% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/deprecated.R
\name{deprecated-matrixCorr}
\alias{deprecated-matrixCorr}
\alias{bland_altman}
\alias{bland_altman_repeated}
\alias{biweight_mid_corr}
\alias{distance_corr}
\alias{partial_correlation}
\alias{ccc_lmm_reml}
\alias{ccc_pairwise_u_stat}
\title{Deprecated Compatibility Wrappers}
\usage{
bland_altman(
  group1,
  group2,
  two = 1.96,
  mode = 1L,
  conf_level = 0.95,
  n_threads = getOption("matrixCorr.threads", 1L),
  verbose = FALSE
)

bland_altman_repeated(
  data = NULL,
  response,
  subject,
  method,
  time,
  two = 1.96,
  conf_level = 0.95,
  n_threads = getOption("matrixCorr.threads", 1L),
  include_slope = FALSE,
  use_ar1 = FALSE,
  ar1_rho = NA_real_,
  max_iter = 200L,
  tol = 1e-06,
  verbose = FALSE
)

biweight_mid_corr(
  data,
  c_const = 9,
  max_p_outliers = 1,
  pearson_fallback = c("hybrid", "none", "all"),
  na_method = c("error", "pairwise", "complete"),
  mad_consistent = FALSE,
  w = NULL,
  sparse_threshold = NULL,
  n_threads = getOption("matrixCorr.threads", 1L),
  output = c("matrix", "sparse", "edge_list"),
  threshold = 0,
  diag = TRUE
)

distance_corr(data, na_method = c("error", "pairwise", "complete"), ...)

partial_correlation(
  data,
  method = c("oas", "ridge", "sample"),
  lambda = 0.001,
  return_cov_precision = FALSE,
  ci = FALSE,
  conf_level = 0.95,
  output = c("matrix", "sparse", "edge_list"),
  threshold = 0,
  diag = TRUE
)

ccc_lmm_reml(
  data,
  response,
  rind,
  method = NULL,
  time = NULL,
  interaction = FALSE,
  max_iter = 100,
  tol = 1e-06,
  Dmat = NULL,
  Dmat_type = c("time-avg", "typical-visit", "weighted-avg", "weighted-sq"),
  Dmat_weights = NULL,
  Dmat_rescale = TRUE,
  ci = FALSE,
  conf_level = 0.95,
  ci_mode = c("auto", "raw", "logit"),
  verbose = FALSE,
  digits = 4,
  use_message = TRUE,
  ar = c("none", "ar1"),
  ar_rho = NA_real_,
  slope = c("none", "subject", "method", "custom"),
  slope_var = NULL,
  slope_Z = NULL,
  drop_zero_cols = TRUE,
  vc_select = c("auto", "none"),
  vc_alpha = 0.05,
  vc_test_order = c("subj_time", "subj_method"),
  include_subj_method = NULL,
  include_subj_time = NULL,
  sb_zero_tol = 1e-10
)

ccc_pairwise_u_stat(
  data,
  response,
  method,
  subject,
  time = NULL,
  Dmat = NULL,
  delta = 1,
  ci = FALSE,
  conf_level = 0.95,
  n_threads = getOption("matrixCorr.threads", 1L),
  verbose = FALSE
)
}
\arguments{
\item{group1, group2}{Numeric vectors of equal length.}

\item{two}{Positive scalar; the multiple of the standard deviation used to
define the limits of agreement.}

\item{mode}{Integer; 1 uses \code{group1 - group2}, 2 uses \code{group2 - group1}.}

\item{conf_level}{Confidence level.}

\item{n_threads}{Integer number of OpenMP threads.}

\item{verbose}{Logical; print brief progress or diagnostic output.}

\item{data}{A \code{data.frame}, matrix, or repeated-measures dataset accepted by
the corresponding replacement function.}

\item{response}{Numeric response vector or column name, depending on the
target method.}

