Added road distance adjacency matrix functionality

.gitignore

@@ -1,4 +1,4 @@
-.Rproj.user
-.Rhistory
-.RData
-.Ruserdata
+*.Rproj.user
+*.Rhistory
+*.RData
+*.Ruserdata

R/INAscene.R

@@ -3,7 +3,7 @@
 #'
 #' This function implements and summarizes multiple simulations across a designated range of parameter values
 #'
-#' Updated 2020-10-13
+#' Updated 2021-10-22
 
 #' @param nreals number of realizations to be evaluated
 #' @param ntimesteps number of time steps to be evaluated
@@ -12,6 +12,8 @@
 
 #' @param readgeocoords if T, read in geocoords - otherwise, generate it in each realization
 #' @param geocoords matrix of x,y coordinates of nodes
+#' @param roaddistfilepath filepath to a R Data (.RData extension) file containing an adjacency matrix with the distances via the road network between nodes in geocoords - mutually exclusive with roadtimefilepath
+#' @param roadtimefilepath filepath to a R Data (.RData extension) file containing an adjacency matrix with the travel times via the road network between nodes in geocoords - mutually exclusive with roaddistfilepath
 
 #' @param numnodes (genlocs) the number of nodes, can be a vector of different numbers of nodes for scenario comparisons (numnodes can be entered as a vector to evaluate multiple scenarios)
 #' @param xrange (genlocs) range of x coordinates, e.g., c(0,50)
@@ -107,7 +109,7 @@
 
 
 
-INAscene <- function(nreals, ntimesteps, doplot=F, outputvol='more', readgeocoords, geocoords=NA, numnodes=NA, xrange=NA, yrange=NA, randgeo=NA, readinitinfo, initinfo=NA, initinfo.norp=NA, initinfo.n=NA, initinfo.p=NA, initinfo.dist=NA, readinitbio, initbio=NA, initbio.norp=NA, initbio.n=NA, initbio.p=NA,  initbio.dist=NA, readseam, seam=NA, seamdist=NA, seamrandp=NA, seampla=NA, seamplb=NA, readbpam, bpam=NA, bpamdist=NA, bpamrandp=NA, bpampla=NA, bpamplb=NA, readprobadoptvec, probadoptvec=NA, probadoptmean=NA, probadoptsd=NA, readprobestabvec, probestabvec=NA, probestabmean=NA, probestabsd=NA, maneffdir=NA, maneffmean=NA, maneffsd=NA, usethreshman, maneffthresh=NA, sampeffort=NA) {
+INAscene <- function(nreals, ntimesteps, doplot=F, outputvol='more', readgeocoords, geocoords=NA, roaddistfilepath=NA, roadtimefilepath=NA, numnodes=NA, xrange=NA, yrange=NA, randgeo=NA, readinitinfo, initinfo=NA, initinfo.norp=NA, initinfo.n=NA, initinfo.p=NA, initinfo.dist=NA, readinitbio, initbio=NA, initbio.norp=NA, initbio.n=NA, initbio.p=NA,  initbio.dist=NA, readseam, seam=NA, seamdist=NA, seamrandp=NA, seampla=NA, seamplb=NA, readbpam, bpam=NA, bpamdist=NA, bpamrandp=NA, bpampla=NA, bpamplb=NA, readprobadoptvec, probadoptvec=NA, probadoptmean=NA, probadoptsd=NA, readprobestabvec, probestabvec=NA, probestabmean=NA, probestabsd=NA, maneffdir=NA, maneffmean=NA, maneffsd=NA, usethreshman, maneffthresh=NA, sampeffort=NA) {
 
