extra formatting changes

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 ... ... @@ -5,12 +5,12 @@ 5 5  \title{Produce random paths modeled on a given path} 6 6  \usage{ 7 7  generateRandomPaths( 8 - path, 9 - from = 1, 10 - to = nrow(path), 11 - d = ncol(path), 12 - randomizationParams, 13 - N 8 +path, 9 +from = 1, 10 +to = nrow(path), 11 +d = ncol(path), 12 +randomizationParams, 13 +N 14 14  ) 15 15  } 16 16  \arguments{ ... ... @@ -47,6 +47,6 @@ randomizationParams. 47 47  \examples{ 48 48  randomizationParams = c('byPermutation','permuteWithinColumns') 49 49  randomPaths = generateRandomPaths(crooked_path,from=6,to=nrow(crooked_path), 50 - d=ncol(crooked_path),randomizationParams=randomizationParams, 51 - N=10) 50 + d=ncol(crooked_path),randomizationParams=randomizationParams, 51 + N=10) 52 52  }

Updated data.R to reference the TrajectoryGeometryData repository and updated the man/... files accordingly.

Michael Shapiro authored on 12/01/2021 16:40:02
Showing1 changed files
 ... ... @@ -5,12 +5,12 @@ 5 5  \title{Produce random paths modeled on a given path} 6 6  \usage{ 7 7  generateRandomPaths( 8 -path, 9 -from = 1, 10 -to = nrow(path), 11 -d = ncol(path), 12 -randomizationParams, 13 -N 8 + path, 9 + from = 1, 10 + to = nrow(path), 11 + d = ncol(path), 12 + randomizationParams, 13 + N 14 14  ) 15 15  } 16 16  \arguments{ ... ... @@ -47,6 +47,6 @@ randomizationParams. 47 47  \examples{ 48 48  randomizationParams = c('byPermutation','permuteWithinColumns') 49 49  randomPaths = generateRandomPaths(crooked_path,from=6,to=nrow(crooked_path), 50 - d=ncol(crooked_path),randomizationParams=randomizationParams, 51 - N=10) 50 + d=ncol(crooked_path),randomizationParams=randomizationParams, 51 + N=10) 52 52  }

whitespace, line-lengths and single-cell data sources sorted

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 ... ... @@ -5,12 +5,12 @@ 5 5  \title{Produce random paths modeled on a given path} 6 6  \usage{ 7 7  generateRandomPaths( 8 - path, 9 - from = 1, 10 - to = nrow(path), 11 - d = ncol(path), 12 - randomizationParams, 13 - N 8 +path, 9 +from = 1, 10 +to = nrow(path), 11 +d = ncol(path), 12 +randomizationParams, 13 +N 14 14  ) 15 15  } 16 16  \arguments{ ... ... @@ -47,6 +47,6 @@ randomizationParams. 47 47  \examples{ 48 48  randomizationParams = c('byPermutation','permuteWithinColumns') 49 49  randomPaths = generateRandomPaths(crooked_path,from=6,to=nrow(crooked_path), 50 - d=ncol(crooked_path),randomizationParams=randomizationParams, 51 - N=10) 50 + d=ncol(crooked_path),randomizationParams=randomizationParams, 51 + N=10) 52 52  }

Removed documentation for functions which are not exported.

Changed names of data, e.g., changed crookedPath to crooked_path.

Michael Shapiro authored on 01/01/2021 16:41:44
Showing1 changed files
 ... ... @@ -5,12 +5,12 @@ 5 5  \title{Produce random paths modeled on a given path} 6 6  \usage{ 7 7  generateRandomPaths( 8 -path, 9 -from = 1, 10 -to = nrow(path), 11 -d = ncol(path), 12 -randomizationParams, 13 -N 8 + path, 9 + from = 1, 10 + to = nrow(path), 11 + d = ncol(path), 12 + randomizationParams, 13 + N 14 14  ) 15 15  } 16 16  \arguments{ ... ... @@ -46,6 +46,7 @@ randomizationParams. 46 46  } 47 47  \examples{ 48 48  randomizationParams = c('byPermutation','permuteWithinColumns') 49 -randomPaths = generateRandomPaths(crookedPath,from=6,to=nrow(crookedPath), 50 - d=ncol(crookedPath),randomizationParams=randomizationParams,N=10) 49 +randomPaths = generateRandomPaths(crooked_path,from=6,to=nrow(crooked_path), 50 + d=ncol(crooked_path),randomizationParams=randomizationParams, 51 + N=10) 51 52  }

most whitespace sorted out

Showing1 changed files
 ... ... @@ -5,12 +5,12 @@ 5 5  \title{Produce random paths modeled on a given path} 6 6  \usage{ 7 7  generateRandomPaths( 8 - path, 9 - from = 1, 10 - to = nrow(path), 11 - d = ncol(path), 12 - randomizationParams, 13 - N 8 +path, 9 +from = 1, 10 +to = nrow(path), 11 +d = ncol(path), 12 +randomizationParams, 13 +N 14 14  ) 15 15  } 16 16  \arguments{ ... ... @@ -47,5 +47,5 @@ randomizationParams. 47 47  \examples{ 48 48  randomizationParams = c('byPermutation','permuteWithinColumns') 49 49  randomPaths = generateRandomPaths(crookedPath,from=6,to=nrow(crookedPath), 50 - d=ncol(crookedPath),randomizationParams=randomizationParams,N=10) 50 + d=ncol(crookedPath),randomizationParams=randomizationParams,N=10) 51 51  }

Wrote a function to measure the progression of a path in a direction and jazzed up the vignette to reflect this.

