Risk.display: 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 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

object obtained from these 'display' functions

...

further arguments passed to or used by methods

Value

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

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.

Examples

Run this code

# NOT RUN {
     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.

# }