Different `knit_print()` output

This package provides some modified knit_print() methods for better output

library(crmPack)
#> Loading required package: ggplot2
#> Registered S3 method overwritten by 'crmPack':
#>   method       from  
#>   print.gtable gtable
#> Type crmPackHelp() to open help browser
#> Type crmPackExample() to open example
library(BLRMeval)

CohortSize

The knit_print() provided in this package have the following improvement:

Better indentation for nested cohort size rules
Move some table caption into preamble string for better compatibility with pdf/word output

If you library(BLRMeval) later than library(crmPack), these knit_print() methods will overwrite the ones in crmPack.

cs1 <- .DefaultCohortSizeDLT()
cs2 <- .DefaultCohortSizeRange()
cs3 <- .DefaultCohortSizeMax()
cs4 <- minSize(cs1, maxSize(cs2, cs3, .DefaultCohortSizeOrdinal()))
cs5 <- CohortSizeOrdinal(
    grade = 1L, rule = cs4)

Their `knit_print()` output in this package:

cs1

Defined by the number of toxicities so far observed

No of toxicities
Lower	Upper	Cohort size
0	1	1
1	Inf	3

cs2

Defined by the dose to be used in the next cohort

Dose
Lower	Upper	Cohort size
0	30	1
30	Inf	3

cs3

The maximum of the cohort sizes defined in the following rules:

Defined by the dose to be used in the next cohort

Dose

Lower Upper Cohort size

0 10 1

10 Inf 3
Defined by the number of toxicities so far observed

No of toxicities

Lower Upper Cohort size

0 1 1

1 Inf 3

Dose
0	10	1
10	Inf	3

No of toxicities
0	1	1
1	Inf	3

cs4

The minimum of the cohort sizes defined in the following rules:

Defined by the number of toxicities so far observed

No of toxicities

Lower

Upper

Cohort size

0

1

1

1

Inf

3
The maximum of the cohort sizes defined in the following rules:
- Defined by the dose to be used in the next cohort
  
  Dose
  
  Lower
  
  Upper
  
  Cohort size
  
  0
  
  30
  
  1
  
  30
  
  Inf
  
  3
- The maximum of the cohort sizes defined in the following rules:
  - Defined by the dose to be used in the next cohort
    
    Dose
    
    Lower Upper Cohort size
    
    0 10 1
    
    10 Inf 3
  - Defined by the number of toxicities so far observed
    
    No of toxicities
    
    Lower Upper Cohort size
    
    0 1 1
    
    1 Inf 3
- Based on a toxicity grade of 1:
  - Defined by the dose to be used in the next cohort
    
    Dose
    
    Lower Upper Cohort size
    
    0 30 1
    
    30 Inf 3

No of toxicities
0	1	1
1	Inf	3

Dose
0	30	1
30	Inf	3

Dose
0	10	1
10	Inf	3

No of toxicities
0	1	1
1	Inf	3

Dose
0	30	1
30	Inf	3

cs5

Based on a toxicity grade of 1:

The minimum of the cohort sizes defined in the following rules:
- Defined by the number of toxicities so far observed
  
  No of toxicities
  
  Lower
  
  Upper
  
  Cohort size
  
  0
  
  1
  
  1
  
  1
  
  Inf
  
  3
- The maximum of the cohort sizes defined in the following rules:
  - Defined by the dose to be used in the next cohort
    
    Dose
    
    Lower
    
    Upper
    
    Cohort size
    
    0
    
    30
    
    1
    
    30
    
    Inf
    
    3
  - The maximum of the cohort sizes defined in the following rules:
    - Defined by the dose to be used in the next cohort
      
      Dose
      
      Lower Upper Cohort size
      
      0 10 1
      
      10 Inf 3
    - Defined by the number of toxicities so far observed
      
      No of toxicities
      
      Lower Upper Cohort size
      
      0 1 1
      
      1 Inf 3
  - Based on a toxicity grade of 1:
    - Defined by the dose to be used in the next cohort
      
      Dose
      
      Lower Upper Cohort size
      
      0 30 1
      
      30 Inf 3

No of toxicities
0	1	1
1	Inf	3

Dose
0	30	1
30	Inf	3

Dose
0	10	1
10	Inf	3

No of toxicities
0	1	1
1	Inf	3

Dose
0	30	1
30	Inf	3

This also works with CohortSizeDLT_AT() and CohortSizeConst2() defined in this package

cs6 <- CohortSizeDLT_AT(intervals = c(0, 1), cohort_size = c(1, 3))
cs6

Defined by the number of toxicities so far observed

No of toxicities
Lower	Upper	Cohort size
0	1	1
1	Inf	3

Note: during the accelerated titration to standard dose escalation transition stage, a cohort size of 2 will be proposed. And the last dose level administrated will be directly recommended as the next dose level if NextBestNCRM_AT() is used.

