Column names: tidy() - Githubissues

alexpghayes commented 6 years ago

This issue thread is for proposals for column names changes. Please read #452 before commenting.

alexpghayes commented 6 years ago

Existing column names (this is fairly complete, but not perfect -- it was scraped from the \value{} section of .Rd files)

column: '...' description: The initial columns correspond to the grouping factors on the right hand side of the model formula. used_by: survdiff
column: cumulative description: Cumulative percentage of variation explained. used_by:
- tidy_irlba
- tidy_svd
- prcomp
column: PC description: An integer vector indicating the principal component. used_by:
- tidy_irlba
- tidy_svd
- prcomp
column: percent description: Percentage of variation explained. used_by:
- tidy_irlba
- tidy_svd
- prcomp
column: row description: Needs custom description used_by:
- tidy_irlba
- tidy_svd
- prcomp
column: std.dev description: Standard deviation explained by this PC. used_by:
- tidy_irlba
- tidy_svd
- prcomp
column: value description: Needs custom desciption. used_by:
- tidy_irlba
- tidy_svd
- prcomp
column: acf description: calculated correlation used_by: acf
column: adj.p.value description: P-value adjusted for multiple comparisons used_by: TukeyHSD
column: alternative description: Alternative hypothesis (character). used_by:
- binWidth
- htest
column: bias description: Bias of the statistic. used_by: boot
column: ci.width description: Expected width of confidence interval. used_by: binWidth
column: class description: The class under consideration. used_by:
- confusionMatrix
- poLCA
column: cluster description: A factor describing the cluster from 1:k used_by: kmeans
column: column1 description: Name or index of the first column being described used_by: rcorr
column: column2 description: Name or index of the second column being described used_by: rcorr
column: comparison description: Levels being compared, separated by - used_by: TukeyHSD
column: component description: Cluster id as a factor. For a model k clusters, these will be as.factor(1:k), or as.factor(0:k) if there's a noise term. used_by: Mclust
column: conf.high description: The upper end of a confidence interval for the term under consideration. Included only if conf.int = TRUE. used_by:
- Arima
- betareg
- biglm
- btergm
- cch
- confusionMatrix
- cv.glmnet
- felm
- glm
- glmRob
- gmm
- htest
- ivreg
- kappa
- lavaan
- lm
- lmodel2
- lmRob
- mjoint
- nlrq
- nls
- plm
- rlm
- rq
- rqs
- speedlm
- survfit
- survreg
- TukeyHSD
column: conf.low description: The lower end of a confidence interval for the term under consideration. Included only if conf.int = TRUE. used_by:
- Arima
- betareg
- biglm
- btergm
- cch
- confusionMatrix
- cv.glmnet
- felm
- glm
- glmRob
- gmm
- htest
- ivreg
- kappa
- lavaan
- lm
- lmodel2
- lmRob
- mjoint
- nlrq
- nls
- plm
- rlm
- rq
- rqs
- speedlm
- survfit
- survreg
- TukeyHSD
column: cutoff description: The cutoff used for classification. Observations with predicted probabilities above this value were assigned class 1, and observations with predicted probabilities below this value were assigned class 0. used_by: roc
column: denominator description: The denominator, which is tau=kendall_score/denominator. used_by: Kendall
column: dev.ratio description: fraction of null deviance explained at each value of lambda used_by: glmnet
column: df description: Degrees of freedom used by this term in the model. used_by:
- anova
- aov
- aovlist
column: distance description: Distance between items used_by: dist
column: estimate description: Estimated value of the term under consideration. Needs additional custom info. used_by:
- aareg
- Arima
- betareg
- biglm
- btergm
- cch
- coeftest
- confusionMatrix
- coxph
- cv.glmnet
- ergm
- felm
- fitdistr
- gamlss
- garch
- glm
- glmnet
- glmRob
- gmm
- htest
- ivreg
- kappa
- lavaan
- lm
- lmodel2
- lmRob
- mjoint
- muhaz
- multinom
- nlrq
- nls
- plm
- poLCA
- rcorr
- ridgelm
- rlm
- rq
- rqs
- speedlm
- survexp
- survfit
- survreg
- TukeyHSD
column: estimate1 description: Sometimes two estimates are computed, such as in a two-sample t-test used_by: htest
