fixing half-closed notation and examples

HopkinsIDD · Dec 17, 2018 · 2782d6d · 2782d6d
1 parent b4d113e
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,14 +1,14 @@
 Package: IDSpatialStats
-Version: 0.3.5
-Date: 2018-06-11
+Version: 0.3.7
+Date: 2018-12-17
 Title: Estimate Global Clustering in Infectious Disease
-Author: Justin Lessler <[email protected]>, Henrik Salje <[email protected]>, John Giles <[email protected]>
+Author: Justin Lessler <[email protected]>, Henrik Salje <[email protected]>, John Giles <[email protected]>
 Maintainer: Justin Lessler <[email protected]>
 License: GPL (>=2)
 Description: Implements various novel and standard
     clustering statistics and other analyses useful for understanding the
     spread of infectious disease.
-RoxygenNote: 6.0.1
+RoxygenNote: 6.1.1
 Encoding: UTF-8
 Imports: igraph, spatstat
 Depends: doParallel, foreach, parallel, R (>= 2.10)

diff --git a/NAMESPACE b/NAMESPACE
@@ -8,7 +8,10 @@ importFrom("igraph", "shortest.paths") # for get.transdist.theta
 importFrom("igraph", "E") # for get.transdist.theta
 importFrom("spatstat", "bounding.box.xy") # for est.transdist
 importFrom("spatstat", "as.ppp") # for est.transdist
+importFrom("spatstat", "ppp") # for est.transdist
 importFrom("spatstat", "crossdist") # for est.transdist
+importFrom("spatstat", "Kcross") # for get.cross.K
+importFrom("spatstat", "pcf") # for get.cross.PCF
 export(get.pi)
 export(get.pi.ci)
 export(get.pi.bootstrap)
@@ -40,5 +43,7 @@ export(est.transdist)
 export(est.transdist.bootstrap.ci)
 export(est.transdist.temporal)
 export(est.transdist.temporal.bootstrap.ci)
+export(get.cross.K)
+export(get.cross.PCF)
 useDynLib(IDSpatialStats, .registration=TRUE, .fixes="C_")
 
diff --git a/R/examples/get_cross_k.R b/R/examples/get_cross_k.R
@@ -1,7 +1,6 @@
 data(DengueSimulationR01)
 
 k <- get.cross.K(epi.data=DengueSimR01, type=5, hom=2, het=NULL, r=NULL, correction='border')
-k.theo <- pi*(k$r)^2
 
-plot(k.theo, type='l', col='red', lty=2, xlab='r', ylab='cross K function')
+plot(k[,2], type='l', col='red', lty=2, xlab='r', ylab='cross K function')
 lines(k$border)
diff --git a/R/examples/get_tau.R b/R/examples/get_tau.R
@@ -7,21 +7,21 @@ r.min<-seq(0,980,20)
 r.mid<-(r.max+r.min)/2
 
 sero.type.func<-function(a,b,tlimit=20){
-  if(a[5]==b[5]&(abs(a[3]-b[3])<=tlimit)){rc=1}
-  else{rc=2}
-  return(rc)
+     if(a[5]==b[5]&(abs(a[3]-b[3])<=tlimit)){rc=1}
+     else{rc=2}
+     return(rc)
 }
 
 geno.type.func<-function(a,b,tlimit=20){
-  if(a[4]==b[4]&(abs(a[3]-b[3])<=tlimit)){rc=1}
-  else{rc=2}
-  return(rc)
+     if(a[4]==b[4]&(abs(a[3]-b[3])<=tlimit)){rc=1}
+     else{rc=2}
+     return(rc)
 }
 
 sero.type.rep.func<-function(a,b,tlimit=20){
-  if(a[5]==1&b[5]==1&(abs(a[3]-b[3])<=tlimit)){rc=1}
-  else{if(a[5]==1&b[5]==-999){rc=2}else{rc=3}}
-  return(rc)
+     if(a[5]==1&b[5]==1&(abs(a[3]-b[3])<=tlimit)){rc=1}
+     else{if(a[5]==1&b[5]==-999){rc=2}else{rc=3}}
+     return(rc)
 }
 
