# Groupwise Statistics, LSmeans, Linear Estimates, Utilities

## Documentation for package ‘doBy’ version 4.7.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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

## -- A --

add | Pipe-friendly arithmetic helpers
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
align_coefs | Align and combine fixed-effect coefficients from multiple models
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
divide | Pipe-friendly arithmetic helpers

## -- 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, years of educations and ethnicity
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
mult | Pipe-friendly arithmetic helpers

## -- N --

NIRmilk | Near infra red light (NIR) measurements in milk
nir_milk | Near infra red light (NIR) measurements in 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
pipe_arithmetic | Pipe-friendly arithmetic helpers
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 | Pipe-friendly arithmetic helpers
prostate | Prostate Tumor Gene Expression Dataset

## -- R --

rbind_list | Bind list of data frames and add list names as a column
reciprocal | Pipe-friendly arithmetic helpers
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 | Set default values in a functions arguments
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 | Wear of shoes
shoes_long | Wear of 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.
subtract | Pipe-friendly arithmetic helpers
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
transform_forecast | Transform forecasts from model scale to data scale by simulation
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