column: estimate2 description: Sometimes two estimates are computed, such as in a two-sample t-test used_by: htest
column: event description: observed number of events used_by: pyears
column: exp description: weighted expected number of events in each group used_by: survdiff
column: expected description: expected number of events (present only if a ratetable term is present) If the data.frame = TRUE argument is supplied to pyears, this is simply the contents of x$data. used_by: pyears
column: flX description: Factor loading of term on factor X. There will be as many columns of this format as there were factors fitted. used_by: factanal
column: fpr description: The false positive rate at the given cutoff. used_by: roc
column: GCV description: generalized cross validation value for this lambda used_by: ridgelm
column: group description: The group (if specified) in the lavaan model used_by: lavaan
column: group1 description: First group being compared used_by: pairwise.htest
column: group2 description: Second group being compared used_by: pairwise.htest
column: index description: Index (i.e. date or time) for a ts or zoo object. used_by:
- ts
- zoo
column: item1 description: First item used_by: dist
column: item2 description: Second item used_by: dist
column: kendall_score description: Kendall score. used_by: Kendall
column: lag description: lag values used_by: acf
column: lambda description: Value of penalty parameter lambda. used_by:
- cv.glmnet
- glmnet
- ridgelm
column: mcmc.error description: The MCMC error used_by: ergm
column: mean description: The mean for each component. In case of 2+ dimensional models, a column with the mean is added for each dimension. NA for noise component used_by: Mclust
column: meansq description: Mean sum of squares. Equal to total sum of squares divided by degrees of freedom. used_by:
- anova
- aov
- aovlist
column: method description: Needs custom info. used_by:
- htest
- lmodel2
column: 'n' description: Needs custom info. used_by:
- binDesign
- binWidth
- pyears
- rcorr
column: 'N' description: number of subjects in each group used_by: survdiff
column: n.censor description: number of censored events used_by: survfit
column: n.event description: number of events at time t used_by: survfit
column: n.risk description: Number of individuals at risk at time zero. used_by:
- survexp
- survfit
column: num.df description: Degrees of freedom used_by: manova
column: nzero description: Number of coefficients that are exactly zero for given lambda. used_by: cv.glmnet
column: obs description: weighted observed number of events in each group used_by: survdiff
column: op description: The operator in the model syntax (e.g. ~~ for covariances, or ~ for regression parameters) used_by: lavaan
column: outcome description: Outcome of manifest variable used_by: poLCA
column: p description: True proportion. used_by: binWidth
column: p.value description: Needs custom information. used_by:
- aareg
- anova
- aov
- aovlist
- betareg
- biglm
- cch
- coeftest
- confusionMatrix
- coxph
- ergm
- felm
- gamlss
- garch
- glm
- glmRob
- gmm
- htest
- ivreg
- Kendall
- lavaan
- lm
- lmRob
- manova
- mjoint
- multinom
- nlrq
- nls
- pairwise.htest
- plm
- rcorr
- rlm
- rq
- rqs
- speedlm
- survreg
column: parameter description: Needs custom info. used_by:
- tidy_optim
- gamlss
- htest
column: power description: Power achieved for given value of n. used_by: binDesign
column: proportion description: The mixing proportion of each component used_by: Mclust
column: pyears description: person-years of exposure used_by: pyears
column: response description: Which response column the coefficients correspond to (typically Y1, Y2, etc). used_by:
- glm
- glmRob
- lm
- lmRob
- rlm
- speedlm
column: robust.se description: robust version of standard error estimate (only when x was called with dfbeta = TRUE) used_by: aareg
column: scale description: Scaling factor of estimated coefficient used_by: ridgelm
column: series description: Name of the series (present only for multivariate time series). used_by:
- ts
- zoo
column: size description: Number of points assigned to cluster. used_by:
- kmeans
- Mclust
