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Fit models over each of a set of independent variables with a response variable

Source: R/modelsum.R
modelsum.Rd

Fit and summarize models for each independent (x) variable with a response variable (y), with options to adjust by variables for each model.

Usage

modelsum(
  formula,
  family = "gaussian",
  data,
  adjust = NULL,
  na.action = NULL,
  subset = NULL,
  weights = NULL,
  id,
  strata,
  control = NULL,
  ...
)

Arguments

formula

an object of class formula; a symbolic description of the variables to be modeled. See "Details" for more information.

family

similar mechanism to glm, where the model to be fit is driven by the family. Options include: binomial, gaussian, survival, poisson, negbin, clog, and ordinal. These can be passed as a string, as a function, or as a list resulting from a call to one of the functions. See modelsum.family for details on survival, ordinal, negbin, and clog families.

data

an optional data.frame, list or environment (or object coercible by as.data.frame to a data frame) containing the variables in the model. If not found in data, the variables are taken from environment(formula), typically the environment from which modelsum is called.

adjust

an object of class formula or a list of formulas, listing variables to adjust by in all models. Specify as a one-sided formula, like: ~Age+ Sex. If a list, the names are used for the summary function. Unadjusted models can be specified as ~ 1 or as a list: list(Unadjusted = NULL).

na.action

a function which indicates what should happen when the data contain NAs. The default (NULL) is to use the defaults of lm, glm, or coxph, depending on the family specifications.

subset

an optional vector specifying a subset of observations (rows of data) to be used in the results. If strata is missing, this works as vector of logicals or an index; otherwise, it should be a logical vector.

weights

an optional vector specifying the weights to apply to each data observation (rows of data)

id

A vector to identify clusters. Only used for relrisk at this time.

strata

a vector of strata to separate model summaries by an additional group. Note that for families like "clog", the "usual" strata term to indicate subject groupings should be given in the adjust argument.

control

control parameters to handle optional settings within modelsum. Arguments for modelsum.control can be passed to modelsum via the ... argument, but if a control object and ... arguments are both supplied, the latter are used. See modelsum.control for other details.

...

additional arguments to be passed to internal modelsum functions.

Value

An object with class c("modelsum", "arsenal_table")

See also

arsenal_table, modelsum.control, summary.modelsum, modelsum.internal, formulize

Author

Jason Sinnwell, Patrick Votruba, Beth Atkinson, Gregory Dougherty, and Ethan Heinzen, adapted from SAS Macro of the same name

Examples


data(mockstudy)

tab1 <- modelsum(bmi ~ sex + age, data = mockstudy)
summary(tab1, text = TRUE)
#> 
#> 
#> |             |estimate |std.error |p.value |adj.r.squared |Nmiss |
#> |:------------|:--------|:---------|:-------|:-------------|:-----|
#> |(Intercept)  |27.491   |0.181     |< 0.001 |0.004         |33    |
#> |sex Female   |-0.731   |0.290     |0.012   |              |      |
#> |(Intercept)  |26.424   |0.752     |< 0.001 |0.000         |33    |
#> |Age in Years |0.013    |0.012     |0.290   |              |      |
#> 

tab2 <- modelsum(alk.phos ~ arm + ps + hgb, adjust = ~ age + sex,
                 family = "gaussian", data = mockstudy)
summary(tab2, text = TRUE)
#> 
#> 
#> |                        |estimate |std.error |p.value |adj.r.squared |Nmiss |
#> |:-----------------------|:--------|:---------|:-------|:-------------|:-----|
#> |(Intercept)             |175.548  |20.587    |< 0.001 |-0.001        |266   |
#> |Treatment Arm F: FOLFOX |-13.701  |8.730     |0.117   |              |      |
#> |Treatment Arm G: IROX   |-2.245   |9.860     |0.820   |              |      |
#> |Age in Years            |-0.017   |0.319     |0.956   |              |      |
#> |sex Female              |3.016    |7.521     |0.688   |              |      |
#> |(Intercept)             |148.391  |19.585    |< 0.001 |0.045         |266   |
#> |ps                      |46.721   |5.987     |< 0.001 |              |      |
#> |Age in Years            |-0.084   |0.311     |0.787   |              |      |
#> |sex Female              |1.169    |7.343     |0.874   |              |      |
#> |(Intercept)             |336.554  |32.239    |< 0.001 |0.031         |266   |
#> |hgb                     |-13.845  |2.137     |< 0.001 |              |      |
#> |Age in Years            |0.095    |0.314     |0.763   |              |      |
#> |sex Female              |-5.980   |7.516     |0.426   |              |      |
#> 

summary(tab2, show.intercept = FALSE, text = TRUE)
#> 
#> 
#> |                        |estimate |std.error |p.value |adj.r.squared |Nmiss |
#> |:-----------------------|:--------|:---------|:-------|:-------------|:-----|
#> |Treatment Arm F: FOLFOX |-13.701  |8.730     |0.117   |-0.001        |266   |
#> |Treatment Arm G: IROX   |-2.245   |9.860     |0.820   |              |      |
#> |Age in Years            |-0.017   |0.319     |0.956   |              |      |
#> |sex Female              |3.016    |7.521     |0.688   |              |      |
#> |ps                      |46.721   |5.987     |< 0.001 |0.045         |266   |
#> |Age in Years            |-0.084   |0.311     |0.787   |              |      |
#> |sex Female              |1.169    |7.343     |0.874   |              |      |
#> |hgb                     |-13.845  |2.137     |< 0.001 |0.031         |266   |
#> |Age in Years            |0.095    |0.314     |0.763   |              |      |
#> |sex Female              |-5.980   |7.516     |0.426   |              |      |
#> 

tab2.df <- as.data.frame(tab2)

tab2.df[1:5,]
#>     y.term  y.label strata.term adjustment model         term
#> 1 alk.phos alk.phos              adjusted1     1  (Intercept)
#> 2 alk.phos alk.phos              adjusted1     1 armF: FOLFOX
#> 3 alk.phos alk.phos              adjusted1     1   armG: IROX
#> 4 alk.phos alk.phos              adjusted1     1          age
#> 5 alk.phos alk.phos              adjusted1     1    sexFemale
#>                     label term.type     estimate  std.error      p.value
#> 1             (Intercept) Intercept 175.54808014 20.5866451 4.343327e-17
#> 2 Treatment Arm F: FOLFOX      Term -13.70061548  8.7296300 1.168035e-01
#> 3   Treatment Arm G: IROX      Term  -2.24497807  9.8600363 8.199294e-01
#> 4            Age in Years  Adjuster  -0.01740894  0.3187823 9.564575e-01
#> 5              sex Female  Adjuster   3.01598411  7.5209656 6.884824e-01
#>   adj.r.squared Nmiss
#> 1 -0.0006968528   266
#> 2 -0.0006968528   266
#> 3 -0.0006968528   266
#> 4 -0.0006968528   266
#> 5 -0.0006968528   266