zhangkaicr / chest

:exclamation: This is a read-only mirror of the CRAN R package repository. chest — Change-in-Estimate Approach to Assess Confounding Effects

Change-in-Estimate (chest) Approach to Assess Confounding Effects

chest package

The ‘chest’ package can be used to assess confounding effects by comparing effect estimates from many models. It calculates the changes in effect estimates by adding one of many variables (potential confounding factors) to the model sequentially in a stepwise fashion. Effect estimates can be regression coefficients, odds ratios and hazard ratios depending on the modelling methods. At each step, only one variable that causes the largest change in the effect estimates among the remaining variables is added to the model. Effect estimates and change (%) values are presented in a graph and data frame table. This approach can be used for assessing confounding effects in epidemiological studies and bio-medical research including clinical trials.

Installation

You can install the released version of chest from CRAN with:

install.packages("chest")

Examples

Data: diabetes and mortality

A data frame ‘diab_df’ is used to examine the association between diabetes (Diabetes) and mortality (Endpoint). The purpose of using this data set is to demonstrate the use of the functions in this package rather than answering any research questions. Assuming it is a cohort design for Cox Proportional Hazards Models, cross-sectional design for Logistic Regression Model and matched cohort design for Conditional logistic regression Models.

chest_speedglm: report odds ratios at all steps with logistic regression models

library(chest)
chest_speedglm(
  crude = "Endpoint ~ Diabetes",
  xlist = c("Age", "Sex", "Married", "Smoke", "Cancer", "CVD","Education", "Income"), 
  zero = 1, data = diab_df)

#>       variables       OR       lb       ub      Change        p    n
#> 1         Crude 2.312758 1.838975 2.908604          NA 7.57e-13 2372
#> 2         + Age 3.348051 2.500654 4.482605  44.7644279 4.83e-16 2372
#> 3      + Income 2.940581 2.153766 4.014836 -12.1703550 1.13e-11 2061
#> 4         + CVD 2.831739 2.068823 3.875994  -3.7013899 8.09e-11 2061
#> 5       + Smoke 2.930687 2.135170 4.022595   3.4942324 2.84e-11 2061
#> 6         + Sex 2.901284 2.113594 3.982528  -1.0032733 4.38e-11 2061
#> 7   + Education 2.881540 2.096819 3.959939  -0.6805040 6.81e-11 2051
#> 8      + Cancer 2.863889 2.083367 3.936828  -0.6125761 9.11e-11 2051
#> 9     + Married 2.878757 2.093150 3.959219   0.5191530 7.88e-11 2048

Odds ratios showing the association between Diabetes and mortality Endpoint after each of other factors added to the model.

When the list of variables is long, generate a variable list first:

vlist <- c("Age", "Sex", "Married", "Smoke", "Cancer", "CVD","Education", "Income")
chest_speedglm(
  crude = "Endpoint ~ Diabetes",
  xlist = vlist,   zero = 1, data = diab_df)

#>       variables       OR       lb       ub      Change        p    n
#> 1         Crude 2.312758 1.838975 2.908604          NA 7.57e-13 2372
#> 2         + Age 3.348051 2.500654 4.482605  44.7644279 4.83e-16 2372
#> 3      + Income 2.940581 2.153766 4.014836 -12.1703550 1.13e-11 2061
#> 4         + CVD 2.831739 2.068823 3.875994  -3.7013899 8.09e-11 2061
#> 5       + Smoke 2.930687 2.135170 4.022595   3.4942324 2.84e-11 2061
#> 6         + Sex 2.901284 2.113594 3.982528  -1.0032733 4.38e-11 2061
#> 7   + Education 2.881540 2.096819 3.959939  -0.6805040 6.81e-11 2051
#> 8      + Cancer 2.863889 2.083367 3.936828  -0.6125761 9.11e-11 2051
#> 9     + Married 2.878757 2.093150 3.959219   0.5191530 7.88e-11 2048

Remove missing values, and change non-effect line

chest_speedglm(
  crude = "Endpoint ~ Diabetes", xlist = vlist, 
  data = diab_df, zero = c(0.98, 1.02),  na_omit = TRUE)

