Hmisc::html output in RMarkdown not displaying certain text correctly.

Publishing Your Results
1

Hello, I'm trying to use the Hmisc package but I'm keep getting strange text defects in Hmisc:html outputs. Here is my code.

## Hmisc package --------------
library(tidyverse)
library(Hmisc)
library(ucidata)

# Load wine data
data(wine)

# Re-code outcome
mydata <- wine %>%
  dplyr::mutate(red_wine = ifelse(color == "Red", 1, 0)) %>%
  dplyr::select(-color)

s <- Hmisc::summaryM(
  fixed_acidity + volatile_acidity + citric_acid + residual_sugar + chlorides + free_sulfur_dioxide +
    total_sulfur_dioxide + density + pH + sulphates + alcohol + quality ~ red_wine,
  data = mydata,
  overall = TRUE,
  test = TRUE,
  continuous = 5
)

html(s, caption='Predictors according to wine type',
     exclude1 = TRUE, npct = 'both', digits = 2,
     prmsd = TRUE, brmsd = TRUE, msdsize = mu$smaller2)

Both in RStudio notebook and preview (nb.html file), it shows this.

image
image895×588 39.6 KB

However, Knit can produce html file without this error. But I would like to see my work in RStudio while working.

Thank you!

2

Reproducibility fails here.

3

This data is from one of the package. What is not mention is that ucidata package is from Github not CRAN.

I don't really know what happens here, but this is due to this special ± character.

Here is a minimal reprex

---
output:
 html_document:
   df_print: paged
editor_options:
 chunk_output_type: inline
---

```{r}
htmltools::HTML(Hmisc::markupSpecs$html$plminus)
```

The markup character print well when knitting the document but does not show correctly on the RStudio IDE as inline output.

I would advice to maybe open an issue in Hmisc repo to get help to investigate

4

Thank you for your help. Interestingly, reprex does render correctly. Below is my reprex.

## Hmisc package --------------
library(tidyverse)
library(Hmisc)
#> Loading required package: lattice
#> Loading required package: survival
#> Loading required package: Formula
#> 
#> Attaching package: 'Hmisc'
#> The following objects are masked from 'package:dplyr':
#> 
#>     src, summarize
#> The following objects are masked from 'package:base':
#> 
#>     format.pval, units
library(ucidata)

# Load wine data
data(wine)

# Re-code outcome
mydata <- wine %>%
  dplyr::mutate(red_wine = ifelse(color == "Red", 1, 0)) %>%
  dplyr::select(-color)

s <- Hmisc::summaryM(
  fixed_acidity + volatile_acidity + citric_acid + residual_sugar + chlorides + free_sulfur_dioxide +
    total_sulfur_dioxide + density + pH + sulphates + alcohol + quality ~ red_wine,
  data = mydata,
  overall = TRUE,
  test = TRUE,
  continuous = 5
)

html(s, caption='Predictors according to wine type',
     exclude1 = TRUE, npct = 'both', digits = 2,
     prmsd = TRUE, brmsd = TRUE, msdsize = mu$smaller2)

Predictors according to wine type.

0
N=4898

1
N=1599

Combined
N=6497

Test Statistic

fixed_acidity

6.30 6.80 7.30
6.85 ± 0.84

7.10 7.90 9.20
8.32 ± 1.74

6.40 7.00 7.70
7.22 ± 1.30

F1<U+2009>6495=1421, P<0.001

volatile_acidity

0.21 0.26 0.32
0.28 ± 0.10

0.39 0.52 0.64
0.53 ± 0.18

0.23 0.29 0.40
0.34 ± 0.16

F1<U+2009>6495=3637, P<0.001

citric_acid

0.27 0.32 0.39
0.33 ± 0.12

0.09 0.26 0.42
0.27 ± 0.19

0.25 0.31 0.39
0.32 ± 0.15

F1<U+2009>6495=173, P<0.001

residual_sugar

1.7 5.2 9.9
6.4 ± 5.1

1.9 2.2 2.6
2.5 ± 1.4

1.8 3.0 8.1
5.4 ± 4.8

F1<U+2009>6495=458, P<0.001

chlorides

0.036 0.043 0.050
0.046 ± 0.022

0.070 0.079 0.090
0.087 ± 0.047

0.038 0.047 0.065
0.056 ± 0.035

F1<U+2009>6495=5156, P<0.001

free_sulfur_dioxide

23 34 46
35 ± 17

7 14 21
16 ± 10

17 29 41
31 ± 18

F1<U+2009>6495=2409, P<0.001

total_sulfur_dioxide

108 134 167
138 ± 42

22 38 62
46 ± 33

77 118 156
116 ± 57

F1<U+2009>6495=5473, P<0.001

density

0.9917 0.9937 0.9961
0.9940 ± 0.0030

0.9956 0.9968 0.9978
0.9967 ± 0.0019

0.9923 0.9949 0.9970
0.9947 ± 0.0030

F1<U+2009>6495=1300, P<0.001

pH

3.09 3.18 3.28
3.19 ± 0.15

3.21 3.31 3.40
3.31 ± 0.15

3.11 3.21 3.32
3.22 ± 0.16

F1<U+2009>6495=829, P<0.001

sulphates

0.41 0.47 0.55
0.49 ± 0.11

0.55 0.62 0.73
0.66 ± 0.17

0.43 0.51 0.60
0.53 ± 0.15

F1<U+2009>6495=2101, P<0.001

alcohol

9.5 10.4 11.4
10.5 ± 1.2

9.5 10.2 11.1
10.4 ± 1.1

9.5 10.3 11.3
10.5 ± 1.2

F1<U+2009>6495=1.8, P=0.18

quality

5.00 6.00 6.00
5.88 ± 0.89

5.00 6.00 6.00
5.64 ± 0.81

5.00 6.00 6.00
5.82 ± 0.87

F1<U+2009>6495=100, P<0.001

a b c represent the lower quartile a, the median b, and the upper quartile c for continuous variables. x ± s represents X ± 1 SD.
Test used: Wilcoxon test .

Created on 2020-09-24 by the reprex package (v0.3.0)

5

I just reinstalled RStudio and it's still the same...

6

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