risk.display: Tables for multivariate odds ratio, incidence density etc

In epiDisplay: Epidemiological Data Display Package

Tables for multivariate odds ratio, incidence density etc

Description

Display of various epidemiological modelling results in a medically understandable format

Usage

logistic.display(logistic.model, alpha = 0.05, crude = TRUE, 
    crude.p.value = FALSE, decimal = 2, simplified = FALSE) 
clogistic.display(clogit.model, alpha = 0.05, crude=TRUE, 
    crude.p.value=FALSE, decimal = 2, simplified = FALSE)
cox.display (cox.model, alpha = 0.05, crude=TRUE, crude.p.value=FALSE, 
    decimal = 2, simplified = FALSE) 
regress.display(regress.model, alpha = 0.05, crude = FALSE, 
    crude.p.value = FALSE, decimal = 2, simplified = FALSE) 
idr.display(idr.model, alpha = 0.05, crude = TRUE, crude.p.value = FALSE, 
    decimal = 2, simplified = FALSE) 
mlogit.display(multinom.model, decimal = 2, alpha = 0.05) 
ordinal.or.display(ordinal.model, decimal = 3, alpha = 0.05)  
tableGlm (model, modified.coeff.array, decimal)
## S3 method for class 'display'
print(x, ...) 

Arguments

logistic.model	a model from a logistic regression
clogit.model	a model from a conditional logistic regression
regress.model	a model from a linear regression
cox.model	a model from a cox regression
idr.model	a model from a Poisson regression or a negative binomial regression
multinom.model	a model from a multinomial or polytomous regression
ordinal.model	a model from an ordinal logistic regression
alpha	significance level
crude	whether crude results and their confidence intervals should also be displayed
crude.p.value	whether crude P values should also be displayed if and only if 'crude=TRUE'
decimal	number of decimal places displayed
simplified	whether the display should be simplified
model	model passed from logistic.display or regress.display to tableGlm
modified.coeff.array	array of model coefficients sent to the function 'tableGlm' to produce the final output
x	object obtained from these 'display' functions
...	further arguments passed to or used by methods

Details

R provides several epidemiological modelling techniques. The functions above display these results in a format easier for medical people to understand.

The function 'tableGlm' is not for general use. It is called by other display functions to receive the 'modified.coeff.array' and produce the output table.

The argument 'simplified' has a default value of 'FALSE'. It works best if the 'data' argument has been supplied during creation of the model. Under this condition, the output has three parts. Part 1 (the first line) indicates the type of the regression and the outcome. For logistic regression, if the outcome is a factor then the referent level is shown. Part 2 shows the main output table where each independent variable coefficient is displayed. If the independent variable is continuous (class numeric) then name of the variable is shown (or the descriptive label if it exists). If the variable is a factor then the name of the level is shown with the referent level omitted. In this case, the name of the referent level and the statistic testing for group effects are displayed. An F-test is used when the model is of class 'lm' or 'glm' with 'family=gaussian' specified. A Likelihood Ratio test is performed when the model is of class 'glm' with 'family = binomial' or 'family = poisson' specified and for models of class 'coxph' and 'clogit'. These tests are carried out with the records available in the model, not necessary all records in the full 'data' argument. The number of records in the model is displayed in the part 3 of the output. When 'simplified=TRUE', the first and the last parts are omitted from the display.

The result is an object of class 'display' and 'list'. Their apparence on the R console is controlled by 'print.display'. The 'table' attribute of these 'display' objects are ready to write (using 'write.csv') to a .csv file which can then be copied to a manuscript document. This approach can substantially reduce both the time and errors produced due to conventional manual copying.

Value

'logistic.display', 'regress.display', 'clogit.display' and 'cox.display', each produces an output table. See 'details'.

Note

Before using these 'display' functions, please note the following limitations.

1) Users should define the 'data' argument of the model.

2) The names of the independent variables must be a subset of the names of the variables in the 'data' argument. Sometimes, one of more variables are omitted by the model due to collinearity. In such a case, users have to specify 'simplified=TRUE' in order to get the display function to work.

