README.md
In UBESP-DCTV/clumpr: Current transpLant sUrplus Management Protocol in R
clumpr 
Current transpLant sUrplus Management Protocol in
R
Last update: 2018-06-11
Description
The clumpr package aims to provide a toolbox of function for model,
validate and visualize dynamics assessed by the “Protocollo Nazionale
per la Gestione delle Eccedenze di Tutti i Programmi di Trapianto” in
Italy.
The first implementation is focused on the lung-transplant centers
management.
Example
This is a basic example which shows you how it works:
library(clumpr)
# setup centers and regions
pavia <- center('Pavia', 'Lombardia', offered = 11, p_accept = 0.8)
bergamo <- center('Bergamo', 'Lombardia', offered = 7, p_accept = 0.5)
milano <- center('Milano', 'Lombardia', offered = 3)
lombardia <- region(set_centers(pavia, bergamo, milano), default_p = 0.2)
# show data
lombardia
#> Region : Lombardia (Italy)
#> Centers : Pavia, Bergamo, Milano (#3)
#> Acceptance rate : 0.92 (at least one center)
#> Offered organs : 21 (from all the centers)
get_centers(lombardia)
#> Center : Pavia (Lombardia --- Italy)
#> Acceptance rate : 0.8
#> Offered organs : 11
#>
#> Center : Bergamo (Lombardia --- Italy)
#> Acceptance rate : 0.5
#> Offered organs : 7
#>
#> Center : Milano (Lombardia --- Italy)
#> Acceptance rate : <inherit from the region rate>
#> Offered organs : 3
# setup macroregions
padova <- center('Padova', 'Veneto', 10, 0.9)
veneto <- region(set_centers(padova))
nitp <- macroregion('NITp', set_regions(lombardia, veneto),
initial_strip = c('lombardia', 'lombardia', 'veneto'))
# show data
nitp
#> Macroregion : NITp (Italy)
#> Regions : Lombardia; Veneto (#2)
#> Centers : Pavia, Bergamo, Milano; Padova (#4)
#> Acceptance rate : 0.992 (at least one center in some region)
#> Offered organs : 31 (from every the centers of every region)
#> Initail strip : Lombardia --> Lombardia --> Veneto
#> Current strip : Lombardia --> Lombardia --> Veneto
#> Time period : 0
get_regions(nitp)
#> Region : Lombardia (Italy)
#> Centers : Pavia, Bergamo, Milano (#3)
#> Acceptance rate : 0.92 (at least one center)
#> Offered organs : 21 (from all the centers)
#>
#> Region : Veneto (Italy)
#> Centers : Padova (#1)
#> Acceptance rate : 0.9 (at least one center)
#> Offered organs : 10 (from all the centers)
get_centers(nitp)
#> $lombardia
#> Center : Pavia (Lombardia --- Italy)
#> Acceptance rate : 0.8
#> Offered organs : 11
#>
#> Center : Bergamo (Lombardia --- Italy)
#> Acceptance rate : 0.5
#> Offered organs : 7
#>
#> Center : Milano (Lombardia --- Italy)
#> Acceptance rate : <inherit from the region rate>
#> Offered organs : 3
#>
#>
#> $veneto
#> Center : Padova (Veneto --- Italy)
#> Acceptance rate : 0.9
#> Offered organs : 10
# add another region and setup a macroarea
torino <- center('Torino', 'Piemonte', 7, 0.6)
piemonte <- region(set_centers(torino))
nord <- macroarea('Nord',
macroregions = set_macroregions(piemonte, nitp)
)
nord
#> Macroarea : Nord (Italy)
#> Macroregions : Piemonte; NITp (#2)
#> Regions : Piemonte; Lombardia, Veneto (#3)
#> Centers : Torino; Pavia, Bergamo, Milano; Padova (#5)
#> Acceptance rate : 0.9968 (at least one center in some region)
#> Offered organs : 38 (from every centers of every region)
#> Initail strip : Piemonte --> Nitp
#> Current strip : Piemonte --> Nitp
#> Time period : 0
get_macroregions(nord)
#> Region : Piemonte (Italy)
#> Centers : Torino (#1)
#> Acceptance rate : 0.6 (at least one center)
#> Offered organs : 7 (from all the centers)
