Residuals for an amerasfit Object

Computes residuals for a fitted amerasfit object.

Usage

# S3 method for class 'amerasfit'
residuals(object,
          method = "RC",
          type = NULL,
          data = NULL,
          dose.col = NULL,
          scaled.schoenfeld = TRUE,
          ...)

Arguments

object

A fitted model object of class amerasfit, as returned by ameras.

method

Character string specifying which estimation method to compute residuals for. One of "RC", "ERC", "MCML", "FMA", or "BMA". Defaults to "RC".

type

The type of residuals to compute. Defaults to "pearson" for all families except "prophaz", for which the default is "schoenfeld". For types other than "schoenfeld", let $Y_i$ and $\mu_i$ denote the observed response and fitted mean response for individual $i$, respectively. Then the residuals are defined as follows:

"pearson": Pearson residuals. For "gaussian": $(Y_i - \mu_i) / \sigma$ where $\sigma$ is the estimated residual standard deviation (note: glm returns raw residuals for Gaussian). For "binomial" and "clogit": $(Y_i - \mu_i) / \sqrt{\mu_i(1 - \mu_i)}$. For "poisson": $(Y_i - \mu_i) / \sqrt{\mu_i}$. For "multinomial": per-category Pearson residuals $(Y_{iz} - \mu_{iz}) / \sqrt{\mu_{iz}(1 - \mu_{iz})}$ where $\mu_{iz}$ is the fitted probability of category $z$ for individual $i$.
"deviance": Deviance residuals, defined as the signed square root of the individual contribution to the deviance. For "gaussian": the raw residual $Y_i - \mu_i$. For "binomial" and "clogit": $\pm\sqrt{-2\log(\hat{p}_i)}$ where $\hat{p}_i = \mu_i$ if $Y_i = 1$ and $\hat{p}_i = 1 - \mu_i$ if $Y_i = 0$, with sign equal to $\text{sign}(Y_i - \mu_i)$. For "poisson": $\pm\sqrt{2(Y_i \log(Y_i/\mu_i) - (Y_i - \mu_i))}$ for $Y_i > 0$ and $\pm\sqrt{2\mu_i}$ for $Y_i = 0$, with sign equal to $\text{sign}(Y_i - \mu_i)$. For "multinomial": per-category deviance residuals as for "binomial".
"response": Raw residuals $Y_i - \mu_i$. For "multinomial": the matrix $\bm{Y} - \hat{\bm{P}}$ where $\bm{Y}$ is the $N \times Z$ indicator matrix of observed categories and $\hat{\bm{P}}$ is the $N \times Z$ matrix of fitted probabilities.
"schoenfeld": Schoenfeld residuals for family="prophaz" only. For each event time, the unscaled residual for the individual experiencing the event is the observed covariate vector minus the risk-set weighted mean covariate vector at that event time. See Details.

data

The original data frame used for fitting. Only required when the model was fitted with keep.data=FALSE.

dose.col

Character string specifying the dose column to use when computing fitted values. If NULL (the default), the dose column is selected automatically: the mean dose across realizations for RC and ERC, the realization with the highest likelihood for MCML and FMA, and the most frequently selected realization for BMA. Can be set to any dose column present in the data to override the automatic selection.

scaled.schoenfeld

Logical. If TRUE (the default), scaled Schoenfeld residuals are returned, obtained by multiplying the raw Schoenfeld residuals by the estimated coefficient variance-covariance matrix following Grambsch and Therneau (1994). If FALSE, raw Schoenfeld residuals are returned. Only used when type="schoenfeld".

...

Additional arguments, currently unused.

Value

For families "gaussian", "binomial", "poisson", and "clogit", a numeric vector of length $N$ containing the residuals.

For family="multinomial", a numeric matrix of dimension $N \times Z$ where $Z$ is the number of outcome categories. Column names correspond to the factor levels. Note that when plotting via plot, the reference category is excluded since its residuals are a linear combination of the other categories.

