Loglinear Models for Three-way tables

Note: This is not an r package but just a set of r functions aiming at one purpose.

Overview

R codes to select the best models fitting three-way tables.

dplyr
broom
plyr

packages would be used. Install these before use this set.

`_common.R`

define find_xname(): used in fitted_val.R, goodness_fit.R
modify broom::tidy.anova() function

`model_threeway.R`

function model_loglin()

fit glm for given data
for every pair of independence model

`goodness_fit.R`

function good_loglin()

for fitted model_loglin,
compute goodness-of-fit
implement with purrr::map() and dplyr::bind_rows()

`fitted_val.R`

function fit_loglin()

for fitted model_loglin,
compute fitted values for every pair of independence model
implement with purrr::map() and plyr::join_all()

Frow now on, this document will show how these functions can be applied.

call tidyverse and broom libraries, and the other functions with r/_common.R
fit with model_loglin()
goodness-of-fit with good_loglin()
choosing the best model based on the goodness-of-fit statistic
compute fitted values with fitted_val

Loading Functions

# install.packages("httr")
library(httr)
git_api <- GET("https://api.github.com/repos/ygeunkim/loglinear3/git/trees/master?recursive=1")
stop_for_status(git_api)
repo_list <- unlist(lapply(content(git_api)$tree, "[", "path"), use.names = FALSE)
# R files in r folder -----------------------------
repo_list <- stringr::str_subset(repo_list, pattern = "^r/")
repo_list <- stringr::str_c("https://raw.githubusercontent.com/ygeunkim/loglinear3/master/", repo_list)
# source every file
sapply(repo_list, source)
#>         https://raw.githubusercontent.com/ygeunkim/loglinear3/master/r/_common.R
#> value   ?                                                                       
#> visible FALSE                                                                   
#>         https://raw.githubusercontent.com/ygeunkim/loglinear3/master/r/fitted_val.R
#> value   ?                                                                          
#> visible FALSE                                                                      
#>         https://raw.githubusercontent.com/ygeunkim/loglinear3/master/r/goodness_fit.R
#> value   ?                                                                            
#> visible FALSE                                                                        
#>         https://raw.githubusercontent.com/ygeunkim/loglinear3/master/r/model_threeway.R
#> value   ?                                                                              
#> visible FALSE

Beginning

tidyverse and broom are loaded. Here we should modify tidy function of tidymodels (2018). tidy.anova() is not defined for anova.glm, so we should add more elements in renamers in the function. Using the original tidy gives warning message.

renamers <- c(
    ...
    "Ref.df" = "ref.df",
    "Deviance" = "deviance", # glm object
    "Resid. Df" = "resid.df", # glm object
    "Resid. Dev" = "resid.dev" # glm object
  )

In addition, find_xname() function would be used later to construct the various independence models.

Data: Alcohol, cigarette, and marijuana use

Data from Agresti (2012) would be used.

refers to a survey by the Wright State University School of Medicine and the United Health Services in Dayton, Ohio. The survey asked 2276 students in their final year of high school in a nonurban area near Dayton, Ohio, whether they had ever used alcohol, cigarettes, or maijuana.

(substance <-
  read_delim("data/Substance_use.dat", delim = " ") %>% 
  mutate(alcohol = str_trim(alcohol)) %>% 
  mutate_if(is.character, factor) %>% 
  mutate_if(is.factor, fct_rev))
#> # A tibble: 8 x 4
#>   alcohol cigarettes marijuana count
#>   <fct>   <fct>      <fct>     <dbl>
#> 1 yes     yes        yes         911
#> 2 yes     yes        no          538
#> 3 yes     no         yes          44
#> 4 yes     no         no          456
#> 5 no      yes        yes           3
#> 6 no      yes        no           43
#> 7 no      no         yes           2
#> 8 no      no         no          279

Long data format as above is easy to fit loglinear model. Against wide format, i.e. contingency table, try tidyr::gather().

Change to the long data format

For example, look at the below table.

(aids <- read_table("data/AIDS.dat"))
#> # A tibble: 4 x 4
#>   race  azt     yes    no
#>   <chr> <chr> <dbl> <dbl>
#> 1 white yes      14    93
#> 2 white no       32    81
#> 3 black yes      11    52
#> 4 black no       12    43

aids %>% 
  gather(yes, no, key = symptom, value = count)
#> # A tibble: 8 x 4
#>   race  azt   symptom count
#>   <chr> <chr> <chr>   <dbl>
#> 1 white yes   yes        14
#> 2 white no    yes        32
#> 3 black yes   yes        11
#> 4 black no    yes        12
#> 5 white yes   no         93
#> 6 white no    no         81
#> 7 black yes   no         52
#> 8 black no    no         43

Finally, we get the long data.

