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R: Calculate design vector for the lsmeans
...the lsmeans Description Calculates the design vector as required to generate the lsmean and standard error. ls_design_equal calculates it by applying an equal weight per covariate combination whilst...
/CRAN/refmans/rbmi/html/ls_design.html
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R: Auxillary functions for computing lsmeans, contrasts etc
...lsmeans, contrasts etc Description Auxillary functions for computing lsmeans, contrasts etc. Usage get_xlevels(obj) ## Default S3 method: get_xlevels(obj) ## S3 method for class 'mer' get_xlevels(obj)...
/CRAN/refmans/doBy/html/linest-get.html
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R: Groupwise Statistics, LSmeans, Linear Estimates, Utilities
...LSmeans, Linear Estimates, Utilities Documentation for package ‘doBy’ version 4.6.20 DESCRIPTION file. User guides, package vignettes and other documentation. Package NEWS. Help Pages A B C D E F...
/CRAN/refmans/doBy/html/00Index.html
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R: Extract Least Square Means from a GEE Model
...Extract Least Square Means from a GEE Model Usage lsmeans(object, conf_level = 0.95, weights = "proportional", ...) ## S3 method for class 'tern_gee_logistic' lsmeans(object, conf_level = 0.95...
/CRAN/refmans/tern.gee/html/lsmeans.html
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R: Least-squares means
lsmeans-package {lsmeans} R Documentation Least-squares means Description This package provides methods for obtaining so-called least-squares means for factor combinations in a variety of fitted linear...
/CRAN/refmans/lsmeans/html/lsmeans-package.html
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R: Least Square Means
...lsmeans(model, ..., .weights = c("proportional", "equal")) Arguments model A model created by lm. ... Fixes specific variables to specific values i.e. trt = 1 or age = 50. The name of the argument...
/CRAN/refmans/rbmi/html/lsmeans.html
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R: Perform t-Tests for Linear Contrasts on LS Means
...lsmeans {VCA} R Documentation Perform t-Tests for Linear Contrasts on LS Means Description Perform custom hypothesis tests on Least Squares Means (LS Means) of fixed effect. Usage test.lsmeans( obj, L...
/CRAN/refmans/VCA/html/test.lsmeans.html
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R: Average daily gain of 65 steers for 3 lines, 9 sires.
harvey.lsmeans {agridat} R Documentation Average daily gain of 65 steers for 3 lines, 9 sires. Description Average daily gain of 65 steers for 3 lines, 9 sires. Usage data("harvey.lsmeans") Format...
/CRAN/refmans/agridat/html/harvey.lsmeans.html
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R: Least Squares Means of Fixed Effects
lsmeans {VCA} R Documentation Least Squares Means of Fixed Effects Description Computes Least Squares Means (LS Means) of fixed effects for fitted mixed models of class 'VCA'. Usage lsmeans( obj, var...
/CRAN/refmans/VCA/html/lsmeans.html
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R: Plot LS means for MMRM
...summarizes adjusted lsmeans and standard error, as well as conducts comparisons between groups' adjusted lsmeans, where the first level of the group is the reference level. Usage g_mmrm_lsmeans...
/CRAN/refmans/tern.mmrm/html/g_mmrm_lsmeans.html
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R: Compute LS-means (aka population means or marginal means)
...types. Usage LSmeans(object, effect = NULL, at = NULL, level = 0.95, ...) ## Default S3 method: LSmeans(object, effect = NULL, at = NULL, level = 0.95, ...) ## S3 method for class 'lmerMod' LSmeans...
/CRAN/refmans/doBy/html/ls-means.html
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R: Example 5.2 from Generalized Linear Mixed Models: Modern...
...Walter W. Stroup(p-164) Description Exam5.2 three factor main effects only design Author(s) Muhammad Yaseen (myaseen208@gmail.com) Adeela Munawar (adeela.uaf@gmail.com) References Stroup, W. W. (2012).
/CRAN/refmans/StroupGLMM/html/Exam5.2.html
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R: Example 3.9 from Generalized Linear Mixed Models: Modern...
...Exam3.9 used to differentiate conditional and marginal binomial models with and without interaction for S2 variable. Author(s) Muhammad Yaseen (myaseen208@gmail.com) Adeela Munawar (adeela.uaf@gmail...
/CRAN/refmans/StroupGLMM/html/Exam3.9.html
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R: Transition to 'emmeans'
...The lsmeans package is being deprecated and further development will take place in its successor, emmeans. Users may use emmeans in almost exactly the same way as lsmeans, but a few function names...