#>       variables       OR       lb       ub       Change        p    n
#> 1         Crude 2.305786 1.809862 2.937600           NA 1.37e-11 2048
#> 2         + Age 3.297099 2.421755 4.488837  42.99238627 3.50e-14 2048
#> 3      + Income 2.902046 2.125534 3.962238 -11.98183743 2.00e-11 2048
#> 4         + CVD 2.797882 2.044220 3.829405  -3.58931015 1.32e-10 2048
#> 5       + Smoke 2.900600 2.113218 3.981361   3.67127605 4.39e-11 2048
#> 6         + Sex 2.872333 2.092484 3.942824  -0.97453037 6.65e-11 2048
#> 7     + Married 2.894543 2.107594 3.975330   0.77324421 5.19e-11 2048
#> 8      + Cancer 2.881019 2.097209 3.957769  -0.46723505 6.52e-11 2048
#> 9   + Education 2.878757 2.093150 3.959219  -0.07851916 7.88e-11 2048

chest_glm: Logistic regression using (generalized linear models, ‘glm’).

‘chest_glm’ is slower than ‘chest_speedglm’. We can use ‘indicate = TRUE’ to monitor the progress. If it is too slow, you may want to try ‘chest_speedglm’.

 chest_glm(crude = "Endpoint ~ Diabetes", xlist = vlist, data = diab_df, indicate = TRUE)

chest_cox: Using Cox Proportional Hazards Models: ‘coxph’ of ‘survival’ package

chest_cox(crude = "Surv(t0, t1, Endpoint) ~ Diabetes", xlist = vlist,
          na_omit = TRUE, data = diab_df, zero = 1)

#>       variables       HR       lb       ub     Change            p    n
#> 1         Crude 1.588134 1.434544 1.758167         NA 4.950249e-19 2048
#> 2         + CVD 1.526276 1.377192 1.691499 -3.8949795 7.454317e-16 2048
#> 3      + Income 1.480726 1.335380 1.641891 -2.9844079 9.581156e-14 2048
#> 4       + Smoke 1.514956 1.366037 1.680108  2.3116907 3.596810e-15 2048
#> 5         + Sex 1.498963 1.351879 1.662049 -1.0556582 1.571022e-14 2048
#> 6     + Married 1.512616 1.363974 1.677456  0.9108110 4.451213e-15 2048
#> 7         + Age 1.526426 1.376076 1.693202  0.9129952 1.305521e-15 2048
#> 8      + Cancer 1.517896 1.368399 1.683726 -0.5587865 3.050629e-15 2048
#> 9   + Education 1.514437 1.365204 1.679982 -0.2279234 4.453189e-15 2048

‘chest_clogit’: Conditional logistic regression: ‘clogit’ of ‘survival’ package

chest_clogit(crude = "Endpoint ~ Diabetes + strata(mid)", 
             xlist = vlist, data = diab_df, indicate= TRUE, zero = 1)
#>  2 out of 9 3 out of 9 4 out of 9 5 out of 9 6 out of 9 7 out of 9 8 out of 9 9 out of 9

#>       variables       OR       lb       ub    Change            p    n
#> 1         Crude 2.586950 1.719871 3.891170        NA 5.033866e-06 2372
#> 2      + Income 2.850010 1.752942 4.633671 10.168718 2.405822e-05 2061
#> 3     + Married 3.133480 1.875838 5.234301  9.946296 1.283423e-05 2058
#> 4   + Education 3.030468 1.810620 5.072149 -3.287484 2.452619e-05 2048
#> 5       + Smoke 3.128331 1.839469 5.320260  3.229314 2.559384e-05 2048
#> 6         + Age 3.212487 1.883223 5.480007  2.690121 1.844153e-05 2048
#> 7         + CVD 3.148114 1.824571 5.431754 -2.003848 3.776568e-05 2048
#> 8      + Cancer 3.100427 1.790709 5.368067 -1.514782 5.340664e-05 2048
#> 9         + Sex 3.100427 1.790709 5.368067  0.000000 5.340664e-05 2048

Note:

Because ‘chest’ fits many models and compares effect estimates, some analyses may take long time to complete. In that case, consider ‘chest_speedglm’ for logistic regression and ‘chest_clogit’ with an argument of approximate method for conditional logistic regression.