cs7 <- CohortSizeConst2(size = 3, max_size = 74)
cs7

A constant size of 3 participants. Note: if the constant cohort size of 3 for the next reocommended dose will make the total sample size exceeds 74, then the next cohort size will be decreased so that the total sample size is at just 74.

maxSize(cs7, cs1, cs6)

The maximum of the cohort sizes defined in the following rules:

A constant size of 3 participants. Note: if the constant cohort size of 3 for the next reocommended dose will make the total sample size exceeds 74, then the next cohort size will be decreased so that the total sample size is at just 74.
Defined by the number of toxicities so far observed

No of toxicities

Lower

Upper

Cohort size

0

1

1

1

Inf

3
Defined by the number of toxicities so far observed

No of toxicities

Lower

Upper

Cohort size

0

1

1

1

Inf

3

Note: during the accelerated titration to standard dose escalation transition stage, a cohort size of 2 will be proposed. And the last dose level administrated will be directly recommended as the next dose level if NextBestNCRM_AT() is used.

No of toxicities
0	1	1
1	Inf	3

No of toxicities
0	1	1
1	Inf	3

Their original `knit_print()` output from `crmPack`

crmPack:::knit_print.CohortSizeDLT(cs1)

Defined by the number of toxicities so far observed
No of toxicities
Lower	Upper	Cohort size
0	1	1
1	Inf	3

crmPack:::knit_print.CohortSizeRange(cs2)

Defined by the dose to be used in the next cohort
Dose
Lower	Upper	Cohort size
0	30	1
30	Inf	3

crmPack:::knit_print.CohortSizeMax(cs3)

The maximum of the cohort sizes defined in the following rules:

Defined by the dose to be used in the next cohort
Dose
Lower	Upper	Cohort size
0	10	1
10	Inf	3

Defined by the number of toxicities so far observed
No of toxicities
Lower	Upper	Cohort size
0	1	1
1	Inf	3

crmPack:::knit_print.CohortSizeMin(cs4)

The minimum of the cohort sizes defined in the following rules:

Defined by the number of toxicities so far observed
No of toxicities
Lower	Upper	Cohort size
0	1	1
1	Inf	3

The maximum of the cohort sizes defined in the following rules:

Defined by the dose to be used in the next cohort
Dose
Lower	Upper	Cohort size
0	30	1
30	Inf	3

The maximum of the cohort sizes defined in the following rules:

Defined by the dose to be used in the next cohort
Dose
Lower	Upper	Cohort size
0	10	1
10	Inf	3

Defined by the number of toxicities so far observed
No of toxicities
Lower	Upper	Cohort size
0	1	1
1	Inf	3

Based on a toxicity grade of 1:

Defined by the dose to be used in the next cohort
Dose
Lower	Upper	Cohort size
0	30	1
30	Inf	3

crmPack:::knit_print.CohortSizeOrdinal(cs5)

Based on a toxicity grade of 1: The minimum of the cohort sizes defined in the following rules:

Defined by the number of toxicities so far observed
No of toxicities
Lower	Upper	Cohort size
0	1	1
1	Inf	3

The maximum of the cohort sizes defined in the following rules:

Defined by the dose to be used in the next cohort
Dose
Lower	Upper	Cohort size
0	30	1
30	Inf	3

The maximum of the cohort sizes defined in the following rules:

Defined by the dose to be used in the next cohort
Dose
Lower	Upper	Cohort size
0	10	1
10	Inf	3

Defined by the number of toxicities so far observed
No of toxicities
Lower	Upper	Cohort size
0	1	1
1	Inf	3

Based on a toxicity grade of 1:

Defined by the dose to be used in the next cohort
Dose
Lower	Upper	Cohort size
0	30	1
30	Inf	3

CohortSize

Their knit_print() output in this package:

Their original knit_print() output from crmPack

Their `knit_print()` output in this package:

Their original `knit_print()` output from `crmPack`