/CRAN/refmans/lsmeans/html/transition.html
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R: Create a reference grid from a fitted model
...{lsmeans} R Documentation Create a reference grid from a fitted model Description These functions are provided in lsmeans because they have been renamed in emmeans Usage ref.grid(object, ...) recover...
/CRAN/refmans/lsmeans/html/ref.grid.html
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R: The 'ref.grid' and 'lsmobj' classes
...emmGrid class defined in emmeans, and are provided as support for objects created in older versions of lsmeans. For details, see emmGrid-class. Author(s) Russell V. Lenth [Package lsmeans version 2.30-...
/CRAN/refmans/lsmeans/html/ref.grid-class.html
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R: Linear estimates matrix
...specifying linear estimate. Usage LE_matrix(object, effect = NULL, at = NULL) ## Default S3 method: LE_matrix(object, effect = NULL, at = NULL) aggregate_linest_list(linest_list) get_linest_list...
/CRAN/refmans/doBy/html/linest-matrix.html
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R: Example 3.2 from Generalized Linear Mixed Models: Modern...
...Concepts, Methods and Applications by Walter W. Stroup(p-73) Description Exam3.2 used binomial data, two treatment samples Author(s) Muhammad Yaseen (myaseen208@gmail.com) Adeela Munawar (adeela.uaf@...
/CRAN/refmans/StroupGLMM/html/Exam3.2.html
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R: Wrappers for alternative naming of EMMs
These functions also provide the functionality formerly provided by the lsmeans package, which is now just a front-end for emmeans. Usage lsmeans(...) lstrends(...) lsmip(...) lsm(...) lsmobj(...) ...
/CRAN/refmans/emmeans/html/wrappers.html
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R: Deprecated functions in RVAideMemoire package
...future versions. Usage back.lsmeans(...) byf.normhist(...) cor.sparse(...) CvM.test(...) DA.confusion(...) DA.valid(...) DA.var(...) dunn.test(...) fc.multcomp(...) friedman.rating.test(...) kruskal...
/CRAN/refmans/RVAideMemoire/html/deprecated.html
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R: Least-Squares Means
...‘lsmeans’ version 2.30-0 DESCRIPTION file. Package NEWS. Help Pages lsmeans-package Least-squares means auto.noise Data sets contrast Create a reference grid from a fitted model emmeans-transition...
/CRAN/refmans/lsmeans/html/00Index.html
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R: Data sets
...a user customarily loads the data from lsmeans. But the same datasets are provided in the emmeans package, and they are documented there. Usage auto.noise Author(s) Russell V. Lenth [Package lsmeans...
/CRAN/refmans/lsmeans/html/auto.noise.html
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R: Tabulation of MMRM Subgroups Results
..."lsmean", "diff", "ci"), .formats = list(n = "xx", n_tot = "xx", lsmean = "xx.x", diff = "xx.x", ci = "(xx.x, xx.x)", pval = "x.xxxx | (<0.0001)"), .labels = list(n = "n", n_tot = "Total n", lsmean...
/CRAN/refmans/tern.mmrm/html/tabulate_mmrm_subgroups.html
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R: Tabulation of a GEE Model
...'tern_gee' as.rtable(x, type = c("coef", "cov"), ...) s_lsmeans_logistic(df, .in_ref_col) a_lsmeans_logistic(df, .in_ref_col) summarize_gee_logistic( lyt, ..., table_names = "lsmeans_logistic_summary"...
/CRAN/refmans/tern.gee/html/tabulate_gee.html
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R: Tables and Graphs for Generalized Estimating Equations (GEE) Model Fits
...tern_gee Tabulation of a GEE Model a_lsmeans_logistic Tabulation of a GEE Model fev_data Example dataset for 'tern.gee' package. fit_gee Fit a GEE Model gee_methods Methods for GEE Models lsmeans...
/CRAN/refmans/tern.gee/html/00Index.html
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R: Example 3.3 from Generalized Linear Mixed Models: Modern...
...by Walter W. Stroup(p-77) Description Exam3.3 use RCBD data with fixed location effect and different forms of estimable functions are shown in this example. Author(s) Muhammad Yaseen (myaseen208@gmail...
/CRAN/refmans/StroupGLMM/html/Exam3.3.html
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R: Helper for Extraction and Formatting of MMRM Subgroups
...treatment arm relative to the reference arm for one MMRM subgroup. Usage h_mmrm_subgroup_df( lsmeans, overall_fit, is_in_subset, visit, treatment_arm, subgroup, var, label ) Arguments lsmeans (named...