column: state description: state if multistate survfit object inputted used_by: survfit
column: statistic description: Needs custom information used_by:
- aareg
- anova
- aov
- aovlist
- betareg
- biglm
- boot
- cch
- coeftest
- coxph
- felm
- gamlss
- garch
- glm
- glmRob
- gmm
- htest
- ivreg
- Kendall
- lavaan
- lm
- lmRob
- manova
- mjoint
- multinom
- nlrq
- nls
- plm
- rlm
- rq
- rqs
- speedlm
- survreg
column: std.all description: Standardized estimates based on both the variances of both (continuous) observed and latent variables. used_by: lavaan
column: std.error description: Standard error of the estimate. boot needs custom info. used_by:
- aareg
- Arima
- betareg
- biglm
- boot
- cch
- coeftest
- coxph
- cv.glmnet
- ergm
- felm
- fitdistr
- gamlss
- garch
- glm
- glmRob
- gmm
- ivreg
- lavaan
- lm
- lmRob
- mjoint
- multinom
- nlrq
- nls
- plm
- poLCA
- rlm
- rq
- rqs
- speedlm
- survfit
- survreg
column: std.lv description: Standardized estimates based on the variances of the (continuous) latent variables only used_by: lavaan
column: std.nox description: Standardized estimates based on both the variances of both (continuous) observed and latent variables, but not the variances of exogenous covariates. used_by: lavaan
column: step description: which step of lambda choices was used used_by: glmnet
column: strata description: strata if stratified survfit object inputted used_by: survfit
column: stratum description: The error stratum used_by: aovlist
column: sumsq description: Sum of squares explained by this term used_by:
- anova
- aov
- aovlist
column: term description: Needs custom info. used_by:
- aareg
- anova
- aov
- aovlist
- Arima
- betareg
- biglm
- boot
- btergm
- cch
- coeftest
- confusionMatrix
- ergm
- felm
- fitdistr
- gamlss
- garch
- glm
- glmnet
- glmRob
- gmm
- ivreg
- lavaan
- lm
- lmodel2
- lmRob
- mjoint
- multinom
- nlrq
- nls
- plm
- ridgelm
- rlm
- rq
- rqs
- speedlm
- survreg
- TukeyHSD
column: time description: Point in time. used_by:
- muhaz
- survexp
- survfit
column: tpr description: The true positive rate at the given cutoff. used_by: roc
column: type description: Either "weighted" or "unweighted" used_by: kappa
column: uniqueness description: Proportion of residual, or unexplained variance used_by: factanal
column: value description: Needs custom info. used_by:
- tidy_optim
- ts
- zoo
column: var_kendall_score description: Variance of the kendall_score. used_by: Kendall
column: variable description: Needs custom info. used_by:
- factanal
- poLCA
column: variance description: In case of one-dimensional and spherical models, the variance for each component, omitted otherwise. NA for noise component used_by: Mclust
column: withinss description: The within-cluster sum of squares used_by: kmeans
column: y.value description: The response level used_by: multinom
column: z description: z score used_by: aareg

alexpghayes commented 6 years ago

Some current conflicts I am aware of for tidy() (some of these not in the list above):

acf / autocorrelation
comp / component
conf.high / upper
conf.low / lower
exp / expected
df / num.df
n / N / size
parameter / term / variable
p / proportion
strata / stratum
response / y.level / y.value
statistic / z

It seems like there's also some redundancy in column names that describe "percent of variance" explained type information.

copernican commented 5 years ago

nzero is used by cv.glmnet(). The description above is "number of coefficients that are exactly zero for given lambda." I think this may be reversed. The documentation for cv.glmnet() states that this is actually the "number of non-zero coefficients at each lambda." If you agree (and if appropriate), I am happy to file an issue in modeltests instead, or to submit a PR.

alexpghayes commented 5 years ago

A PR or an issue would be ideal!

github-actions[bot] commented 3 years ago

This issue has been automatically closed due to inactivity.

github-actions[bot] commented 3 years ago

This issue has been automatically locked. If you believe you have found a related problem, please file a new issue (with a reprex: https://reprex.tidyverse.org) and link to this issue.

tidymodels / broom

Column names: tidy() #455