Groupwise Statistics, LSmeans, Linear Estimates, Utilities

Documentation for package ‘doBy’ version 4.7.0

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A B C D E F G H I L M N O P R S T U V W misc

-- A --

add_int	Add interaction columns to data frame
add_pred	Add predicted values of different types to dataframe
add_resid	Add residuals of different types to dataframe
aggregate_linest_list	Linear estimates matrix
as_lhs_chr	Formula operations and coercion.
as_lhs_frm	Formula operations and coercion.
as_rhs_chr	Formula operations and coercion.
as_rhs_frm	Formula operations and coercion.

-- B --

beets	beets data
binomial_to_bernoulli_data	Convert binomial data to bernoulli data
bquote_fun_list	Backquote a list of functions
breastcancer	Gene expression signatures for p53 mutation status in 250 breast cancer samples
budworm	Budworm data
by-lapply	Formula based version of lapply and sapply
by-lmby	List of lm objects with a common model
by-order	Ordering (sorting) rows of a data frame
by-sample	Sampling from a data frame
by-split	Split a data frame into groups defined by variable(s)
by-subset	Finds subsets of a dataframe which is split by variables in a formula.
by-summary	Groupwise summary statistics
by-transform	Function to make groupwise transformations

-- C --

cad1	Coronary artery disease data
cad2	Coronary artery disease data
carcass	Lean meat contents of 344 pig carcasses
carcassall	Lean meat contents of 344 pig carcasses
child_growth	Berkeley Growth Study data
codstom	Diet of Atlantic cod in the Gulf of St. Lawrence (Canada)
coef.esticon_class	Contrasts for lm, glm, lme, and geeglm objects
coef.linest_class	Compute linear estimates
coef.lmBy	List of lm objects with a common model
coef.summary_lmBy	List of lm objects with a common model
confint.esticon_class	Contrasts for lm, glm, lme, and geeglm objects
confint.linest_class	Compute linear estimates
crickets	crickets data
crimeRate	crimeRate
crime_rate	crimeRate
cropyield	Yield from Danish agricultural production of grain and root crop.
cv_glm_fitlist	Cross-validation for list of glm objects

-- D --

data-wine	Chemical composition of wine
data_breastcancer	Gene expression signatures for p53 mutation status in 250 breast cancer samples
data_budworm	Budworm data
data_cad	Coronary artery disease data
data_mathmark	Mathematics marks for students
data_personality	Personality traits
descStat	Computing simple descriptive statistics of a numeric vector.
dietox	Growth curves of pigs in a 3x3 factorial experiment

-- E --

esticon	Contrasts for lm, glm, lme, and geeglm objects
expr_to_fun	Convert expression into function object.

-- F --

fatacid	Fish oil in pig food
fev	Forced expiratory volume in children
firstlastobs	Locate the index of the first/last unique value
firstobs	Locate the index of the first/last unique value
firstobs.default	Locate the index of the first/last unique value
firstobs.formula	Locate the index of the first/last unique value
fitted.lmBy	List of lm objects with a common model
formula_add	Formula operations and coercion.
formula_add_str	Formula operations and coercion.
formula_chr_to_form	Formula operations and coercion.
formula_nth	Formula operations and coercion.
formula_ops	Formula operations and coercion.
formula_poly	Formula operations and coercion.
formula_to_interaction_matrix	Formula operations and coercion.

-- G --

generate_data_list	Generate data list
getBy	List of lm objects with a common model
get_contrasts	Auxillary functions for computing lsmeans, contrasts etc
get_contrasts.default	Auxillary functions for computing lsmeans, contrasts etc
get_contrasts.merMod	Auxillary functions for computing lsmeans, contrasts etc
get_formulas	Get formulas from model_stability_glm_class object
get_fun	Section a function and set default values in function
get_linest_list	Linear estimates matrix
get_section	Section a function and set default values in function
get_vartypes	Auxillary functions for computing lsmeans, contrasts etc
get_X	Auxillary functions for computing lsmeans, contrasts etc
get_X.default	Auxillary functions for computing lsmeans, contrasts etc
get_X.merMod	Auxillary functions for computing lsmeans, contrasts etc
get_xlevels	Auxillary functions for computing lsmeans, contrasts etc
get_xlevels.default	Auxillary functions for computing lsmeans, contrasts etc
get_xlevels.mer	Auxillary functions for computing lsmeans, contrasts etc
get_xlevels.merMod	Auxillary functions for computing lsmeans, contrasts etc

-- H --

haldCement	Heat development in cement under hardening.
head.splitByData	Split a data frame into groups defined by variable(s)
head2	head and tail for matrices
head_matrix	head and tail for matrices

-- I --

income	income data
interaction-plot	Two-way interaction plot
interaction_plot	Two-way interaction plot
is_estimable	Determines if contrasts are estimable.