/CRAN/refmans/tern.mmrm/html/h_mmrm_subgroup_df.html
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R: Analysis of Covariance
...ancova(data, vars, visits = NULL, weights = c("proportional", "equal")) Arguments data A data.frame containing the data to be used in the model. vars A vars object as generated by set_vars(). Only...
/CRAN/refmans/rbmi/html/ancova.html
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R: Dataset for Unit-Testing of LS Means
...in SAS PROC MIXED and rounded to two decimals as covariance parameter estimates slightly differ. Usage data(LSMeans_Data) Format data.frame with 200 rows and 6 variables. [Package VCA version 1.5.1...
/CRAN/refmans/VCA/html/LSMeans_Data.html
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R: Compute the least squares means from a prediction grid and...
...and estimated coefficients Usage get_lsmeans(data, xmatrix, pred_grid, Betas, continuous_covar_inds = NULL) Arguments data The raw data from which the estimates were computed xmatrix The design matrix...
/CRAN/refmans/pmartR/html/get_lsmeans.html
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R: Compute linear estimates
...population means (also known as LSMEANS). Usage linest(object, L = NULL, ...) ## S3 method for class 'linest_class' confint(object, parm, level = 0.95, ...) ## S3 method for class 'linest_class' coef...
/CRAN/refmans/doBy/html/linest.html
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R: Construct Linear Contrast Matrix for Hypothesis Tests
.../contrast matrices from a string-representation of linear hypotheses. Usage getL(obj, s, what = c("fixef", "lsmeans")) Arguments obj (VCA) object s (character) string or vector of strings, denoting one...
/CRAN/refmans/VCA/html/getL.html
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R: Example 3.5 from Generalized Linear Mixed Models: Modern...
...Applications by Walter W. Stroup(p-85) Description Exam3.5 fixed location, factorial treatment structure, Gaussian response Author(s) Muhammad Yaseen (myaseen208@gmail.com) Adeela Munawar (adeela.uaf@...
/CRAN/refmans/StroupGLMM/html/Exam3.5.html
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R: Least Square Means
...g2 inverse. Usage LSM(Formula, Data, Term, conf.level=0.95, adj="lsd", hideNonEst=TRUE, PLOT=FALSE, descend=FALSE, ...) Arguments Formula a conventional formula of model Data data.frame Term term name...
/CRAN/refmans/sasLM/html/LSM.html
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R: Extract Least Square Means from 'MMRM'
...Extracts the least square means from an MMRM fit. Usage get_mmrm_lsmeans(fit, vars, conf_level, weights, averages = list()) Arguments fit (mmrm) result of mmrm::mmrm(). vars (named list of string or...
/CRAN/refmans/tern.mmrm/html/get_mmrm_lsmeans.html
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R: Reference Based Multiple Imputation
...NEWS. Help Pages A C D E F G H I L M P Q R S T V -- A -- add_class Add a class adjust_trajectories Adjust trajectories due to the intercurrent event (ICE) adjust_trajectories_single Adjust trajectory...
/CRAN/refmans/rbmi/html/00Index.html
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R: Tidy a(n) emmGrid object
...single hypothesis, a cluster, or a class. Exactly what tidy considers to be a model component varies across models but is usually self-evident. If a model has several distinct types of components, you...
/CRAN/refmans/broom/html/tidy.emmGrid.html
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R: Tidy a(n) summary_emm object
...component might be a single term in a regression, a single hypothesis, a cluster, or a class. Exactly what tidy considers to be a model component varies across models but is usually self-evident. If...
/CRAN/refmans/broom/html/tidy.summary_emm.html
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R: Tidy a(n) ref.grid object
...component might be a single term in a regression, a single hypothesis, a cluster, or a class. Exactly what tidy considers to be a model component varies across models but is usually self-evident. If...
/CRAN/refmans/broom/html/tidy.ref.grid.html
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R: Tidy a(n) lsmobj object
...about the components of a model. A model component might be a single term in a regression, a single hypothesis, a cluster, or a class. Exactly what tidy considers to be a model component varies across...
/CRAN/refmans/broom/html/tidy.lsmobj.html
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R: (V)ariance (C)omponent (A)nalysis.
...fitted by REML the typical VCA-table is derived, also containing the variances of VC, which are approximated by the method outlined in Giesbrecht & Burns (1985). REML-estimation is available via...
/CRAN/refmans/VCA/html/VCA-Package.html
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R: Extract a tidy data frame of draws of posterior distributions...
