Package ms.sev. R topics documented: December 21, Type Package
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1 Type Package Package ms.sev December 21, 2016 Title Package for Calculation of ARMSS, Local MSSS and Global MSSS Version Date Author Maintainer Helga Westerlind Calculates ARMSS (age related multiple sclerosis severity), and both local and global MSSS (multiple sclerosis severity score). License GPL-2 NeedsCompilation no Repository CRAN Date/Publication :02:13 R topics documented: ms_sev-package edss globalarmss globalmsss global_armss global_msss local_armss local_msss ms_sev oldmsss Index 9 1
2 2 edss ms_sev-package Estimation of severity scores for multiple sclerosis. Details Estimation of severity scores for multiple sclerosis. Package: ms_sev Type: Package Version: 1.0 Date: License: GPL 2 Maintainer: Helga Westerlind <Helga.Westerlind@ki.se> edss Data for testing ms.sev package Mock for 2,000 individuals to test the ms.sev package. (edss) Format A frame consisting of 6 columns and 2,000 rows. The rows corresponds to EDSS value, age at which the EDSS score was assessed and disease duration.
3 globalarmss 3 globalarmss Global ARMSS matrix The global ARMSS-matrix provided with the ms.sev-package (globalarmss) Format A frame consisting of 20 columns and 30 rows, corresponding to EDSS-scores in 0.5-increments, and disease duration. The first row marks the disease duration. globalmsss Global MSSS matrix The global MSSS-matrix provided with the ms.sev-package (globalmsss) Format This is the new, updated MSSS-matrix. A frame consisting of 20 columns and 30 rows, corresponding to EDSS-scores in 0.5-increments, and disease duration. The first column is corresponding to disease duration.
4 4 global_msss global_armss ARMSS Calculates and returns the global ARMSS-score for every individual in the set. global_armss(, matrix=false) matrix A frame containing the variable "ageatedss" and the variable "edss" for every individual. If the global ARMSS table should be returned or not. Returns the initially supplied frame with the added variable "garmss". (edss) out <- global_armss(edss) global_msss Global MSSS Estimation of global MSSS-scores. global_msss(, matrix=false, omsss=false)
5 local_armss 5 matrix omsss A frame containing the variable "dd" (disease duration) and the variable "edss" for every individual. If the global MSSS-matrix should be returned or not. If true, the old MSSS score is returned for every individual. Details Estimation of global MSSS-scores. Returns the provided frame with an added column of global msss-scores. globalmsss The supplied frame with an added ugmsss column representing the global msss-score. If omsss is requested, an additional variable named ogmsss is also added. The global MSSS-matrix with columns representing EDSS-scores and rows disease duration, starting at 1 and truncated at 30. This item is only returned if matrix=t. If omsss is requested, the old MSSS matrix is also returned. (edss) out <- global_msss(edss, matrix=true, omsss=true) local_armss ARMSS Calculates and returns the local ARMSS-score for every individual in the set. local_armss(, range = 2)
6 6 local_msss range A frame containing the variable "ageatedss" and the variable "edss" for every individual. The age-range from which to include individuals in the ARMSS-estimation. Default=2. Returns the initially supplied frame with the added variable "armss". (edss) out <- local_armss(edss) local_msss Local MSSS Estimation of local MSSS-scores. local_msss(, range=2) A frame including the variables "edss"" and "dd" (disease duration), which is estimating the disease duration from onset to edss. range The age range in which to include individuals in the msss calculation. The default value is set to two. The supplied frame with an added column "lmsss" including the estimated local MSSS for every individual.
7 ms_sev 7 (edss) out <- local_msss(edss) ms_sev MS-Severity Estimates the severity score for the user supplied frame of patients. ms_sev(, type="global_armss", range = 2, matrix=f, omsss=false) type range matrix omsss A frame containing the variable "edss" for every individual and "age" if "armss" is requested. For MSSS estimation, a variable "dd", corresponding to the disease duration, is needed. Specification of the type of severity calculation. Default is global armss. Other options are "local_armss", "local_msss" and "global_msss". The age-range from which to include individuals in the local ARMSS and local MSSS-estimations. The default age-range is 2 years. If true, the global MSSS-matrix is returned. Please note that this option only works for global MSSS and global ARMSS. If true, the old MSSS-score will be estimated and returned. Please note that this option only works for the global MSSS. Returns the initially supplied frame with a column added with the requested type of severity score. If "matrix" is set to true, the ms\_sev will return a list where the first element is the frame with the added severity score, and the second item is the requested ARMSS/MSSS matrix. If omsss is set to TRUE, both the old and the updated MSSS matrix will be returned.
8 8 oldmsss (edss) out <- ms_sev(edss) head(out$) out <- ms_sev(edss, type="global_msss", matrix=true) head(out$) oldmsss the old Global MSSS matrix Format The global MSSS-matrix provided with the ms.sev-package (oldmsss) A frame consisting of 20 columns and 30 rows, corresponding to EDSS-scores in 0.5-increments, and disease duration. This is the original MSSS matrix. The first column is corresponding to disease duration.
9 Index Topic ARMSS global_armss, 4 local_armss, 5 Topic EDSS global_armss, 4 global_msss, 4 local_armss, 5 local_msss, 6 Topic MSSS global_msss, 4 Topic SEVERITY local_msss, 6 Topic sets Topic package ms_sev-package, 2 Topic severity global_armss, 4 local_armss, 5 global_armss, 4 global_msss, 4 local_armss, 5 local_msss, 6 ms_sev-package, 2 9
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