#>
#> Macroregion : NITp (Italy)
#> Regions : Lombardia; Veneto (#2)
#> Centers : Pavia, Bergamo, Milano; Padova (#4)
#> Acceptance rate : 0.992 (at least one center in some region)
#> Offered organs : 31 (from every the centers of every region)
#> Initail strip : Lombardia --> Lombardia --> Veneto
#> Current strip : Lombardia --> Lombardia --> Veneto
#> Time period : 0
get_regions(nord)
#> Region : Piemonte (Italy)
#> Centers : Torino (#1)
#> Acceptance rate : 0.6 (at least one center)
#> Offered organs : 7 (from all the centers)
#>
#> Region : Lombardia (Italy)
#> Centers : Pavia, Bergamo, Milano (#3)
#> Acceptance rate : 0.92 (at least one center)
#> Offered organs : 21 (from all the centers)
#>
#> Region : Veneto (Italy)
#> Centers : Padova (#1)
#> Acceptance rate : 0.9 (at least one center)
#> Offered organs : 10 (from all the centers)
get_centers(nord)
#> $piemonte
#> Center : Torino (Piemonte --- Italy)
#> Acceptance rate : 0.6
#> Offered organs : 7
#>
#>
#> $lombardia
#> Center : Pavia (Lombardia --- Italy)
#> Acceptance rate : 0.8
#> Offered organs : 11
#>
#> Center : Bergamo (Lombardia --- Italy)
#> Acceptance rate : 0.5
#> Offered organs : 7
#>
#> Center : Milano (Lombardia --- Italy)
#> Acceptance rate : <inherit from the region rate>
#> Offered organs : 3
#>
#>
#> $veneto
#> Center : Padova (Veneto --- Italy)
#> Acceptance rate : 0.9
#> Offered organs : 10
roma <- center('Roma', 'Lazio', 10, 0.9)
lazio <- region(set_centers(roma))
sud <- macroarea('Sud',
macroregions = set_macroregions(lazio)
)
italy <- state('Italy', set_macroareas(nord, sud))
italy
#> State : Italy
#> Macroareas : Nord; Sud (#2)
#> Macroregions : Piemonte, NITp; Lazio (#3)
#> Regions : Piemonte; Lombardia, Veneto; Lazio (#4)
#> Centers : Torino; Pavia, Bergamo, Milano; Padova; Roma (#6)
#> Acceptance rate : 0.99968 (at least one center in some region)
#> Offered organs : 48 (from every centers of every region)
#> Initail strip : Nord --> Sud
#> Current strip : Nord --> Sud
#> Time period : 0
get_macroareas(italy)
#> Macroarea : Nord (Italy)
#> Macroregions : Piemonte; NITp (#2)
#> Regions : Piemonte; Lombardia, Veneto (#3)
#> Centers : Torino; Pavia, Bergamo, Milano; Padova (#5)
#> Acceptance rate : 0.9968 (at least one center in some region)
#> Offered organs : 38 (from every centers of every region)
#> Initail strip : Piemonte --> Nitp
#> Current strip : Piemonte --> Nitp
#> Time period : 0
#>
#> Macroarea : Sud (Italy)
#> Macroregions : Lazio (#1)
#> Regions : Lazio (#1)
#> Centers : Roma (#1)
#> Acceptance rate : 0.9 (at least one center in some region)
#> Offered organs : 10 (from every centers of every region)
#> Initail strip : Lazio
#> Current strip : Lazio
#> Time period : 0
get_macroregions(italy)
#> Region : Piemonte (Italy)
#> Centers : Torino (#1)
#> Acceptance rate : 0.6 (at least one center)
#> Offered organs : 7 (from all the centers)
#>
#> Macroregion : NITp (Italy)
#> Regions : Lombardia; Veneto (#2)
#> Centers : Pavia, Bergamo, Milano; Padova (#4)
#> Acceptance rate : 0.992 (at least one center in some region)
#> Offered organs : 31 (from every the centers of every region)
#> Initail strip : Lombardia --> Lombardia --> Veneto
#> Current strip : Lombardia --> Lombardia --> Veneto
#> Time period : 0
#>
#> Region : Lazio (Italy)
#> Centers : Roma (#1)
#> Acceptance rate : 0.9 (at least one center)
#> Offered organs : 10 (from all the centers)
get_regions(italy)
#> Region : Piemonte (Italy)