 ### error message(s)
 
@@ -311,7 +313,7 @@ for (j22 in 1:ncombs) {
   }
 
 
-  temp <- multsame2(nreals2=nreals, ntimesteps2=ntimesteps, doplot2=doplot, readgeocoords2=readgeocoords, geocoords2=geocoords, numnodes2=numnodes, xrange2=xrange, yrange2=yrange, randgeo2=randgeo, readinitinfo2=readinitinfo, initinfo2=initinfo, initinfo.norp2=initinfo.norp, initinfo.n2=initinfo.n, initinfo.p2=initinfo.p, initinfo.dist2=initinfo.dist, readinitbio2=readinitbio, initbio2=initbio, initbio.norp2=initbio.norp, initbio.n2=initbio.n, initbio.p2=initbio.p, initbio.dist2=initbio.dist, readseam2=readseam, seam2=seam,  seamdist2=seamdist, seamrandp2=seamrandp, seampla2=seampla, seamplb2=seamplb, readbpam2=readbpam, bpam2=bpam, bpamdist2=bpamdist, bpamrandp2=bpamrandp, bpampla2=bpampla, bpamplb2=bpamplb, readprobadoptvec2=readprobadoptvec, probadoptvec2=probadoptvec, probadoptmean2=probadoptmean, probadoptsd2=probadoptsd, readprobestabvec2=readprobestabvec, probestabvec2=probestabvec, probestabmean2=probestabmean, probestabsd2=probestabsd, maneffdir2=maneffdir, maneffmean2=maneffmean, maneffsd2=maneffsd, usethreshman2=usethreshman, maneffthresh2=maneffthresh, sampeffort2=sampeffort)
+  temp <- multsame2(nreals2=nreals, ntimesteps2=ntimesteps, doplot2=doplot, readgeocoords2=readgeocoords, geocoords2=geocoords, roaddistfilepath2=roaddistfilepath, roadtimefilepath2=roadtimefilepath, numnodes2=numnodes, xrange2=xrange, yrange2=yrange, randgeo2=randgeo, readinitinfo2=readinitinfo, initinfo2=initinfo, initinfo.norp2=initinfo.norp, initinfo.n2=initinfo.n, initinfo.p2=initinfo.p, initinfo.dist2=initinfo.dist, readinitbio2=readinitbio, initbio2=initbio, initbio.norp2=initbio.norp, initbio.n2=initbio.n, initbio.p2=initbio.p, initbio.dist2=initbio.dist, readseam2=readseam, seam2=seam,  seamdist2=seamdist, seamrandp2=seamrandp, seampla2=seampla, seamplb2=seamplb, readbpam2=readbpam, bpam2=bpam, bpamdist2=bpamdist, bpamrandp2=bpamrandp, bpampla2=bpampla, bpamplb2=bpamplb, readprobadoptvec2=readprobadoptvec, probadoptvec2=probadoptvec, probadoptmean2=probadoptmean, probadoptsd2=probadoptsd, readprobestabvec2=readprobestabvec, probestabvec2=probestabvec, probestabmean2=probestabmean, probestabsd2=probestabsd, maneffdir2=maneffdir, maneffmean2=maneffmean, maneffsd2=maneffsd, usethreshman2=usethreshman, maneffthresh2=maneffthresh, sampeffort2=sampeffort)
 
 
   multdetails[[rowcount]] <- temp
@@ -342,4 +344,4 @@ if (outputvol=='more') {
     list(multout=multout)
 }
 
