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

[jamesly]

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.

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

Thank you!

[technocrat]

@jamesly

data(wine)

Reproducibility fails here.

[cderv]

@technocrat

@jamesly

data(wine)

Reproducibility fails here.

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

@jamesly

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

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

harrelfe/Hmisc

[jamesly]

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)}

[jamesly]

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