\item{subject}{Subject identifier or subject column name.}

\item{method}{Method label or method column name.}

\item{time}{Replicate/time index or time column name.}

\item{include_slope}{Logical; whether to estimate proportional bias.}

\item{use_ar1}{Logical; whether to use AR(1) within-subject correlation.}

\item{ar1_rho}{AR(1) parameter.}

\item{max_iter, tol}{EM control parameters.}

\item{c_const}{Positive numeric Tukey biweight tuning constant.}

\item{max_p_outliers}{Numeric in \verb{(0, 1]}; optional cap on the maximum
proportion of outliers on each side.}

\item{pearson_fallback}{Character fallback policy used by \code{bicor()}.}

\item{na_method}{Missing-data policy forwarded to the replacement function
when supported.}

\item{mad_consistent}{Logical; if \code{TRUE}, uses the consistency-corrected MAD.}

\item{w}{Optional vector of case weights.}

\item{sparse_threshold}{Optional threshold controlling sparse output.}

\item{output}{Output representation for the computed estimates.}

\item{threshold}{Non-negative absolute-value filter for non-matrix outputs.}

\item{diag}{Logical; whether to include diagonal entries in non-matrix outputs.}

\item{...}{Additional arguments forwarded to the replacement function when
supported.}

\item{lambda}{Numeric regularisation strength used by \code{pcorr()}.}

\item{return_cov_precision}{Logical; if \code{TRUE}, also return covariance and
precision matrices.}

\item{ci}{Logical; if \code{TRUE}, request confidence intervals when supported by
the replacement function.}

\item{rind}{Character; column identifying subjects, forwarded as \code{subject}
to \code{ccc_rm_reml()}.}

\item{interaction}{Logical; forwarded to \code{ccc_rm_reml()}.}

\item{Dmat}{Optional distance matrix forwarded to \code{ccc_rm_reml()}.}

\item{Dmat_type}{Character selector controlling how \code{Dmat} is constructed.}

\item{Dmat_weights}{Optional weights used when \code{Dmat_type} requires them.}

\item{Dmat_rescale}{Logical; whether to rescale \code{Dmat}.}

\item{ci_mode}{Character selector for the confidence-interval scale used by
\code{ccc_rm_reml()}.}

\item{digits}{Display precision forwarded to \code{ccc_rm_reml()}.}

\item{use_message}{Logical; whether the deprecated wrapper emits a lifecycle
message.}

\item{ar}{Character selector for the within-subject residual correlation
model.}

\item{ar_rho}{Numeric AR(1) parameter.}

\item{slope}{Character selector for the proportional-bias slope structure.}

\item{slope_var}{Optional covariance matrix for custom slopes.}

\item{slope_Z}{Optional design matrix for custom slopes.}

\item{drop_zero_cols}{Logical; whether zero-variance design columns are
dropped.}

\item{vc_select}{Character selector controlling variance-component
selection.}

\item{vc_alpha}{Significance level used in variance-component selection.}

\item{vc_test_order}{Character vector controlling the variance-component
test order.}

\item{include_subj_method}{Optional logical override for the
subject-by-method component.}

\item{include_subj_time}{Optional logical override for the subject-by-time
component.}

\item{sb_zero_tol}{Numerical tolerance used when stabilising the scale-bias
term.}

\item{delta}{Numeric power exponent for U-statistics distances.}
}
\description{
Temporary wrappers for functions renamed in \code{matrixCorr} 1.0.0. These
wrappers preserve the pre-1.0 entry points while warning that they will be
removed in 2.0.0.
}
\details{
Renamed functions:
\itemize{
\item \code{bland_altman()} -> \code{ba()}
\item \code{bland_altman_repeated()} -> \code{ba_rm()}
\item \code{biweight_mid_corr()} -> \code{bicor()}
\item \code{distance_corr()} -> \code{dcor()}
\item \code{partial_correlation()} -> \code{pcorr()}
\item \code{ccc_lmm_reml()} -> \code{ccc_rm_reml()}
\item \code{ccc_pairwise_u_stat()} -> \code{ccc_rm_ustat()}
}

The deprecated wrappers will be removed in \code{matrixCorr} 2.0.0.
}
