_NUM_THREADS = "1",
VECLIB_MAXIMUM_THREADS = "1"
)
library(reticulate)
# this vignette requires python 3.7 or newer to run
eval_is <- tryCatch({
numeric_version(py_config()$version) >= "3.7" && py_numpy_available() &&
py_module_available("scipy") && py_module_available("sklearn")
}, error = function(e) FALSE)
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
eval = eval_is
)
## ----pkg and data loading, eval=TRUE------------------------------------------
library(CytOpT)
data("HIPC_Stanford")
## ----Stanford_1228_1A_head, echo=FALSE----------------------------------------
knitr::kable(head(HIPC_Stanford_1228_1A))
## ----goldstandard-------------------------------------------------------------
gold_standard_manual_prop <- c(table(HIPC_Stanford_1369_1A_labels) /
length(HIPC_Stanford_1369_1A_labels))
## ----optimization-------------------------------------------------------------
set.seed(123)
res <- CytOpT(X_s = HIPC_Stanford_1228_1A, X_t = HIPC_Stanford_1369_1A,
Lab_source = HIPC_Stanford_1228_1A_labels,
theta_true = gold_standard_manual_prop,
method="minmax", monitoring = TRUE)
## ----results------------------------------------------------------------------
summary(res)
## ----plots, fig.width = 7, fig.asp = .8, fig.retina=2-------------------------
plot(res)
## ----BA, fig.width = 7, fig.asp = .6, fig.retina = 2--------------------------
Bland_Altman(res$proportions)
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