[R] Print hypothesis warning- Car package

[Bert Gunter]

The factor names are legal but the Warnings tell you pretty clearly that
Car doesn't like such things. So why don't you just use something else that
is more conventional.

-- Bert

On Sat, Sep 16, 2023 at 1:40 PM Robert Baer <rbaer using atsu.edu> wrote:

> 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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