On Wed, 24 Feb 2010, chipmaney wrote:
Recently, I ran a series of Kruskal-Wallace tests [kruskal.test()] using by()
to group by site Output is a list:
Herb.KW
Herb.df$ID: 10-1
Kruskal-Wallis rank sum test
data: Indicator_Rating by Year
Kruskal-Wallis chi-squared = 15.24, df = 7, p-value = 0.03302
-----------------------------------------------------------------------------------------------------
Herb.df$ID: 18-1
Kruskal-Wallis rank sum test
data: Indicator_Rating by Year
Kruskal-Wallis chi-squared = 13.56, df = 7, p-value = 0.05963
-----------------------------------------------------------------------------------------------------
Herb.df$ID: 18-10
Kruskal-Wallis rank sum test
data: Indicator_Rating by Year
Kruskal-Wallis chi-squared = 16.65, df = 5, p-value = 0.005213
------------------------------------------------------------------------------------------------------
I used the following code to extract a vector of p.values for each list
element:
sapply(Herb.KW, '[[', 'p.value')
10-1 18-1 18-10 18-11 18-12 18-13 18-2
18-3 18-4 18-5 18-6
3.302e-02 5.963e-02 5.213e-03 1.321e-09 4.483e-04 2.823e-02 2.893e-03
2.535e-02 5.701e-03
3-1 37-15 37-16 37-17 37-20 37-21 37-23
37-24 37-25 37-26
3.552e-18 9.189e-01 4.051e-03 2.122e-09 1.325e-01 2.128e-03 4.543e-01
9.940e-02 1.748e-02
I then used wilcoxon_test for post-hoc analysis, which also returns a LIST
with sites as elements. However, when I try to extract a pvalue from the
list elements, I get the following message:
The test functions in "coin" do not return "htest" objects like
kruskal.test() but have their own S4 class. But there is an extractor
function pvalue() which can be easily employed:
R> wt <- wilcox_test(extra ~ group, data = sleep, distribution = "exact")
R> pvalue(wt)
[1] 0.06581654
Similarly, you can extract both the standardized statistic as well as the
underlying linear statistic (aka rank sum) via statistic():
R> statistic(wt)
1
-1.854118
R> statistic(wt, "linear")
1 80.5
Thus, your code line should just be
sapply(Herb.Wilcox, pvalue)
instead of
sapply(Herb.Wilcox, '[[', 'p.value')
For more implementation details, see:
http://www.jstatsoft.org/v28/i08/
(as pointed out in citation("coin")).
Best,
Z
Error in FUN(X[[1L]], ...) : object of type 'S4' is not subsettable
First, how do I determine what the "values" (e.g., statistic, pvalue) of the
model output are, because the reference manual does not say (unlike for
kruskal.test)...is the value object named "p.value" or "pvalue" or
"p-value"??? Is the statistic named "statistic" or "Z.statistic" or
"U.statistic"????
Second, why isn't this object not subsettable even though class=list? how do
i get around this problem and extract the statistic and p-value for each
element in the list?
--
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