Fitting GLMs

in hand

We can write every formula in hand. However, it is annoying.

(subs_hierarchy <-
  substance %>% 
  do(
    indep = glm(count ~ alcohol + cigarettes + marijuana, data = ., family = poisson()),
    ac_m = glm(count ~ alcohol + cigarettes + marijuana + alcohol:cigarettes, 
               data = ., family = poisson()),
    amcm = glm(count ~ alcohol + cigarettes + marijuana + alcohol:marijuana + cigarettes:marijuana, 
               data = ., family = poisson()),
    acamcm = glm(count ~ alcohol + cigarettes + marijuana + alcohol:cigarettes + alcohol:marijuana + cigarettes:marijuana, 
                 data = ., family = poisson()),
    acm = glm(count ~ alcohol * cigarettes * marijuana, 
              data = ., family = poisson())
  ))
#> # A tibble: 1 x 5
#>   indep  ac_m   amcm   acamcm acm   
#>   <list> <list> <list> <list> <list>
#> 1 <glm>  <glm>  <glm>  <glm>  <glm>

Defining function

Function can be defined for more general usage. See r/model_threeway.R

model_loglin() fits loglinear model for every pair of independence model.

.data: data
yname: character, response variable
glm_fam: random component of glm, option for family of glm(). Since we are fitting loglinear model, poisson() is set to be default.

It returns tibble with list element.

(subs_hierarchy <- model_loglin(substance, yname = "count", glm_fam = poisson()))
#> # A tibble: 1 x 9
#>   indep joint1 joint2 joint3 conditional1 conditional2 conditional3 homogen
#>   <lis> <list> <list> <list> <list>       <list>       <list>       <list> 
#> 1 <glm> <glm>  <glm>  <glm>  <glm>        <glm>        <glm>        <glm>  
#> # … with 1 more variable: threefac <list>

Each list has glm object with [[1]].

subs_hierarchy$indep[[1]]
#> 
#> Call:  glm(formula = mutual, family = glm_fam, data = .)
#> 
#> Coefficients:
#>  (Intercept)     alcoholno  cigarettesno   marijuanano  
#>        6.292        -1.785        -0.649         0.315  
#> 
#> Degrees of Freedom: 7 Total (i.e. Null);  4 Residual
#> Null Deviance:       2850 
#> Residual Deviance: 1290  AIC: 1340

Chi-square Goodness-of-fit tests

Statistic

$G^2 = 2\sum n_{ijk}\ln\frac{n_{ijk}}{\hat\mu_{ijk}}$

$X^2 = \sum\frac{(n_{ijk} - \hat\mu_{ijk})^2}{\hat\mu_{ijk}}$

with residual df = the number of cell count - the number of non-redundant parameters

good_loglin() calculates the above statistic for given option test. test = "LRT" option of anova.glm() produces . test = Chisq gives . As noticed, this function is designed to be applied with purrr::map() and dplyr::bind_rows().

(subs_good <-
  subs_hierarchy %>% 
  map(good_loglin, test = "LRT") %>% 
  bind_rows()) %>% 
  pander::pander()

model	df	resid.df	resid.dev
alcohol + cigarettes + marijuana	1	4	1286
alcohol + cigarettes + marijuana + cigarettes:marijuana	1	3	534.2
alcohol + cigarettes + marijuana + alcohol:marijuana	1	3	939.6
alcohol + cigarettes + marijuana + alcohol:cigarettes	1	3	843.8
alcohol + cigarettes + marijuana + alcohol:marijuana + cigarettes:marijuana	1	2	187.8
alcohol + cigarettes + marijuana + alcohol:cigarettes + cigarettes:marijuana	1	2	92.02
alcohol + cigarettes + marijuana + alcohol:cigarettes + alcohol:marijuana	1	2	497.4
alcohol + cigarettes + marijuana + alcohol:cigarettes + alcohol:marijuana + cigarettes:marijuana	1	1	0.374
alcohol + cigarettes + marijuana + alcohol:cigarettes + alcohol:marijuana + cigarettes:marijuana + alcohol:cigarettes:marijuana	1	0	0