#> Centers : Torino (#1)
#> Acceptance rate : 0.6 (at least one center)
#> Offered organs : 7 (from all the centers)
#>
#> Region : Lombardia (Italy)
#> Centers : Pavia, Bergamo, Milano (#3)
#> Acceptance rate : 0.92 (at least one center)
#> Offered organs : 21 (from all the centers)
#>
#> Region : Veneto (Italy)
#> Centers : Padova (#1)
#> Acceptance rate : 0.9 (at least one center)
#> Offered organs : 10 (from all the centers)
#>
#> Region : Lazio (Italy)
#> Centers : Roma (#1)
#> Acceptance rate : 0.9 (at least one center)
#> Offered organs : 10 (from all the centers)
get_centers(italy)
#> $piemonte
#> Center : Torino (Piemonte --- Italy)
#> Acceptance rate : 0.6
#> Offered organs : 7
#>
#>
#> $lombardia
#> Center : Pavia (Lombardia --- Italy)
#> Acceptance rate : 0.8
#> Offered organs : 11
#>
#> Center : Bergamo (Lombardia --- Italy)
#> Acceptance rate : 0.5
#> Offered organs : 7
#>
#> Center : Milano (Lombardia --- Italy)
#> Acceptance rate : <inherit from the region rate>
#> Offered organs : 3
#>
#>
#> $veneto
#> Center : Padova (Veneto --- Italy)
#> Acceptance rate : 0.9
#> Offered organs : 10
#>
#>
#> $lazio
#> Center : Roma (Lazio --- Italy)
#> Acceptance rate : 0.9
#> Offered organs : 10
# TODO
Installation
You can install clumpr from GitHub with:
# install.packages("devtools")
devtools::install_github("UBESP-DCTV/clumpr")
Bug reports
If you encounter a bug, please file a
reprex (minimal reproducible
example) to https://github.com/UBESP-DCTV/clumpr/issues
Code of conduct
Please note that this project is released with a Contributor Code of
Conduct. By participating in this project you agree
to abide by its terms.
References
Protocollo Nazionale per la Gestione delle Eccedenze di Tutti i
Programmi di Trapianto
(pdf)
UBESP-DCTV/clumpr documentation built on July 3, 2021, 11:23 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
clumpr
Current transpLant sUrplus Management Protocol in R
Last update: 2018-06-11
Description
The clumpr package aims to provide a toolbox of function for model,
validate and visualize dynamics assessed by the “Protocollo Nazionale
per la Gestione delle Eccedenze di Tutti i Programmi di Trapianto” in
Italy.
The first implementation is focused on the lung-transplant centers management.
Example
This is a basic example which shows you how it works:
library(clumpr)
# setup centers and regions
pavia <- center('Pavia', 'Lombardia', offered = 11, p_accept = 0.8)
bergamo <- center('Bergamo', 'Lombardia', offered = 7, p_accept = 0.5)
milano <- center('Milano', 'Lombardia', offered = 3)
lombardia <- region(set_centers(pavia, bergamo, milano), default_p = 0.2)
# show data
lombardia
#> Region : Lombardia (Italy)
#> Centers : Pavia, Bergamo, Milano (#3)
#> Acceptance rate : 0.92 (at least one center)
#> Offered organs : 21 (from all the centers)
get_centers(lombardia)
#> Center : Pavia (Lombardia --- Italy)
#> Acceptance rate : 0.8
#> Offered organs : 11
#>
#> Center : Bergamo (Lombardia --- Italy)
#> Acceptance rate : 0.5
#> Offered organs : 7
#>
#> Center : Milano (Lombardia --- Italy)
#> Acceptance rate : <inherit from the region rate>
#> Offered organs : 3
# setup macroregions
padova <- center('Padova', 'Veneto', 10, 0.9)
veneto <- region(set_centers(padova))
nitp <- macroregion('NITp', set_regions(lombardia, veneto),
initial_strip = c('lombardia', 'lombardia', 'veneto'))
# show data
nitp
#> Macroregion : NITp (Italy)
#> Regions : Lombardia; Veneto (#2)
#> Centers : Pavia, Bergamo, Milano; Padova (#4)