 sero.tau.R01<-get.tau(DengueSimR01,sero.type.func,r=r.max,r.low=r.min,comparison.type="independent")
@@ -31,7 +31,7 @@ sero.tau.R02<-get.tau(DengueSimR02,sero.type.func,r=r.max,r.low=r.min,comparison
 geno.tau.R02<-get.tau(DengueSimR02,geno.type.func,r=r.max,r.low=r.min,comparison.type="independent")
 
 sero.tau.representative<-get.tau(DengueSimRepresentative,
-    sero.type.rep.func,r=r.max,r.low=r.min,comparison.type="representative")
+                                 sero.type.rep.func,r=r.max,r.low=r.min,comparison.type="representative")
 
 ## R0 of 1
 plot(r.mid,sero.tau.R01,ylim=c(0.3,max(geno.tau.R01)),log="y",
@@ -42,8 +42,8 @@ abline(v=100,lty=1,lwd=2)
 lines(r.mid,geno.tau.R01,pch=20,col=rgb(t(col2rgb("dark green")/255),alpha=0.6),lwd=1)
 lines(r.mid,sero.tau.representative,pch=20,col=rgb(t(col2rgb("dark blue")/255),alpha=0.6),lty=2)
 legend("topright",legend=c("Genotype","Serotype","Serotype (representative population)",
-     "Maximum transmission distance"),lwd=1,col=c("dark green","blue","blue","black"),
-      lty=c(1,1,2,1),bty="n")
+                           "Maximum transmission distance"),lwd=1,col=c("dark green","blue","blue","black"),
+       lty=c(1,1,2,1),bty="n")
 
 ## R0 of 2
 plot(r.mid,sero.tau.R02,ylim=c(0.3,max(geno.tau.R02)),log="y",

diff --git a/R/spatialfuncs.r b/R/spatialfuncs.r
@@ -5,29 +5,32 @@
 ##' specified by the passed in function with that point.
 ##'
 ##' @param posmat a matrix with columns x, y and any other named columns
-##'    columns needed by fun
-##' @param fun a function that takes in two rows of posmat and returns:
+##'    columns needed by \code{fun}
+##' @param fun a function that takes in two rows of \code{posmat} and returns:
 ##' \enumerate{
-##'      \item  for pairs included in the numerator and denominator
+##'      \item for pairs included in the numerator and denominator
 ##'      \item for pairs that should only be included in the denominator
 ##'      \item for pairs that should be ignored all together}
 ##' Note that names from \code{posmat} are not preserved in calls to \code{fun}, so the columns of the matrix should be
 ##' referenced numerically
-##' so this is not available to the fun
+##' so this is not available to the \code{fun}
 ##' @param r the series of spatial distances (or there maximums) we are
 ##'          interested in
 ##' @param r.low the low end of each range, 0 by default
 ##'
 ##' @return  pi value for each distance range that we look at. Where:
 ##'
-##' \deqn{ \pi(d_1,d_2) = \frac{\sum \boldsymbol{1} (d_{ij} \in (d_1,d_2)) \boldsymbol{1} (f(i,j)=1) }{\sum \sum \boldsymbol{1} (d_{ij} \in (d_1,d_2)) \boldsymbol{1} (f(i,j) \in \{1,2\}) }}
+##'\deqn{ \pi(d_1, d_2) = \frac{\sum \boldsymbol{1} (d_{ij} \in [d_1,d_2)) \boldsymbol{1} (f(i,j)=1) }{\sum \sum \boldsymbol{1} [d_{ij} \in (d_1,d_2)) \boldsymbol{1} (f(i,j) \in \{1,2\}) }}
 ##'
 ##' @author Justin Lessler and Henrik Salje
 ##'
 ##' @family get.pi
 ##' @family spatialtau
 ##'
-##' @example R/examples/get_pi.R
+##' @example 
+##' \dontrun{
+##' R/examples/get_pi.R
+##' }
 ##'
 