For family="prophaz" with type="schoenfeld", a data frame with columns id (row index of the event), time (event time), and one additional column per model parameter containing the Schoenfeld residuals. Only rows corresponding to events (status=1) are included.

Details

Fitted values are computed using the dose column specified by dose.col.

For family="clogit", fitted values $\mu_i$ are the conditional probabilities of being a case within each matched set, computed as $R_i / \sum_{j \in \text{set}(i)} R_j$ where $R_i$ is the relative risk for individual $i$ and the sum is over all individuals in the same matched set.

For family="prophaz" and type="schoenfeld", the Schoenfeld residual for the individual failing at time $t$ is: $$\bm{r} = \bm{x} - \bar{\bm{x}}(t)$$ where $\bm{x}$ is the observed covariate vector for the failing individual and $$\bar{\bm{x}}(t) = \frac{\sum_{j \in \mathcal{R}(t)} \bm{x}_j R_j} {\sum_{j \in \mathcal{R}(t)} R_j}$$ is the weighted mean covariate vector in the risk set $\mathcal{R}(t)$ at time $t$, with weights equal to the relative risks $R_j$. Ties in event times are handled using the Breslow approximation.

References

Schoenfeld, D. (1982). Partial residuals for the proportional hazards regression model. Biometrika, 69(1), 239–241. doi:10.1093/biomet/69.1.239

Grambsch, P. M. and Therneau, T. M. (1994). Proportional hazards tests and diagnostics based on weighted residuals. Biometrika, 81(3), 515–526. doi:10.1093/biomet/81.3.515

Examples

data("data", package="ameras")
dosevars <- paste0("V", 1:10)

fit <- ameras(Y.binomial ~ dose(all_of(dosevars), model="ERR"),
              data=data, family="binomial", methods="RC")
#> Error in resolve_dose_selection(sel_args, data): ℹ In argument: `all_of(dosevars)`.
#> Caused by error:
#> ! object 'dosevars' not found

## Pearson residuals (default)
res <- residuals(fit)
#> Error: object 'fit' not found
summary(res)
#> Error: object 'res' not found

## Deviance residuals
res_dev <- residuals(fit, type="deviance")
#> Error: object 'fit' not found

## Response residuals
res_raw <- residuals(fit, type="response")
#> Error: object 'fit' not found

## Specific dose column
res_v1 <- residuals(fit, dose.col="V1")
#> Error: object 'fit' not found

## Multiple methods
# \donttest{
fit2 <- ameras(Y.binomial ~ dose(all_of(dosevars), model="ERR"),
               data=data, family="binomial", methods=c("RC", "ERC"))
#> Error in resolve_dose_selection(sel_args, data): ℹ In argument: `all_of(dosevars)`.
#> Caused by error:
#> ! object 'dosevars' not found
res_erc <- residuals(fit2, method="ERC")
#> Error: object 'fit2' not found
# }

## With keep.data=FALSE
# \donttest{
fit3 <- ameras(Y.binomial ~ dose(all_of(dosevars), model="ERR"),
               data=data, family="binomial", methods="RC",
               keep.data=FALSE)
#> Error in resolve_dose_selection(sel_args, data): ℹ In argument: `all_of(dosevars)`.
#> Caused by error:
#> ! object 'dosevars' not found
res <- residuals(fit3, data=data)
#> Error: object 'fit3' not found
# }

## Schoenfeld residuals for proportional hazards model
# \donttest{
fit4 <- ameras(Surv(time, status) ~ dose(all_of(dosevars), model="ERR"),
               data=data, family="prophaz", methods="RC")
#> Error in resolve_dose_selection(sel_args, data): ℹ In argument: `all_of(dosevars)`.
#> Caused by error:
#> ! object 'dosevars' not found
res_sch <- residuals(fit4)
#> Error: object 'fit4' not found
res_raw_sch <- residuals(fit4, scaled.schoenfeld=FALSE)
#> Error: object 'fit4' not found
# }