-}
+}

R/cities.csv

@@ -0,0 +1,327 @@
+id,lon,lat
+NewYork[d],-73.93,40.66
+LosAngeles,-118.41,34.01
+Chicago,-87.68,41.83
+Houston,-95.39,29.78
+Phoenix,-112.09,33.57
+Philadelphia[e],-75.13,40
+SanAntonio,-98.52,29.47
+SanDiego,-117.13,32.81
+Dallas,-96.76,32.79
+SanJose,-121.81,37.29
+Austin,-97.75,30.3
+Jacksonville[f],-81.66,30.33
+FortWorth,-97.34,32.78
+Columbus,-82.98,39.98
+Indianapolis[g],-86.14,39.77
+Charlotte,-80.83,35.2
+SanFrancisco[h],-123.03,37.72
+Seattle,-122.35,47.62
+Denver[i],-104.88,39.76
+Washington[j],-77.01,38.9
+Nashville[k],-86.78,36.17
+OklahomaCity,-97.51,35.46
+ElPaso,-106.42,31.84
+Boston,-71.02,42.33
+Portland,-122.65,45.53
+LasVegas,-115.26,36.22
+Detroit,-83.1,42.38
+Memphis,-89.97,35.1
+Louisville[l],-85.64,38.16
+Baltimore[m],-76.61,39.3
+Milwaukee,-87.96,43.06
+Albuquerque,-106.64,35.1
+Tucson,-110.87,32.15
+Fresno,-119.79,36.78
+Sacramento,-121.46,38.56
+KansasCity,-94.55,39.12
+Mesa,-111.71,33.4
+Atlanta,-84.42,33.76
+Omaha,-96.04,41.26
+ColoradoSprings,-104.76,38.86
+Raleigh,-78.64,35.83
+LongBeach,-118.15,33.8
+VirginiaBeach[m],-76.02,36.78
+Miami,-80.2,25.77
+Oakland,-122.22,37.76
+Minneapolis,-93.26,44.96
+Tulsa,-95.9,36.12
+Bakersfield,-119.01,35.32
+Wichita,-97.34,37.69
+Arlington,-97.12,32.7
+Aurora,-104.68,39.68
+Tampa,-82.47,27.97
+NewOrleans[n],-89.93,30.05
+Cleveland,-81.67,41.47
+Honolulu[b],-157.84,21.32
+Anaheim,-117.76,33.85
+Lexington[o],-84.45,38.04
+Stockton,-121.31,37.97
+CorpusChristi,-97.17,27.75
+Henderson,-115.03,36
+Riverside,-117.39,33.93
+Newark,-74.17,40.72
+SaintPaul,-93.1,44.94
+SantaAna,-117.88,33.73
+Cincinnati,-84.5,39.14
+Irvine,-117.77,33.67
+Orlando,-81.27,28.41
+Pittsburgh,-79.97,40.43
+St.Louis[m],-90.24,38.63
+Greensboro,-79.82,36.09
+JerseyCity,-74.06,40.71
+Anchorage[p],-149.28,61.17
+Lincoln,-96.68,40.81
+Plano,-96.74,33.05
+Durham,-78.9,35.98
+Buffalo,-78.85,42.89
+Chandler,-111.85,33.28
+ChulaVista,-117.01,32.62
+Toledo,-83.58,41.66
+Madison,-89.42,43.08
+Gilbert[q],-111.74,33.31
+Reno,-119.84,39.54
+FortWayne,-85.14,41.08
+NorthLasVegas,-115.09,36.28
+St.Petersburg,-82.64,27.76
+Lubbock,-101.88,33.56
+Irving,-96.97,32.85
+Laredo,-99.48,27.56
+WinstonSalem,-80.26,36.1
+Chesapeake[m],-76.3,36.67
+Glendale,-112.18,33.53
+Garland,-96.63,32.9
+Scottsdale,-111.86,33.68
+Norfolk[m],-76.24,36.92
+Boise[r],-116.23,43.6
+Fremont,-121.94,37.49
+Spokane,-117.43,47.66
+SantaClarita,-118.5,34.4
+BatonRouge[s],-91.13,30.44
+Richmond[m],-77.47,37.53
+Hialeah,-80.3,25.86
+SanBernardino,-117.29,34.14
+Tacoma,-122.45,47.25
+Modesto,-121,37.63
+Huntsville,-86.67,34.69
+DesMoines,-93.61,41.57
+Yonkers,-73.86,40.94