 get.pi <- function(posmat,
@@ -79,15 +82,19 @@ get.pi <- function(posmat,
 ##'
 ##' @return  theta value for each distance range that we look at. Where:
 ##'
-##' \deqn{ \theta(d_1,d_2) = \frac{\sum \boldsymbol{1} (d_{ij} \in (d_1,d_2)) \boldsymbol{1} (f(i,j)=1) }{\sum \sum \boldsymbol{1} (d_{ij} \in (d_1,d_2)) \boldsymbol{1} (f(i,j)=2) }}
+##' \deqn{ \theta(d_1,d_2) = \frac{\sum \boldsymbol{1} d_{ij} \in [d_1,d_2)) \boldsymbol{1} (f(i,j)=1) }{\sum \sum \boldsymbol{1} d_{ij} \in [d_1,d_2)) \boldsymbol{1} (f(i,j)=2) }}
 ##'
 ##' @author Justin Lessler and Henrik Salje
 ##'
 ##' @family get.theta
 ##' @family spatialtau
 ##'
-##' @example R/examples/get_theta.R
+##' @example 
+##' \dontrun{
+##' R/examples/get_theta.R
+##' }
 ##'
+
 get.theta <- function(posmat,
                       fun,
                       r = 1,
@@ -132,7 +139,10 @@ get.theta <- function(posmat,
 ##'
 ##' @family get.pi
 ##'
-##' @example R/examples/get_pi_typed.R
+##' @example 
+##' \dontrun{
+##' R/examples/get_pi_typed.R
+##' }
 ##'
 get.pi.typed <- function(posmat,
                          typeA = -1,
@@ -176,7 +186,10 @@ get.pi.typed <- function(posmat,
 ##'
 ##' @family get.theta
 ##'
-##' @example R/examples/get_theta_typed.R
+##' @example 
+##' \dontrun{
+##' R/examples/get_theta_typed.R
+##' }
 ##'
 get.theta.typed <- function(posmat,
                             typeA = -1,
@@ -221,10 +234,10 @@ get.theta.typed <- function(posmat,
 ##'
 ##' @family get.pi
 ##'
-##' @examples
+##' @example 
 ##' \dontrun{
-##'  R/examples/get_pi_ci.R
-##'  }
+##' R/examples/get_pi_ci.R
+##' }
 ##'
 get.pi.ci <- function(posmat,
                       fun,
@@ -270,10 +283,10 @@ get.pi.ci <- function(posmat,
 ##'
 ##' @family get.theta
 ##'
-##' @examples
+##' @example 
 ##' \dontrun{
-##'  R/examples/get_theta_ci.R
-##'  }
+##' R/examples/get_theta_ci.R
+##' }
 ##'
 get.theta.ci <- function(posmat,
                          fun,
@@ -319,7 +332,7 @@ get.theta.ci <- function(posmat,
 ##'
 ##' @family get.pi
 ##'
-##' @examples
+##' @example
 ##' \dontrun{
 ##'  R/examples/get_pi_bootstrap.R
 ##'  }
@@ -377,7 +390,7 @@ get.pi.bootstrap <- function(posmat,
 ##'
 ##' @family get.theta
 ##'
-##' @examples
+##' @example
 ##' \dontrun{
 ##'  R/examples/get_theta_bootstrap.R
 ##'  }
@@ -430,7 +443,7 @@ get.theta.bootstrap <- function(posmat,
 ##'
 ##' @family get.pi
 ##'
-##' @examples
+##' @example
 ##' \dontrun{
 ##'  R/examples/get_pi_typed_bootstrap.R
 ##'  }
@@ -481,7 +494,7 @@ get.pi.typed.bootstrap <- function(posmat,
 ##'
 ##' @family get.theta
 ##'
-##' @examples
+##' @example
 ##' \dontrun{
 ##'  R/examples/get_theta_typed_bootstrap.R
 ##'  }
@@ -514,7 +527,6 @@ get.theta.typed.bootstrap <- function(posmat,
   return(rc)
 }
 
