[R] Print hypothesis warning- Car package

Robert Baer rb@er @end|ng |rom @t@u@edu
Sat Sep 16 22:39:49 CEST 2023


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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