+Rochester,-77.61,43.16
+MorenoValley,-117.2,33.92
+Fayetteville,-78.97,35.08
+Fontana,-117.46,34.1
+Columbus[t],-84.87,32.51
+Worcester,-71.8,42.26
+PortSt.Lucie,-80.38,27.28
+LittleRock,-92.35,34.72
+Augusta[u],-82.07,33.36
+Oxnard,-119.2,34.2
+Birmingham,-86.79,33.52
+Montgomery,-86.26,32.34
+Frisco,-96.82,33.15
+Amarillo,-101.83,35.19
+SaltLakeCity,-111.93,40.77
+GrandRapids,-85.65,42.96
+HuntingtonBeach,-118,33.69
+OverlandPark,-94.69,38.88
+Glendale,-118.24,34.18
+Tallahassee,-84.25,30.45
+GrandPrairie,-97.02,32.68
+McKinney,-96.66,33.19
+CapeCoral,-81.99,26.64
+SiouxFalls,-96.73,43.53
+Peoria,-112.3,33.78
+Providence,-71.41,41.82
+Vancouver,-122.59,45.63
+Knoxville,-83.94,35.97
+Akron,-81.52,41.08
+Shreveport,-93.79,32.46
+Mobile,-88.1,30.66
+Brownsville,-97.45,25.99
+NewportNews[m],-76.52,37.07
+FortLauderdale,-80.14,26.14
+Chattanooga,-85.24,35.06
+Tempe,-111.93,33.38
+Aurora,-88.29,41.76
+SantaRosa,-122.7,38.44
+Eugene,-123.11,44.05
+ElkGrove,-121.38,38.41
+Salem,-123.02,44.92
+Ontario,-117.6,34.03
+Cary[v],-78.81,35.78
+RanchoCucamonga,-117.56,34.12
+Oceanside,-117.3,33.22
+Lancaster,-118.17,34.69
+GardenGrove,-117.96,33.77
+PembrokePines,-80.34,26.02
+FortCollins,-105.06,40.54
+Palmdale,-118.1,34.59
+Springfield,-93.29,37.19
+Clarksville,-87.34,36.56
+Salinas,-121.63,36.69
+Hayward,-122.1,37.62
+Paterson,-74.16,40.91
+Alexandria[m],-77.08,38.82
+Macon[w],-83.69,32.8
+Corona,-117.56,33.86
+KansasCity[x],-94.74,39.12
+Lakewood,-105.11,39.69
+Springfield,-72.54,42.11
+Sunnyvale,-122.02,37.38
+Jackson,-90.21,32.31
+Killeen,-97.73,31.07
+Hollywood,-80.16,26.03
+Murfreesboro,-86.41,35.85
+Pasadena,-95.15,29.65
+Bellevue,-122.15,47.59
+Pomona,-117.76,34.05
+Escondido,-117.07,33.13
+Joliet,-88.14,41.51
+Charleston,-79.95,32.81
+Mesquite,-96.58,32.76
+Naperville,-88.16,41.74
+Rockford,-89.06,42.25
+Bridgeport,-73.19,41.18
+Syracuse,-76.14,43.04
+Savannah,-81.15,32
+Roseville,-121.31,38.76
+Torrance,-118.34,33.83
+Fullerton,-117.92,33.88
+Surprise,-112.45,33.67
+McAllen,-98.24,26.23
+Thornton,-104.94,39.91
+Visalia,-119.32,36.32
+Olathe,-94.81,38.88
+Gainesville,-82.34,29.67
+WestValleyCity,-112.01,40.68
+Orange,-117.86,33.78
+Denton,-97.14,33.21
+Warren,-83.02,42.49
+Pasadena,-118.13,34.16
+Waco,-97.18,31.56
+CedarRapids,-91.67,41.96
+Dayton,-84.19,39.77
+Elizabeth,-74.19,40.66
+Hampton[m],-76.29,37.04
+Columbia,-80.89,34.02
+Kent,-122.21,47.38
+Stamford,-73.54,41.07
+Lakewood,-74.21,40.08
+Victorville,-117.35,34.52
+Miramar,-80.33,25.97
+CoralSprings,-80.25,26.27
+SterlingHeights,-83.03,42.58
+NewHaven,-72.92,41.31
+Carrollton,-96.89,32.98
+Midland,-102.11,32.02