Choosing the best model

From , we compare reduced model to complex model

$G^2(M_0 \mid M_1) = G^2(M_0) - G^2(M_1) \approx \chi^2\Big(df = df(M_0) - df(M_1)\Big)$

subs_good %>% 
  rename(alternative = model) %>% 
  group_by(resid.df) %>% 
  slice(which.min(resid.dev)) %>% 
  arrange(resid.df) %>% 
  mutate(
    goodness = c(resid.dev[1], -diff(resid.dev)),
    df_good = c(resid.df[1], -diff(resid.df))
  ) %>% 
  mutate(p_value = pchisq(goodness, df = df_good, lower.tail = FALSE)) %>% 
  pander::pander()

alternative	df	resid.df	resid.dev	goodness
alcohol + cigarettes + marijuana + alcohol:cigarettes + alcohol:marijuana + cigarettes:marijuana + alcohol:cigarettes:marijuana	1	0	0	0
alcohol + cigarettes + marijuana + alcohol:cigarettes + alcohol:marijuana + cigarettes:marijuana	1	1	0.374	0.374
alcohol + cigarettes + marijuana + alcohol:cigarettes + cigarettes:marijuana	1	2	92.02	92.02
alcohol + cigarettes + marijuana + cigarettes:marijuana	1	3	534.2	534.2
alcohol + cigarettes + marijuana	1	4	1286	1286

Table continues below

df_good	p_value
0	1
1	0.541
2	0
3	0
4	0

(AC, AM, CM) vs saturated model (ACM): cannot reject with p-value 0.5408, so we choose (AC, AM, CM)
(A, CM) vs (AC, AM, CM): reject

Thus, we use the model (AC, AM, CM)

Fitted values

fit_loglin() computes fitted values for each independent model. Use this function with purrr::map() and plyr::join_all(). In plyr::join_all(), every variable name including response is written.

subs_hierarchy %>% 
  map(fit_loglin) %>% 
  plyr::join_all(by = c("count", "alcohol", "cigarettes", "marijuana")) %>% 
  pander::pander()

count	alcohol	cigarettes	marijuana	alcohol + cigarettes + marijuana
911	yes	yes	yes	540
538	yes	yes	no	740.2
44	yes	no	yes	282.1
456	yes	no	no	386.7
3	no	yes	yes	90.6
43	no	yes	no	124.2
2	no	no	yes	47.33
279	no	no	no	64.88

Table continues below

alcohol + cigarettes + marijuana + cigarettes:marijuana	alcohol + cigarettes + marijuana + alcohol:marijuana
782.7	627.3
497.5	652.9
39.39	327.7
629.4	341.1
131.3	3.284
83.47	211.5
6.609	1.716
105.6	110.5

Table continues below

alcohol + cigarettes + marijuana + alcohol:cigarettes	alcohol + cigarettes + marijuana + alcohol:marijuana + cigarettes:marijuana
611.2	909.2
837.8	438.8
210.9	45.76
289.1	555.2
19.4	4.76
26.6	142.2
118.5	0.24
162.5	179.8

Table continues below

alcohol + cigarettes + marijuana + alcohol:cigarettes + cigarettes:marijuana	alcohol + cigarettes + marijuana + alcohol:cigarettes + alcohol:marijuana
885.9	710
563.1	739
29.45	245
470.6	255
28.12	0.703
17.88	45.3
16.55	4.297
264.4	276.7

Table continues below

alcohol + cigarettes + marijuana + alcohol:cigarettes + alcohol:marijuana + cigarettes:marijuana	alcohol + cigarettes + marijuana + alcohol:cigarettes + alcohol:marijuana + cigarettes:marijuana + alcohol:cigarettes:marijuana
910.4	911
538.6	538
44.62	44
455.4	456
3.617	3
42.38	43
1.383	2
279.6	279

References

Agresti, Alan. 2012. Categorical Data Analysis. 3rd ed. Wiley.

tidymodels. 2018. “Stats-Anova-tidiers.R.” https://github.com/tidymodels/broom/blob/master/R/stats-anova-tidiers.R.

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Loglinear Models for Three-way tables

Overview

`_common.R`

`model_threeway.R`

`goodness_fit.R`

`fitted_val.R`

Loading Functions

Beginning

Data: Alcohol, cigarette, and marijuana use

Change to the long data format

Fitting GLMs

in hand

Defining function

Chi-square Goodness-of-fit tests

Statistic

Choosing the best model

Fitted values

References

About

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ygeunkim/loglinear3

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Loglinear Models for Three-way tables

Overview

_common.R

model_threeway.R

goodness_fit.R

fitted_val.R

Loading Functions

Beginning

Data: Alcohol, cigarette, and marijuana use

Change to the long data format

Fitting GLMs

in hand

Defining function

Chi-square Goodness-of-fit tests

Statistic

Choosing the best model

Fitted values

References

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`_common.R`

`model_threeway.R`

`goodness_fit.R`

`fitted_val.R`

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