...marginal means" (emmeans/lsmeans) from a Bayesian model fit. Description Extract draws from the result of a call to emmeans::emmeans() (formerly lsmeans) or emmeans::ref_grid() applied to a Bayesian...
/CRAN/refmans/tidybayes/html/gather_emmeans_draws.html
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R: Helpers for Processing Least Square Means
...h_get_emmeans_res(fit, vars, weights) h_get_average_visit_specs(emmeans_res, vars, averages, fit) h_get_spec_visit_estimates(emmeans_res, specs, conf_level, tests = FALSE) h_get_single_visit_estimates...
/CRAN/refmans/tern.mmrm/html/lsmeans_helpers.html
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R: 'MMRM' Analysis
..."AVAL", covariates = c(), id = "USUBJID", arm = "ARM", visit = "AVISIT"), data, conf_level = 0.95, cor_struct = "unstructured", weights_emmeans = "proportional", averages_emmeans = list(), parallel...
/CRAN/refmans/tern.mmrm/html/fit_mmrm.html
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R: Implements an Analysis of Covariance (ANCOVA)
ancova_single {rbmi} R Documentation Implements an Analysis of Covariance (ANCOVA) Description Performance analysis of covariance. See ancova() for full details. Usage ancova_single( data, outcome...
/CRAN/refmans/rbmi/html/ancova_single.html
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R: Examp2.5.2.1 from Duchateau, L. and Janssen, P. and Rowlands,...
...Examp2.5.2.1 from Duchateau, L. and Janssen, P. and Rowlands, G. J. (1998).Linear Mixed Models. An Introduction with applications in Veterinary Research. International Livestock Research Institute.
/CRAN/refmans/VetResearchLMM/html/Examp2.5.2.1.html
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R: Summary for analysis of covariance (ANCOVA).
...summarize_ancova( lyt, vars, variables, conf_level, interaction_y = FALSE, interaction_item = NULL, var_labels, na_str = default_na_str(), nested = TRUE, ..., show_labels = "visible", table_names...
/CRAN/refmans/tern/html/summarize_ancova.html
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R: Examp3.2 from Duchateau, L. and Janssen, P. and Rowlands, G....
...Examp3.2 from Duchateau, L. and Janssen, P. and Rowlands, G. J. (1998).Linear Mixed Models. An Introduction with applications in Veterinary Research. International Livestock Research Institute.
/CRAN/refmans/VetResearchLMM/html/Examp3.2.html
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R: Variance Component Analysis
...file. User guides, package vignettes and other documentation. Help Pages VCA-package (V)ariance (C)omponent (A)nalysis. anovaMM ANOVA-Type Estimation of Mixed Models anovaVCA ANOVA-Type Estimation...
/CRAN/refmans/VCA/html/00Index.html
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R: 'SAS' Linear Model
...'SAS'. A different result does not necessarily mean incorrectness. However, many want the same result with 'SAS'. This package aims to achieve that. Reference: Littell RC, Stroup WW, Freund RJ (2002, ...
/CRAN/refmans/sasLM/html/sasLM-package.html
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R: Fit Linear Mixed Models via REML
...Function fits Linear Mixed Models (LMM) using Restricted Maximum Likelihood (REML). Usage remlMM( form, Data, by = NULL, VarVC = TRUE, cov = TRUE, quiet = FALSE, order.data = TRUE ) Arguments form...
/CRAN/refmans/VCA/html/remlMM.html
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R: Matrix of Coefficients in a Linear Model
...glm, gls, lme, and lmer. Usage Kmatrix(model, modelterm, covariate=NULL, covariateV=NULL, data=NULL, prtnum=FALSE) Arguments model Model object returned by aov, lm, glm, gls, lme, and lmer. modelterm...
/CRAN/refmans/predictmeans/html/Kmatrix.html
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R: Convert to and from 'emmGrid' objects
...These are useful utility functions for creating a compact version of an emmGrid object that may be saved and later reconstructed, or for converting old ref.grid or lsmobj objects into emmGrid objects.
/CRAN/refmans/emmeans/html/as.emmGrid.html
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R: General Linear Model similar to SAS PROC GLM
...a conventional formula for a linear model. Data a data.frame to be analyzed BETA if TRUE, coefficients (parameters) of REG will be returned. This is equivalent to SOLUTION option of SAS PROC GLM EMEAN...
/CRAN/refmans/sasLM/html/GLM.html
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R: Extraction of MMRM Subgroup Results based on Population Model...
...and corresponding (grouped) factor levels. Usage extract_mmrm_subgroups( fit, visit, subgroups = NULL, groups_lists = list(), treatment_arm = fit$treatment_levels[1L], label_all = "All Patients"...