+Norman,-97.34,35.24
+SantaClara,-121.96,37.36
+Athens[y],-83.37,33.94
+ThousandOaks,-118.87,34.19
+Topeka,-95.69,39.03
+SimiValley,-118.74,34.26
+Columbia,-92.32,38.95
+Vallejo,-122.26,38.1
+Fargo,-96.82,46.86
+Allentown,-75.47,40.59
+Pearland,-95.32,29.55
+Concord,-122,37.97
+Abilene,-99.73,32.45
+Arvada,-105.15,39.83
+Berkeley,-122.29,37.86
+AnnArbor,-83.73,42.27
+Independence,-94.35,39.08
+Rochester,-92.47,44.01
+Lafayette[z],-92.02,30.2
+Hartford,-72.68,41.76
+CollegeStation,-96.29,30.58
+Clovis,-119.68,36.82
+Fairfield,-122.03,38.25
+PalmBay,-80.66,27.98
+Richardson,-96.7,32.97
+RoundRock,-97.66,30.52
+Cambridge,-71.11,42.37
+Meridian,-116.39,43.61
+WestPalmBeach,-80.12,26.74
+Evansville,-87.53,37.98
+Clearwater,-82.76,27.97
+Billings,-108.54,45.78
+WestJordan,-112,40.6
+Richmond,-122.36,37.95
+Westminster,-105.06,39.88
+Manchester,-71.44,42.98
+Lowell,-71.32,42.63
+Wilmington,-77.88,34.2
+Antioch,-121.79,37.97
+Beaumont,-94.14,30.08
+Provo,-111.64,40.24
+NorthCharleston,-80.06,32.91
+Elgin,-88.32,42.03
+Carlsbad,-117.28,33.12
+Odessa,-102.34,31.88
+Waterbury,-73.03,41.55
+Springfield,-89.64,39.79
+LeagueCity,-95.1,29.49
+Downey,-118.13,33.93
+Gresham,-122.44,45.5
+HighPoint,-79.99,35.99
+BrokenArrow,-95.78,36.03
+Peoria,-89.61,40.75
+Lansing,-84.55,42.71
+Lakeland,-81.95,28.05
+PompanoBeach,-80.13,26.24
+CostaMesa,-117.91,33.66
+Pueblo,-104.61,38.26
+Lewisville,-96.98,33.04
+MiamiGardens,-80.24,25.94
+LasCruces,-106.78,32.32
+SugarLand,-95.61,29.59
+Murrieta,-117.19,33.57
+Ventura[aa],-119.25,34.26
+Everett,-122.19,47.95
+Temecula,-117.13,33.49
+Dearborn,-83.21,42.31
+SantaMaria,-120.44,34.93
+WestCovina,-117.9,34.05
+ElMonte,-118.02,34.07
+Greeley,-104.76,40.41
+Sparks,-119.73,39.55
+Centennial,-104.86,39.59
+Boulder,-105.25,40.02
+SandySprings,-84.36,33.93
+Inglewood,-118.34,33.95
+Edison,-74.41,40.52
+SouthFulton,-84.67,33.59
+GreenBay,-87.98,44.52
+Burbank,-118.32,34.19
+Renton,-122.19,47.47
+Hillsboro,-122.93,45.52
+ElCajon,-116.96,32.8
+Tyler,-95.3,32.31
+Davie[ac],-80.28,26.07
+SanMateo,-122.31,37.56
+Brockton,-71.02,42.08
+Concord,-80.6,35.4
+JurupaValley,-117.46,34
+DalyCity,-122.46,37.7
+Allen,-96.66,33.09
+RioRancho,-106.67,35.29
+Rialto,-117.38,34.11
+Woodbridge,-74.28,40.56
+SouthBend,-86.26,41.67
+SpokaneValley,-117.23,47.67
+Norwalk,-118.08,33.9
+Menifee,-117.19,33.69
+Vacaville,-121.97,38.35
+WichitaFalls,-98.52,33.9
+Davenport,-90.6,41.55
+Quincy,-71,42.25
+Chico,-121.83,39.74
+Lynn,-70.95,42.47
+Lee'sSummit,-94.37,38.92
+NewBedford,-70.93,41.64
+FederalWay,-122.35,47.32
+Clinton,-82.92,42.59
+Edinburg,-98.16,26.3
+Nampa,-116.56,43.57
+Roanoke[m],-79.93,37.27