-
 ##' get the null distribution of the \code{get.pi} function
 ##'
 ##' Does permutations to calculate the null distribution of get pi
@@ -531,7 +543,7 @@ get.theta.typed.bootstrap <- function(posmat,
 ##'
 ##' @family get.pi
 ##'
-##' @examples
+##' @example
 ##' \dontrun{
 ##'  R/examples/get_pi_permute.R
 ##'  }
@@ -586,7 +598,7 @@ get.pi.permute <- function(posmat,
 ##'
 ##' @family get.theta
 ##'
-##' @examples
+##' @example
 ##' \dontrun{
 ##'  R/examples/get_theta_permute.R
 ##'  }
@@ -644,7 +656,7 @@ get.theta.permute <- function(posmat,
 ##'
 ##' @family get.pi
 ##'
-##' @examples
+##' @example
 ##' \dontrun{
 ##'  R/examples/get_pi_typed_permute.R
 ##'  }
@@ -705,7 +717,7 @@ get.pi.typed.permute <- function(posmat,
 ##'
 ##' @family get.theta
 ##'
-##' @examples
+##' @example
 ##' \dontrun{
 ##'  R/examples/get_theta_typed_permute.R
 ##'  }
@@ -776,18 +788,18 @@ get.theta.typed.permute <- function(posmat,
 ##'
 ##' @return The tau value for each distance we look at. If \code{comparison.type} is "representative", this is:
 ##'
-##' \code{tau = get.pi(posmat, fun, r, r.low)/get.pi(posmat,fun,0,infinity)}
+##' \code{tau = get.pi(posmat, fun, r, r.low)/get.pi(posmat,fun,infinity,0)}
 ##'
 ##' If \code{comparison.type} is "independent", this is:
 ##'
-##' \code{tau = get.theta(posmat, fun, r, r.low)/get.theta(posmat,fun,0,infinity)}
+##' \code{tau = get.theta(posmat, fun, r, r.low)/get.theta(posmat,fun,infinity,0)}
 ##'
 ##' @author Justin Lessler and Henrik Salje
 ##'
 ##' @family get.tau
 ##' @family spatialtau
 ##'
-##' @examples
+##' @example 
 ##' \dontrun{
 ##' R/examples/get_tau.R
 ##' }
@@ -827,7 +839,7 @@ get.tau <- function(posmat,
   return(rc)
 }
 ##'
-##' Optimizewd version of \code{get.tau} for typed data
+##' Optimized version of \code{get.tau} for typed data
 ##'
 ##' Version of th e \code{get.tau} function that is optimized for
 ##' statically typed data. That is data where we want the relationship between
@@ -850,8 +862,10 @@ get.tau <- function(posmat,
 ##'
 ##' @family get.tau
 ##'
-##' @example R/examples/get_tau_typed.R
-##'
+##' @example 
+##' \dontrun{
+##' R/examples/get_tau_typed.R
+##'}
 get.tau.typed <- function(posmat,
                           typeA = -1,
                           typeB = -1,
@@ -906,7 +920,7 @@ get.tau.typed <- function(posmat,
 ##'
 ##' @family get.tau
 ##'
-##' @examples
+##' @example
 ##' \dontrun{
 ##'  R/examples/get_tau_ci.R
 ##'  }
@@ -955,7 +969,7 @@ get.tau.ci <- function(posmat,
 ##'
 ##' @family get.tau
 ##'
-##' @examples
+##' @example
 ##' \dontrun{
 ##'  R/examples/get_tau_bootstrap.R
 ##'  }
@@ -1022,7 +1036,7 @@ get.tau.bootstrap <- function(posmat,
 ##'
 ##' @family get.tau
 ##'
-##' @examples
+##' @example
 ##' \dontrun{
 ##'  R/examples/get_tau_typed_bootstrap.R
 ##'  }
@@ -1086,7 +1100,7 @@ get.tau.typed.bootstrap <- function(posmat,
 ##'
 ##' @family get.tau
 ##'
-##' @examples
+##' @example
 ##' \dontrun{
 ##'  R/examples/get_tau_permute.R
 ##'  }
@@ -1159,7 +1173,7 @@ get.tau.permute <- function(posmat,
 ##'
 ##' @family get.tau
 ##'
-##' @examples
+##' @example
 ##' \dontrun{
 ##' R/examples/get_tau_typed_permute.R
 ##' }