/CRAN/refmans/tern.mmrm/html/extract_mmrm_subgroups.html
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R: Plot Bayes dose response curve and dose group means
...length(y)), dgrid=sort(unique(c(seq(0,max(dose),length=50), dose))), predict= TRUE,plotDif=FALSE,plotMed=FALSE, plotResid=FALSE,clev=0.9, binary=c('no','logit','probit','BinRes'),BinResLev, BinResDir...
/CRAN/refmans/clinDR/html/plotB.html
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R: Tidy Data and 'Geoms' for Bayesian Models
...NEWS. Help Pages A C D E F G H L M N P R S T U X tidybayes-package Tidy Data and 'Geoms' for Bayesian Models -- A -- add_draws Add draws to a data frame in tidy format add_epred_draws Add draws from...
/CRAN/refmans/tidybayes/html/00Index.html
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R: Examp3.1 from Duchateau, L. and Janssen, P. and Rowlands, G....
...Examp3.1 from Duchateau, L. and Janssen, P. and Rowlands, G. J. (1998).Linear Mixed Models. An Introduction with applications in Veterinary Research. International Livestock Research Institute.
/CRAN/refmans/VetResearchLMM/html/Examp3.1.html
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R: Testing and Plotting Procedures for Biostatistics
...B C D E F G I K L M O P Q R S T U W RVAideMemoire-package Testing and Plotting Procedures for Biostatistics -- A -- adonis.II Type II permutation MANOVA using distance matrices Anova.clm Anova Tables...
/CRAN/refmans/RVAideMemoire/html/00Index.html
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R: Perform t-Tests for Linear Contrasts on Fixed Effects
...combinations (contrasts) of estimated fixed effects. Usage test.fixef( obj, L, ddfm = c("contain", "residual", "satterthwaite"), method.grad = "simple", tol = 1e-12, quiet = FALSE, opt = TRUE, onlyDF...
/CRAN/refmans/VCA/html/test.fixef.html
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R: teal Module: Mixed Model Repeated Measurements (MMRM)...
...tm_a_mmrm( label, dataname, parentname = ifelse(inherits(arm_var, "data_extract_spec"), teal.transform::datanames_input(arm_var), "ADSL"), aval_var, id_var, arm_var, visit_var, cov_var, arm_ref_comp...
/CRAN/refmans/teal.modules.clinical/html/tm_a_mmrm.html
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R: Estimated Marginal Means, aka Least-Squares Means
...NEWS. Help Pages A C D E F G H I J L M N O P Q R S T U V W X misc emmeans-package Estimated marginal means (aka Least-squares means) -- A -- add_grouping Manipulate factors in a reference grid as...
/CRAN/refmans/emmeans/html/00Index.html
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R: Standardize a formula and data frame for regression.
...making regression output easier to interpret. For mixed effects regressions, this also offers computational benefits, and for Bayesian regressions, it also makes determining reasonable priors easier.
/CRAN/refmans/standardize/html/standardize.html
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R: General Linear Hypotheses
...glht(model, linfct, alternative = c("two.sided", "less", "greater"), rhs = 0, ...) ## S3 method for class 'character' glht(model, linfct, ...) ## S3 method for class 'expression' glht(model, linfct...
/CRAN/refmans/multcomp/html/glht.html
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R: ANOVA-Type Estimation of Mixed Models
...any linear mixed model including random models and linear models. Usage anovaMM( form, Data, by = NULL, VarVC.method = c("scm", "gb"), NegVC = FALSE, quiet = FALSE, order.data = TRUE ) Arguments form...
/CRAN/refmans/VCA/html/anovaMM.html
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R: Estimated marginal means (Least-squares means)
...among them. EMMs are also known as least-squares means. Usage emmeans(object, specs, by = NULL, fac.reduce = function(coefs) apply(coefs, 2, mean), contr, options = get_emm_option("emmeans"), weights...
/CRAN/refmans/emmeans/html/emmeans.html
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R: Datasets from agricultural experiments
...publications relating to agriculture, including field crops, tree crops, animal studies, and a few others. Details If you use these data, please cite both the agridat package and the original source...
/CRAN/refmans/agridat/html/agridat.html
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R: Agricultural Datasets
...B C D E F G H I J K L M N O P R S T U V W Y Z agridat-package Datasets from agricultural experiments -- A -- aastveit.barley Barley heights and environmental covariates in Norway aastveit.barley.covs...
/CRAN/refmans/agridat/html/00Index.html
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