Package: doBy 4.6.22.9004

doBy: Groupwise Statistics, LSmeans, Linear Estimates, Utilities

Utility package containing: 1) Facilities for working with grouped data: 'do' something to data stratified 'by' some variables. 2) LSmeans (least-squares means), general linear estimates. 3) Restrict functions to a smaller domain. 4) Miscellaneous other utilities.

Authors:Søren Højsgaard <[email protected]> and Ulrich Halekoh <[email protected]>

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doBy.pdf |doBy.html✨
doBy/json (API)
NEWS

# Install 'doBy' in R:
install.packages('doBy', repos = c('https://hojsgaard.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/hojsgaard/doby/issues

Datasets:
  • NIRmilk - NIRmilk
  • beets - Beets data
  • breastcancer - Gene expression signatures for p53 mutation status in 250 breast cancer samples
  • budworm - Budworm data
  • 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
  • codstom - Diet of Atlantic cod in the Gulf of St. Lawrence
  • crickets - Crickets data
  • crimeRate - CrimeRate
  • crime_rate - CrimeRate
  • cropyield - Yield from Danish agricultural production of grain and root crop.
  • dietox - Growth curves of pigs in a 3x3 factorial experiment
  • fatacid - Fish oil in pig food
  • fev - Forced expiratory volume in children
  • haldCement - Heat development in cement under hardening.
  • income - Income data
  • math - Mathematics marks for students
  • mathmark - Mathematics marks for students
  • milkman - Milk yield data for manually milked cows.
  • milkman_rdm1 - Milk yield data for manually milked cows.
  • nir_milk - Nir_milk
  • personality - Personality traits
  • potatoes - Weight and size of 20 potatoes
  • prostate - Prostate Tumor Gene Expression Dataset

On CRAN:

93 exports 1 stars 12.16 score 43 dependencies 885 dependents 64 mentions 3.0k scripts 198.6k downloads

Last updated 12 days agofrom:df9a1c0e96. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 06 2024
R-4.5-winOKSep 06 2024
R-4.5-linuxOKSep 06 2024
R-4.4-winOKSep 06 2024
R-4.4-macOKSep 06 2024
R-4.3-winOKSep 06 2024
R-4.3-macOKSep 06 2024

Exports:aggregate_linest_listas_lhs_chras_lhs_frmas_rhs_chras_rhs_frmbinomial_to_bernoulli_databquote_fun_listchr_to_matrixcv_glm_fitlistdescStatdoby.xtabsesticonexpr_to_funfirstobsformula_addformula_add_strformula_chr_to_formformula_nthformula_polyformula_to_interaction_matrixgenerate_data_listget_contrastsget_formulasget_funget_linest_listget_sectionget_vartypesget_Xget_xlevelsgetByinteraction_plotis_estimableis_groupedlapply_bylapplyBylastobsLE_matrixlinestlm_bylmByLSmeansmatrix_opmatrix2set_listmb_summarymodel_stability_glmnull_basisorder_byorderByparseGroupFormulaplot_lmpopMeansrecode_varrecodeVarrecover_pca_datarenameColrle2sample_bysampleBysapply_bysapplyByscale_byscale_dfscale2scaleBysection_funsection_fun_envsection_fun_subset_covariate_valset_defaultset_list2matrixset_xlevelssimplify_rhssplit_bysplit_bycolsplit_byrowsplitBysub_seqsubSeqsubset_bysubsetBysummary_bysummary_mbsummaryBytaylorterms_labelstimeSinceEventto_strtransform_bytransformBytruncate0unique_formulawhich.maxnwhich.minn

Dependencies:backportsbootbroomclicolorspacecowplotcpp11Derivdplyrfansifarvergenericsggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmicrobenchmarkmodelrmunsellnlmepillarpkgconfigpurrrR6RColorBrewerrlangscalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr

doby: Groupwise computations and miscellaneous utilities

Søren Højsgaard

Rendered fromdoby.rmdusingknitr::knitron Sep 06 2024.

Last update: 2024-06-21
Started: 2024-06-07

doBy: Linear estimates and LSmeans

Rendered fromlinest_lsmeans.rnwusingknitr::knitron Sep 06 2024.

Last update: 2024-04-23
Started: 2023-03-13

Sectioning a function

Søren Højsgaard

Rendered fromsection_fun.rmdusingknitr::knitron Sep 06 2024.