#> Acceptance rate : 0.992 (at least one center in some region)
#> Offered organs : 31 (from every the centers of every region)
#> Initail strip : Lombardia --> Lombardia --> Veneto
#> Current strip : Lombardia --> Lombardia --> Veneto
#> Time period : 0
get_regions(nitp)
#> Region : Lombardia (Italy)
#> Centers : Pavia, Bergamo, Milano (#3)
#> Acceptance rate : 0.92 (at least one center)
#> Offered organs : 21 (from all the centers)
#>
#> Region : Veneto (Italy)
#> Centers : Padova (#1)
#> Acceptance rate : 0.9 (at least one center)
#> Offered organs : 10 (from all the centers)
get_centers(nitp)
#> $lombardia
#> Center : Pavia (Lombardia --- Italy)
#> Acceptance rate : 0.8
#> Offered organs : 11
#>
#> Center : Bergamo (Lombardia --- Italy)
#> Acceptance rate : 0.5
#> Offered organs : 7
#>
#> Center : Milano (Lombardia --- Italy)
#> Acceptance rate : <inherit from the region rate>
#> Offered organs : 3
#>
#>
#> $veneto
#> Center : Padova (Veneto --- Italy)
#> Acceptance rate : 0.9
#> Offered organs : 10
# add another region and setup a macroarea
torino <- center('Torino', 'Piemonte', 7, 0.6)
piemonte <- region(set_centers(torino))
nord <- macroarea('Nord',
macroregions = set_macroregions(piemonte, nitp)
)
nord
#> Macroarea : Nord (Italy)
#> Macroregions : Piemonte; NITp (#2)
#> Regions : Piemonte; Lombardia, Veneto (#3)
#> Centers : Torino; Pavia, Bergamo, Milano; Padova (#5)
#> Acceptance rate : 0.9968 (at least one center in some region)
#> Offered organs : 38 (from every centers of every region)
#> Initail strip : Piemonte --> Nitp
#> Current strip : Piemonte --> Nitp
#> Time period : 0
get_macroregions(nord)
#> Region : Piemonte (Italy)
#> Centers : Torino (#1)
#> Acceptance rate : 0.6 (at least one center)
#> Offered organs : 7 (from all the centers)
#>
#> Macroregion : NITp (Italy)
#> Regions : Lombardia; Veneto (#2)
#> Centers : Pavia, Bergamo, Milano; Padova (#4)
#> Acceptance rate : 0.992 (at least one center in some region)
#> Offered organs : 31 (from every the centers of every region)
#> Initail strip : Lombardia --> Lombardia --> Veneto
#> Current strip : Lombardia --> Lombardia --> Veneto
#> Time period : 0
get_regions(nord)
#> Region : Piemonte (Italy)
#> Centers : Torino (#1)
#> Acceptance rate : 0.6 (at least one center)
#> Offered organs : 7 (from all the centers)
#>
#> Region : Lombardia (Italy)
#> Centers : Pavia, Bergamo, Milano (#3)
#> Acceptance rate : 0.92 (at least one center)
#> Offered organs : 21 (from all the centers)
#>
#> Region : Veneto (Italy)
#> Centers : Padova (#1)
#> Acceptance rate : 0.9 (at least one center)
#> Offered organs : 10 (from all the centers)
get_centers(nord)
#> $piemonte
#> Center : Torino (Piemonte --- Italy)
#> Acceptance rate : 0.6
#> Offered organs : 7
#>
#>
#> $lombardia
#> Center : Pavia (Lombardia --- Italy)
#> Acceptance rate : 0.8
#> Offered organs : 11
#>
#> Center : Bergamo (Lombardia --- Italy)
#> Acceptance rate : 0.5
#> Offered organs : 7
#>
#> Center : Milano (Lombardia --- Italy)
#> Acceptance rate : <inherit from the region rate>
#> Offered organs : 3
#>
#>
#> $veneto
#> Center : Padova (Veneto --- Italy)
#> Acceptance rate : 0.9
#> Offered organs : 10
roma <- center('Roma', 'Lazio', 10, 0.9)
lazio <- region(set_centers(roma))
sud <- macroarea('Sud',
macroregions = set_macroregions(lazio)
)
italy <- state('Italy', set_macroareas(nord, sud))
italy
#> State : Italy
#> Macroareas : Nord; Sud (#2)
#> Macroregions : Piemonte, NITp; Lazio (#3)
