TLF examples
TLF examples through R Markdown
This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see http://rmarkdown.rstudio.com.
two different layouts from two package
This table (used package 'table1') can be displayed in HTML. But not in word because word enviroment does not convert the layout format.
| Alive (N=134) |
Melanoma death (N=57) |
Non-melanoma death (N=14) |
Overall (N=205) |
|
|---|---|---|---|---|
| factor(sex) | ||||
| 0 | 91 (67.9%) | 28 (49.1%) | 7 (50.0%) | 126 (61.5%) |
| 1 | 43 (32.1%) | 29 (50.9%) | 7 (50.0%) | 79 (38.5%) |
| age | ||||
| Mean (SD) | 50.0 (15.9) | 55.1 (17.9) | 65.3 (10.9) | 52.5 (16.7) |
| Median [Min, Max] | 52.0 [4.00, 84.0] | 56.0 [14.0, 95.0] | 65.0 [49.0, 86.0] | 54.0 [4.00, 95.0] |
| factor(ulcer) | ||||
| 0 | 92 (68.7%) | 16 (28.1%) | 7 (50.0%) | 115 (56.1%) |
| 1 | 42 (31.3%) | 41 (71.9%) | 7 (50.0%) | 90 (43.9%) |
| thickness | ||||
| Mean (SD) | 2.24 (2.33) | 4.31 (3.57) | 3.72 (3.63) | 2.92 (2.96) |
| Median [Min, Max] | 1.36 [0.100, 12.9] | 3.54 [0.320, 17.4] | 2.26 [0.160, 12.6] | 1.94 [0.100, 17.4] |
This table (used package 'gtsummary') can be displayed in HTML and in word with most of the layout format elements.
| Characteristic | Alive, N = 134 (65%) |
Melanoma death, N = 57 (28%) |
Non-melanoma death, N = 14 (6.8%) |
Overall, N = 205 |
|---|---|---|---|---|
| Sex | ||||
| 0 | 91 / 134 (67.910%) | 28 / 57 (49.123%) | 7 / 14 (50.000%) | 126 / 205 (61.463%) |
| 1 | 43 / 134 (32.090%) | 29 / 57 (50.877%) | 7 / 14 (50.000%) | 79 / 205 (38.537%) |
| Age | ||||
| Mean (SD) | 50 (15.92) | 55 (17.91) | 65 (10.90) | 52 (16.67) |
| Range | 4, 84 | 14, 95 | 49, 86 | 4, 95 |
| Ulcer | ||||
| 0 | 92 / 134 (68.657%) | 16 / 57 (28.070%) | 7 / 14 (50.000%) | 115 / 205 (56.098%) |
| 1 | 42 / 134 (31.343%) | 41 / 57 (71.930%) | 7 / 14 (50.000%) | 90 / 205 (43.902%) |
| thickness | ||||
| Mean (SD) | 2 (2.33) | 4 (3.57) | 4 (3.63) | 3 (2.96) |
| Range | 0, 13 | 0, 17 | 0, 13 | 0, 17 |
Another example with other dataset
Table 1: basic descriptive stat table 1
| Characteristic | N = 2001 |
|---|---|
| Chemotherapy Treatment | |
| Drug A | 98 (49.00%) |
| Drug B | 102 (51.00%) |
| Age | 47 (38, 57) |
| Unknown | 11 |
| Grade | |
| I | 68 (34.00%) |
| II | 68 (34.00%) |
| III | 64 (32.00%) |
| Tumor Response | 61 (31.61%) |
| Unknown | 7 |
|
1
Statistics presented: n (%); Median (IQR)
|
|
Table 2: basic descriptive stat by treatment and overall
| Characteristic | Drug A, N = 98 (49%) |
Drug B, N = 102 (51%) |
Overall, N = 200 |
|---|---|---|---|
| Age | |||
| Mean (SD) | 47 (14.71) | 47 (14.01) | 47 (14.31) |
| Range | 6, 78 | 9, 83 | 6, 83 |
| Unknown | 7 | 4 | 11 |
| Tumor Grade | |||
| I | 35 / 98 (35.71%) | 33 / 102 (32.35%) | 68 / 200 (34.00%) |
| II | 32 / 98 (32.65%) | 36 / 102 (35.29%) | 68 / 200 (34.00%) |
| III | 31 / 98 (31.63%) | 33 / 102 (32.35%) | 64 / 200 (32.00%) |
| Tumor Response | 28.0 / 95.0 (29.474%) | 33.0 / 98.0 (33.673%) | 61.0 / 193.0 (31.606%) |
| Unknown | 3 | 4 | 7 |
Table 3: basic test
| Variable | N | Drug A, N = 981 | Drug B, N = 1021 | p-value2 |
|---|---|---|---|---|
| Age | 189 | 46 (37, 59) | 48 (39, 56) | 0.7 |
| Grade | 200 | 0.9 | ||
| I | 35 (35.71%) | 33 (32.35%) | ||
| II | 32 (32.65%) | 36 (35.29%) | ||
| III | 31 (31.63%) | 33 (32.35%) | ||
| Tumor Response | 193 | 28 (29.47%) | 33 (33.67%) | 0.6 |
|
1
Statistics presented: Median (IQR); n (%)
2
Statistical tests performed: Wilcoxon rank-sum test; chi-square test of independence
|
||||
Table 4: logistic regression result
| Characteristic | OR1 | 95% CI1 | p-value |
|---|---|---|---|
| Chemotherapy Treatment | |||
| Drug A | — | — | |
| Drug B | 1.13 | 0.60, 2.13 | 0.7 |
| Age | 1.02 | 1.00, 1.04 | 0.10 |
| Grade | |||
| I | — | — | |
| II | 0.85 | 0.39, 1.85 | 0.7 |
| III | 1.01 | 0.47, 2.15 | >0.9 |
|
1
OR = Odds Ratio, CI = Confidence Interval
|
|||
Table 5: Result from logistic and Cox regression side by side table
| Characteristic | Tumor Response | Time to Death | ||||
|---|---|---|---|---|---|---|
| OR1 | 95% CI1 | p-value | HR1 | 95% CI1 | p-value | |
| Chemotherapy Treatment | ||||||
| Drug A | — | — | — | — | ||
| Drug B | 1.13 | 0.60, 2.13 | 0.7 | 1.30 | 0.88, 1.92 | 0.2 |
| Age | 1.02 | 1.00, 1.04 | 0.10 | 1.01 | 0.99, 1.02 | 0.3 |
| Grade | ||||||
| I | — | — | — | — | ||
| II | 0.85 | 0.39, 1.85 | 0.7 | 1.21 | 0.73, 1.99 | 0.5 |
| III | 1.01 | 0.47, 2.15 | >0.9 | 1.79 | 1.12, 2.86 | 0.014 |
|
1
OR = Odds Ratio, CI = Confidence Interval, HR = Hazard Ratio
|
||||||
Including Plots
You can also embed plots, for example:
Figure 1: a forest plot based on table 4
Figure 2: Forest plot with table
plotly pakcage cannot display inside of Rstudio to show interactive plot( but can be displayed in HTML output) need to install extra js to knit into WORD But no interactive plot in WORD
#install.packages("webshot")
#webshot::install_phantomjs()
library(plotly)
ggplotly(p)Figure 3: Kaplan-Meier plot based on the same dataset