Michael Shapiro authored on 09/06/2020 15:54:24
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 ... ... @@ -35,7 +35,7 @@ details.} 35 35  } 36 36  \value{ 37 37  This function returns a list of random paths. Each path is 38 - a matrix. Note that each random path begins at the origin. 38 + a matrix. 39 39  } 40 40  \description{ 41 41  This function takes a path and produces N random paths of the same

This modifies the path randomization so that paths can be randomized either by permutation of the matrix or by taking steps.

Michael Shapiro authored on 03/06/2020 16:40:36
Showing1 changed files
 ... ... @@ -9,7 +9,7 @@ generateRandomPaths( 9 9  from = 1, 10 10  to = nrow(path), 11 11  d = ncol(path), 12 - preserveLengths = TRUE, 12 + randomizationParams, 13 13  N 14 14  ) 15 15  } ... ... @@ -26,9 +26,10 @@ nrow(path).} 26 26  \item{d}{- The dimension under consideration. This defaults to 27 27  ncol(path)} 28 28   29 -\item{preserveLengths}{- If this is set to TRUE, the steps of the 30 -random paths have the same euclidean length as those of the 31 -give path. Otherwise they hav length 1.} 29 +\item{randomizationParams}{- A character vector controling the 30 +randomization method used. It's first entry must be either 31 +'byPermutation' or 'bySteps' See the vignette for further 32 +details.} 32 33   33 34  \item{N}{- The number of random paths required.} 34 35  } ... ... @@ -38,12 +39,13 @@ This function returns a list of random paths. Each path is 38 39  } 39 40  \description{ 40 41  This function takes a path and produces N random paths of the same 41 -dimension and length based on it. The steps along the random paths 42 -are based on uniform sampling of the unit sphere. If  43 -preserveLengths is set to TRUE, the random paths of steps of the 44 -same length as the original path. Otherwise, the steps are all 45 -length 1. 42 +dimension and length based on it. This can be done either by 43 +permuting the entries in path or by taking steps from the initial 44 +point of path. Exact behaviour is controlled by 45 +randomizationParams. 46 46  } 47 47  \examples{ 48 -randomPaths = generateRandomPaths(crookedPath,from=6,N=10) 48 +randomizationParams = c('byPermutation','permuteWithinColumns') 49 +randomPaths = generateRandomPaths(crookedPath,from=6,to=nrow(crookedPath), 50 + d=ncol(crookedPath),randomizationParams=randomizationParams,N=10) 49 51  }

Documented the data in R/data.R

Michael Shapiro authored on 26/05/2020 14:25:19
Showing1 changed files
 ... ... @@ -44,3 +44,6 @@ preserveLengths is set to TRUE, the random paths of steps of the 44 44  same length as the original path. Otherwise, the steps are all 45 45  length 1. 46 46  } 47 +\examples{ 48 +randomPaths = generateRandomPaths(crookedPath,from=6,N=10) 49 +}

The changes to the documentaion are the result of a misconception as to the source of some problems. HOWEVER I was able to track down and fix some bugs and successfully run testPathForDirectionality using straightPath as my test data.

Michael Shapiro authored on 21/05/2020 16:56:41
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 ... ... @@ -6,8 +6,8 @@ 6 6  \usage{ 7 7  generateRandomPaths( 8 8  path, 9 - start = 1, 10 - end = nrow(path), 9 + from = 1, 10 + to = nrow(path), 11 11  d = ncol(path), 12 12  preserveLengths = TRUE, 13 13  N ... ... @@ -17,10 +17,10 @@ generateRandomPaths( 17 17  \item{path}{- This is an mxn dimensional matrix. Each row is 18 18  considered a point.} 19 19   20 -\item{start}{- The starting place along the path which will be 20 +\item{from}{- The starting place along the path which will be 21 21  treated as the center of the sphere. This defaults to 1.} 22 22   23 -\item{end}{- The end point of the path. This defaults to 23 +\item{to}{- The end point of the path. This defaults to 24 24  nrow(path).} 25 25   26 26  \item{d}{- The dimension under consideration. This defaults to

This now contains code and documentation.

Michael Shapiro authored on 10/04/2020 11:42:19
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 1 1 new file mode 100644 ... ... @@ -0,0 +1,46 @@ 1 +% Generated by roxygen2: do not edit by hand 2 +% Please edit documentation in R/TrajectoryGeometry.R 3 +\name{generateRandomPaths} 4 +\alias{generateRandomPaths} 5 +\title{Produce random paths modeled on a given path} 6 +\usage{ 7 +generateRandomPaths( 8 + path, 9 + start = 1, 10 + end = nrow(path), 11 + d = ncol(path), 12 + preserveLengths = TRUE, 13 + N 14 +) 15 +} 16 +\arguments{ 17 +\item{path}{- This is an mxn dimensional matrix. Each row is 18 +considered a point.} 19 + 20 +\item{start}{- The starting place along the path which will be 21 +treated as the center of the sphere. This defaults to 1.} 22 + 23 +\item{end}{- The end point of the path. This defaults to 24 +nrow(path).} 25 + 26 +\item{d}{- The dimension under consideration. This defaults to 27 +ncol(path)} 28 + 29 +\item{preserveLengths}{- If this is set to TRUE, the steps of the 30 +random paths have the same euclidean length as those of the 31 +give path. Otherwise they hav length 1.} 32 + 33 +\item{N}{- The number of random paths required.} 34 +} 35 +\value{ 36 +This function returns a list of random paths. Each path is 37 + a matrix. Note that each random path begins at the origin. 38 +} 39 +\description{ 40 +This function takes a path and produces N random paths of the same 41 +dimension and length based on it. The steps along the random paths 42 +are based on uniform sampling of the unit sphere. If  43 +preserveLengths is set to TRUE, the random paths of steps of the 44 +same length as the original path. Otherwise, the steps are all 45 +length 1. 46 +}