#> Regions : Piemonte; Lombardia, Veneto; Lazio (#4)
#> Centers : Torino; Pavia, Bergamo, Milano; Padova; Roma (#6)
#> Acceptance rate : 0.99968 (at least one center in some region)
#> Offered organs : 48 (from every centers of every region)
#> Initail strip : Nord --> Sud
#> Current strip : Nord --> Sud
#> Time period : 0
get_macroareas(italy)
#> Macroarea : Nord (Italy)
#> Macroregions : Piemonte; NITp (#2)
#> Regions : Piemonte; Lombardia, Veneto (#3)
#> Centers : Torino; Pavia, Bergamo, Milano; Padova (#5)
#> Acceptance rate : 0.9968 (at least one center in some region)
#> Offered organs : 38 (from every centers of every region)
#> Initail strip : Piemonte --> Nitp
#> Current strip : Piemonte --> Nitp
#> Time period : 0
#>
#> Macroarea : Sud (Italy)
#> Macroregions : Lazio (#1)
#> Regions : Lazio (#1)
#> Centers : Roma (#1)
#> Acceptance rate : 0.9 (at least one center in some region)
#> Offered organs : 10 (from every centers of every region)
#> Initail strip : Lazio
#> Current strip : Lazio
#> Time period : 0
get_macroregions(italy)
#> Region : Piemonte (Italy)
#> Centers : Torino (#1)
#> Acceptance rate : 0.6 (at least one center)
#> Offered organs : 7 (from all the centers)
#>
#> Macroregion : NITp (Italy)
#> Regions : Lombardia; Veneto (#2)
#> Centers : Pavia, Bergamo, Milano; Padova (#4)
#> Acceptance rate : 0.992 (at least one center in some region)
#> Offered organs : 31 (from every the centers of every region)
#> Initail strip : Lombardia --> Lombardia --> Veneto
#> Current strip : Lombardia --> Lombardia --> Veneto
#> Time period : 0
#>
#> Region : Lazio (Italy)
#> Centers : Roma (#1)
#> Acceptance rate : 0.9 (at least one center)
#> Offered organs : 10 (from all the centers)
get_regions(italy)
#> Region : Piemonte (Italy)
#> Centers : Torino (#1)
#> Acceptance rate : 0.6 (at least one center)
#> Offered organs : 7 (from all the centers)
#>
#> Region : Lombardia (Italy)
#> Centers : Pavia, Bergamo, Milano (#3)
#> Acceptance rate : 0.92 (at least one center)
#> Offered organs : 21 (from all the centers)
#>
#> Region : Veneto (Italy)
#> Centers : Padova (#1)
#> Acceptance rate : 0.9 (at least one center)
#> Offered organs : 10 (from all the centers)
#>
#> Region : Lazio (Italy)
#> Centers : Roma (#1)
#> Acceptance rate : 0.9 (at least one center)
#> Offered organs : 10 (from all the centers)
get_centers(italy)
#> $piemonte
#> Center : Torino (Piemonte --- Italy)
#> Acceptance rate : 0.6
#> Offered organs : 7
#>
#>
#> $lombardia
#> Center : Pavia (Lombardia --- Italy)
#> Acceptance rate : 0.8
#> Offered organs : 11
#>
#> Center : Bergamo (Lombardia --- Italy)
#> Acceptance rate : 0.5
#> Offered organs : 7
#>
#> Center : Milano (Lombardia --- Italy)
#> Acceptance rate : <inherit from the region rate>
#> Offered organs : 3
#>
#>
#> $veneto
#> Center : Padova (Veneto --- Italy)
#> Acceptance rate : 0.9
#> Offered organs : 10
#>
#>
#> $lazio
#> Center : Roma (Lazio --- Italy)
#> Acceptance rate : 0.9
#> Offered organs : 10
# TODO
Installation
You can install clumpr from GitHub with:
# install.packages("devtools")
devtools::install_github("UBESP-DCTV/clumpr")
Bug reports
If you encounter a bug, please file a reprex (minimal reproducible example) to https://github.com/UBESP-DCTV/clumpr/issues
Code of conduct
Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.
References
Protocollo Nazionale per la Gestione delle Eccedenze di Tutti i Programmi di Trapianto (pdf)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.