3) Under the following conditions, 'simplified' will be forced to TRUE and 'crude' forced to FALSE.

3.1) The names of the independent variables contain a function such as 'factor()' or any '\$' sign.

3.2) The levels of the factor variables contain any ':' sign.

3.3) There are more than one interaction terms in the model

3.4) The 'data' argument is missing in the conditional logistic regression and Cox regression model

4) For any other problems with these display results, users are advised to run 'summary(model)' or 'summary(model)$coefficients' to check the consistency between variable names in the model and those in the coefficients. The number in the latter may be fewer than that in the former due to collinearity. In this case, it is advised to specify 'simplified=TRUE' to turn off the attempt to tidy up the rownames of the output from 'summary(model)$coeffients'. The output when 'simplified=TRUE' is more reliable but less understandable.

Author(s)

Virasakdi Chongsuvivatwong [e-mail]

See Also

'glm', 'confint'

Examples

     model0 <- glm(case ~ induced + spontaneous, family=binomial, data=infert)
     summary(model0)
     logistic.display(model0)

     data(ANCdata)
     glm1 <- glm(death ~ anc + clinic, family=binomial, data=ANCdata)
     logistic.display(glm1)
     logistic.display(glm1, simplified=TRUE)

     library(MASS) # necessary for negative binomial regression
     data(DHF99); .data <- DHF99
     attach(.data)
     model.poisson <- glm(containers ~ education + viltype, 
         family=poisson, data=DHF99)
     
     model.nb <- glm.nb(containers ~ education + viltype, 
         data=.data)
     idr.display(model.poisson)  -> poiss
     print(poiss) # or print.display(poiss) or poiss
     idr.display(model.nb) 
     detach(.data) 
      
     data(VC1to6)
     .data <- VC1to6
     .data$fsmoke <- factor(.data$smoking)
     levels(.data$fsmoke) <- list("no"=0, "yes"=1)
     clr1 <- clogit(case ~ alcohol + fsmoke + strata(matset), data=.data)
     clogistic.display(clr1)
     rm(list=ls())
      
     data(BP)
     .data <- BP
     attach(.data)
     age <- as.numeric(as.Date("2000-01-01") - birthdate)/365.25
     agegr <- pyramid(age,sex, bin=20)$ageGroup
     .data$hypertension <- sbp >= 140 | dbp >=90
     detach(.data)
     model1 <- glm(hypertension ~ sex + agegr + saltadd, family=binomial, 
               data=.data)
     logistic.display(model1) -> table3
     attributes(table3)
     table3
     table3$table
     # You may want to save table3 into a spreadsheet
     write.csv(table3$table, file="table3.csv") # Note $table
     ## Have a look at this file in Excel, or similar spreadsheet program
     
     file.remove(file="table3.csv")
     model2 <- glm(hypertension ~ sex * age + sex * saltadd, family=binomial, 
               data=.data)
     logistic.display(model2) 
     # More than 1 interaction term so 'simplified turned to TRUE

     reg1 <- lm(sbp ~ sex + agegr + saltadd, data=.data)
     regress.display(reg1)

     reg2 <- glm(sbp ~ sex + agegr + saltadd, family=gaussian, data=.data)
     regress.display(reg2)
     
     data(Compaq)
     cox1 <- coxph(Surv(year, status) ~ hospital + stage * ses, data=Compaq)
     cox.display(cox1, crude.p.value=TRUE)

     # Ordinal logistic regression
     library(nnet)
     options(contrasts = c("contr.treatment", "contr.poly"))
     house.plr <- polr(Sat ~ Infl + Type + Cont, weights = Freq, data = housing)
     house.plr
     ordinal.or.display(house.plr)

     # Polytomous or multinomial logistic regression
     house.multinom <- multinom(Sat ~ Infl + Type + Cont, weights = Freq, 
             data = housing)
     summary(house.multinom)
     mlogit.display(house.multinom, alpha=.01) # with 99% confidence limits.

epiDisplay documentation built on May 18, 2022, 5:11 p.m.