On 17 Sep 2023, at 16:43 , John Fox <j...@mcmaster.ca> wrote:
Dear Robert,
Anova() calls linearHypothesis(), also in the car package, to compute sums of
squares and df, supplying appropriate hypothesis matrices. linearHypothesis()
usually tries to express the hypothesis matrix in symbolic equation form for
printing, but won't do this if coefficient names include arithmetic operators,
in your case - and +, which can confuse it.
The symbolic form of the hypothesis isn't really relevant for Anova(), which
doesn't use the printed representation of each hypothesis, and so, despite the
warnings, you get the correct ANOVA table. In your case, where the data are
balanced, with 4 cases per cell, Anova(mod) and summary(mod) are equivalent,
which makes me wonder why you would use Anova() in the first place.
To elaborate a bit, linearHypothesis() does tolerate arithmetic operators in
coefficient names if you specify the hypothesis symbolically rather than as a
hypothesis matrix. For example, to test, the interaction:
------- snip --------
linearHypothesis(mod,
+ c("TreatmentDabrafenib:ExpressionCD271+ = 0",
+ "TreatmentTrametinib:ExpressionCD271+ = 0",
+ "TreatmentCombination:ExpressionCD271+ = 0"))
Linear hypothesis test
Hypothesis:
TreatmentDabrafenib:ExpressionCD271+ = 0
TreatmentTrametinib:ExpressionCD271+ = 0
TreatmentCombination:ExpressionCD271+ = 0
Model 1: restricted model
Model 2: Viability ~ Treatment * Expression
Res.Df RSS Df Sum of Sq F Pr(>F)
1 27 18966
2 24 16739 3 2226.3 1.064 0.3828
------- snip --------
Alternatively:
------- snip --------
H <- matrix(0, 3, 8)
H[1, 6] <- H[2, 7] <- H[3, 8] <- 1
H
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
[1,] 0 0 0 0 0 1 0 0
[2,] 0 0 0 0 0 0 1 0
[3,] 0 0 0 0 0 0 0 1
linearHypothesis(mod, H)
Linear hypothesis test
Hypothesis:
Model 1: restricted model
Model 2: Viability ~ Treatment * Expression
Res.Df RSS Df Sum of Sq F Pr(>F)
1 27 18966
2 24 16739 3 2226.3 1.064 0.3828
Warning message:
In printHypothesis(L, rhs, names(b)) :
one or more coefficients in the hypothesis include
arithmetic operators in their names;
the printed representation of the hypothesis will be omitted
------- snip --------
There's no good reason that linearHypothesis() should try to express each
hypothesis symbolically for Anova(), since Anova() doesn't use that
information. When I have some time, I'll arrange to avoid the warning.
Best,
John
--
John Fox, Professor Emeritus
McMaster University
Hamilton, Ontario, Canada
web: https://www.john-fox.ca/
On 2023-09-16 4:39 p.m., Robert Baer wrote:
Caution: External email.
When doing Anova using the car package, I get a print warning that is
unexpected. It seemingly involves have my flow cytometry factor levels
named CD271+ and CD171-. But I am not sure this warning should be
intended behavior. Any explanation about whether I'm doing something
wrong? Why can't I have CD271+ and CD271- as factor levels? Its legal
text isn't it?
library(car) mod = aov(Viability ~ Treatment*Expression, data = dat1)
Anova(mod, type =2) Anova Table (Type II tests) Response: Viability Sum
Sq Df F value Pr(>F) Treatment 19447.3 3 9.2942 0.0002927 *** Expression
2669.8 1 3.8279 0.0621394 . Treatment:Expression 2226.3 3 1.0640
0.3828336 Residuals 16739.3 24 --- Signif. codes: 0 ‘***’ 0.001 ‘**’
0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Warning messages: 1: In printHypothesis(L,
rhs, names(b)) : one or more coefficients in the hypothesis include
arithmetic operators in their names; the printed representation of the
hypothesis will be omitted 2: In printHypothesis(L, rhs, names(b)) : one
or more coefficients in the hypothesis include arithmetic operators in
their names; the printed representation of the hypothesis will be
omitted 3: In printHypothesis(L, rhs, names(b)) : one or more
coefficients in the hypothesis include arithmetic operators in their
names; the printed representation of the hypothesis will be omitted
The code to reproduce:
```
dat1 <-structure(list(Treatment = structure(c(1L, 1L, 1L, 1L, 3L, 1L,
1L, 1L, 1L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L), levels = c("Control",
"Dabrafenib", "Trametinib", "Combination"), class = "factor"),
Expression = structure(c(2L, 2L, 2L, 2L, 2L, 1L,
1L, 1L,
1L, 2L, 2L, 2L, 2L, 1L,
1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L,
1L, 2L, 2L, 2L, 2L, 1L,
1L, 1L, 1L), levels = c("CD271-",
"CD271+"), class = "factor"),
Viability = c(128.329809725159, 24.2360176821065,
76.3597924274457, 11.0128771862387, 21.4683836248318,
140.784162982894, 87.4303286565443,
118.181818181818, 53.603690178743,
51.2973284643475, 5.47760907168941,
27.1574091870075, 50.8360561214684,
56.5250816836441, 28.6949836632712,
93.2731116663463, 71.900826446281,
32.2314049586777, 24.2360176821065,
27.4649240822602, 24.0822602344801,
26.542379396502, 30.693830482414,
27.772438977513, 13.4729963482606,
8.24524312896406, 18.5469921199308,
13.9342686911397, 13.3192389006342,
19.9308091485681, 17.6244474341726,
16.2406304055353)),
row.names = c(NA,
-32L),
class = c("tbl_df", "tbl", "data.frame"))
mod = aov(Viability ~ Treatment*Expression, data = dat1)
summary(mod)
library(car)
Anova(mod, type =2)
```
sessionInfo() R version 4.3.1 (2023-06-16 ucrt) Platform:
x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 11 x64 (build
25951) Matrix products: default locale: [1] LC_COLLATE=English_United
States.utf8 LC_CTYPE=English_United States.utf8
LC_MONETARY=English_United States.utf8 [4] LC_NUMERIC=C
LC_TIME=English_United States.utf8 time zone: America/Chicago tzcode
source: internal attached base packages: [1] stats graphics grDevices
utils datasets methods base other attached packages: [1] car_3.1-2
carData_3.0-5 tidyr_1.3.0 readr_2.1.4 readxl_1.4.3 ggplot2_3.4.3
dplyr_1.1.3 loaded via a namespace (and not attached): [1] crayon_1.5.2
vctrs_0.6.3 cli_3.6.1 rlang_1.1.1 purrr_1.0.2 generics_0.1.3
labeling_0.4.3 [8] bit_4.0.5 glue_1.6.2 colorspace_2.1-0 hms_1.1.3
scales_1.2.1 fansi_1.0.4 grid_4.3.1 [15] cellranger_1.1.0 abind_1.4-5
munsell_0.5.0 tibble_3.2.1 tzdb_0.4.0 lifecycle_1.0.3 compiler_4.3.1
[22] pkgconfig_2.0.3 rstudioapi_0.15.0 farver_2.1.1 R6_2.5.1
tidyselect_1.2.0 utf8_1.2.3 parallel_4.3.1 [29] vroom_1.6.3 pillar_1.9.0
magrittr_2.0.3 bit64_4.0.5 tools_4.3.1 withr_2.5.0 gtable_0.3.4
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