Last update: 2024-04-29
Started: 2024-04-29

Readme and manuals

Help Manual

Help pageTopics
Convert right hand sided formula to a list.rhsf2list
beets databeets
Convert binomial data to bernoulli databinomial_to_bernoulli_data
Backquote a list of functionsbquote_fun_list
Scale a dataframe or matrixby_scale scaleBy scale_by
Formula based version of lapply and sapplyby-lapply lapplyBy lapply_by sapplyBy sapply_by
List of lm objects with a common modelby-lmby coef.lmBy coef.summary_lmBy fitted.lmBy getBy lmBy lm_by residuals.lmBy summary.lmBy
Ordering (sorting) rows of a data frameby-order orderBy order_by
Sampling from a data frameby-sample sampleBy sample_by
Split a data frameby-split head.splitByData splitBy split_by tail.splitByData
Finds subsets of a dataframe which is split by variables in a formula.by-subset subsetBy subset_by
Function to calculate groupwise summary statisticsby-summary summaryBy summary_by
Function to make groupwise transformationsby-transform transformBy transform_by
Lean meat contents of 344 pig carcassescarcass carcassall
Character vector to matrixchr_to_matrix
Diet of Atlantic cod in the Gulf of St. Lawrence (Canada)codstom
crickets datacrickets
crimeRatecrime_rate
crimeRatecrimeRate
Yield from Danish agricultural production of grain and root crop.cropyield
Cross-validation for list of glm objectscv_glm_fitlist
Gene expression signatures for p53 mutation status in 250 breast cancer samplesbreastcancer data_breastcancer
Budworm databudworm data_budworm
Coronary artery disease datacad1 cad2 data_cad
Mathematics marks for studentsdata_mathmark math mathmark
Personality traitsdata_personality personality
Computing simple descriptive statistics of a numeric vector.descStat
Growth curves of pigs in a 3x3 factorial experimentdietox
Contrasts for lm, glm, lme, and geeglm objectscoef.esticon_class confint.esticon_class esticon summary.esticon_class vcov.esticon_class
Convert expression into function object.expr_to_fun
Fish oil in pig foodfatacid
Forced expiratory volume in childrenfev
Locate the index of the first/last unique valuefirstlastobs firstobs firstobs.default firstobs.formula lastobs lastobs.default lastobs.formula
Formula operations and coercion.as_lhs_chr as_lhs_frm as_rhs_chr as_rhs_frm formula_add formula_add_str formula_chr_to_form formula_nth formula_ops formula_poly formula_to_interaction_matrix simplify_rhs simplify_rhs.character simplify_rhs.formula terms_labels to_str unique_formula
Generate data listgenerate_data_list
Get formulas from model_stability_glm_class objectget_formulas
Heat development in cement under hardening.haldCement
income dataincome
Two-way interaction plotinteraction-plot interaction_plot
Determines if contrasts are estimable.is-estimable is_estimable
Compute linear estimatescoef.linest_class confint.linest_class linest linest.default linest.geeglm linest.glm linest.lm linest.lmerMod linest.merMod summary.linest_class
Auxillary functions for computing lsmeans, contrasts etcget_contrasts get_contrasts.default get_contrasts.merMod get_vartypes get_X get_X.default get_X.merMod get_xlevels get_xlevels.default get_xlevels.mer get_xlevels.merMod linest-get set_covariate_val set_xlevels
Linear estimates matrixaggregate_linest_list get_linest_list LE_matrix LE_matrix.default linest-matrix
Compute LS-means (aka population means or marginal means)ls-means LSmeans LSmeans.default LSmeans.lmerMod popMeans popMeans.default popMeans.lmerMod
Matrix operations based on matching dimensionsmatrix_op
Fast summary of microbenchmark objectmb_summary summary_mb
Milk yield data for manually milked cows.milkman milkman_rdm1
Model stability for glm objectsmodel_stability_glm
nir_milknir_milk
NIRmilkNIRmilk
Finds the basis of the (right) null space.null-basis null_basis
Extract components from a formula with "conditioning bar"parseGroupFormula
Plot linear model objectplot_lm
Weight and size of 20 potatoespotatoes
Prostate Tumor Gene Expression Datasetprostate
Recode values of a vectorrecodeVar recode_var
Recover data from principal component analysisrecover_pca_data
Rename columns in a matrix or a dataframe.renameCol
Scaling numerical valuesscale2 scale_df
Section a function and set default values in functionget_fun get_section section_fun section_fun_env section_fun_sub set_default
Matrix representatation of list of vectors and vice versamatrix2set_list set_list2matrix set_list_set_matrix
Split matrix or dataframe into listsplit_bycol split_byrow split_byrow_bycol
Find sub-sequences of identical elements in a vector.is_grouped rle2 subSeq sub_seq
Taylor expansion (one dimension)taylor
Tidy an esticon objecttidy-esticon tidy.esticon_class
Tidy a linest objecttidy-linest tidy.linest_class
Calculate "time since event" in a vector.timeSinceEvent
Truncate values in a matrix / vector to zero if they are below a certain threshold.truncate0
Where are the n largest or n smallest elements in a numeric vector ?which.maxn which.minn