-- L --

lapplyBy	Formula based version of lapply and sapply
lapply_by	Formula based version of lapply and sapply
lastobs	Locate the index of the first/last unique value
lastobs.default	Locate the index of the first/last unique value
lastobs.formula	Locate the index of the first/last unique value
LE_matrix	Linear estimates matrix
LE_matrix.default	Linear estimates matrix
linest	Compute linear estimates
linest-get	Auxillary functions for computing lsmeans, contrasts etc
linest-matrix	Linear estimates matrix
linest.default	Compute linear estimates
linest.geeglm	Compute linear estimates
linest.glm	Compute linear estimates
linest.lm	Compute linear estimates
linest.lmerMod	Compute linear estimates
linest.merMod	Compute linear estimates
lmBy	List of lm objects with a common model
lm_by	List of lm objects with a common model
ls-means	Compute LS-means (aka population means or marginal means)
LSmeans	Compute LS-means (aka population means or marginal means)
LSmeans.default	Compute LS-means (aka population means or marginal means)
LSmeans.lmerMod	Compute LS-means (aka population means or marginal means)

-- M --

math	Mathematics marks for students
mathmark	Mathematics marks for students
math_teachers	Height of math teachers
matrix2set_list	Matrix representatation of list of vectors and vice versa
mb_summary	Fast summary of microbenchmark object
milkman	Milk yield data for manually milked cows.
milkman_rdm1	Milk yield data for manually milked cows.
model_stability_glm	Model stability for glm objects

-- N --

NIRmilk	NIRmilk
nir_milk	nir_milk

-- O --

orderBy	Ordering (sorting) rows of a data frame
order_by	Ordering (sorting) rows of a data frame

-- P --

parseGroupFormula	Extract components from a formula with "conditioning bar"
personality	Personality traits
pick1	Extract (pick) elements without using brackets
pick2	Extract (pick) elements without using brackets
pick_elements	Extract (pick) elements without using brackets
plot_lm	Plot linear model object
popMeans	Compute LS-means (aka population means or marginal means)
popMeans.default	Compute LS-means (aka population means or marginal means)
popMeans.lmerMod	Compute LS-means (aka population means or marginal means)
potatoes	Weight and size of 20 potatoes
pow	Power function
prostate	Prostate Tumor Gene Expression Dataset

-- R --

rbind_list	Bind list of data frames and add list names as a column
reciprocal	Reciprocal function
recodeVar	Recode values of a vector
recode_var	Recode values of a vector
recover_pca_data	Recover data from principal component analysis
renameCol	Rename columns in a matrix or a dataframe.
residuals.lmBy	List of lm objects with a common model
response	Get response variable from model
response_plot	Plot the response variable against the predictor variables.

-- S --

sampleBy	Sampling from a data frame
sample_by	Sampling from a data frame
sapplyBy	Formula based version of lapply and sapply
sapply_by	Formula based version of lapply and sapply
scaleBy	Group-wise scaling of data
scale_by	Group-wise scaling of data
scale_df	Scale numeric variables in a data frame
section_fun	Section a function and set default values in function
section_fun_env	Section a function and set default values in function
section_fun_sub	Section a function and set default values in function
set_covariate_val	Auxillary functions for computing lsmeans, contrasts etc
set_default	Section a function and set default values in function
set_list2matrix	Matrix representatation of list of vectors and vice versa
set_list_set_matrix	Matrix representatation of list of vectors and vice versa
set_xlevels	Auxillary functions for computing lsmeans, contrasts etc
shoes	shoes
simplify_rhs	Formula operations and coercion.
simplify_rhs.character	Formula operations and coercion.
simplify_rhs.formula	Formula operations and coercion.
splitBy	Split a data frame into groups defined by variable(s)
splitBy.legacy	Split a data frame into groups defined by variable(s)
split_by	Split a data frame into groups defined by variable(s)
split_by.legacy	Split a data frame into groups defined by variable(s)
split_bycol	Split matrix or dataframe into list
split_byrow	Split matrix or dataframe into list
split_byrow_bycol	Split matrix or dataframe into list
subSeq	Find sub-sequences of identical elements in a vector.
subsetBy	Finds subsets of a dataframe which is split by variables in a formula.
subset_by	Finds subsets of a dataframe which is split by variables in a formula.
sub_seq	Find sub-sequences of identical elements in a vector.
summary.esticon_class	Contrasts for lm, glm, lme, and geeglm objects
summary.linest_class	Compute linear estimates
summary.lmBy	List of lm objects with a common model
summaryBy	Groupwise summary statistics
summary_by	Groupwise summary statistics
summary_mb	Fast summary of microbenchmark object

-- T --

tail.splitByData	Split a data frame into groups defined by variable(s)
tail2	head and tail for matrices
taylor	Taylor expansion (one dimension)
terms_labels	Formula operations and coercion.
tidy-esticon	Tidy an esticon object
tidy-linest	Tidy a linest object
tidy.esticon_class	Tidy an esticon object
tidy.linest_class	Tidy a linest object
timeSinceEvent	Calculate "time since event" in a vector
time_since_event	Calculate "time since event" in a vector
to_str	Formula operations and coercion.
transformBy	Function to make groupwise transformations
transform_by	Function to make groupwise transformations
truncate0	Truncate values in a matrix / vector to zero if they are below a certain threshold.

-- U --

unique_formula

Formula operations and coercion.

-- V --

v	Shorthand for vparse()
vcheck	Check if variables exist in a data frame
vcov.esticon_class	Contrasts for lm, glm, lme, and geeglm objects
vmap	Apply a function to each parsed variable name
vparse	Variable utilities: parse, select, check, map, rename
vrename	Rename columns in a data frame
vselect	Select columns from a data frame using flexible input

-- W --

which.maxn	Where are the n largest or n smallest elements in a numeric vector ?
which.minn	Where are the n largest or n smallest elements in a numeric vector ?
wine	Chemical composition of wine

-- misc --

.rhsf2list

Convert right hand sided formula to a list