Calculating percentiles for distance and velocity based on the NICHD Fetal Growth Standard

FetalGrowth_Calculator_Velocity_0730.R

###################################### Inputs #################################

# Gestational Age
cat("Please enter Gestational Age\n")
GA= scan(n=2)
if(length(GA)==0|length(GA)==1){
cat("Please enter Gestational Age\n")
GA= scan(n=2)
if(length(GA)==0|length(GA)==1){
cat("If you have your Gestational Age information, please enter Gestational Age
\nIf you do not have your Please enter Gestational Age, please hit any button to continue\n")
GA=scan(n=2)
if(length(GA)==0){
GA=40
}#set default value for GA
}
}

## Race
race_index= c("White", "Black" ,"Hispanic", "Asian")
cat("Please enter # of race\nRace Index: 1-White 2-Black 3-Hispanic 4-Asian\n")
Race= scan(n=1)
if(length(Race)==0){
cat("Please enter # of race\nRace Index: 1-White 2-Black 3-Hispanic 4-Asian\n")
Race= scan(n=1)
if(length(Race)==0){
cat("If you have your race information, please enter # of race
\nIf you do not have your race information, please hit any button to continue
\nRace Index: 1-White 2-Black 3-Hispanic 4-Asian\n")
Race= scan(n=1)
if(length(Race)==0){
Race=1
}#set default value for race
}
}

## Ultrasonograpy TypeUltrasonograpy
ultra_index= c("EFW1" , "EFW2" , "EFW3" , "EFW4" , "AC" , "BPD" , "FL", "HC","HUMERUS", "HCAC")
cat("Please enter # of ultrasonograpy typeUltrasonograpy
\nUltra Index: 1-EFW1, 2-EFW2, 3-EFW3, 4-EFW4, 5-AC, 6-BPD, 7-FL, 8-HC, 9-HUMERUS, 10-HCAC\n")
Ultra= scan(n=1)
if(length(Ultra)==0){
cat("Please enter # of ultrasonograpy typeUltrasonograpy
\nUltra Index: 1-EFW1, 2-EFW2, 3-EFW3, 4-EFW4, 5-AC, 6-BPD, 7-FL, 8-HC, 9-HUMERUS, 10-HCAC\n")
Ultra= scan(n=1)
if(length(Ultra)==0){
cat("If you have your Ultra information\nPlease enter # of Ultra
\nIf you do not have your Ultra information, please hit any button to continue
\nUltra Index: 1-EFW1, 2-EFW2, 3-EFW3, 4-EFW4, 5-AC, 6-BPD, 7-FL, 8-HC, 9-HUMERUS, 10-HCAC\n")
Ultra=scan(n=1)
if(length(Ultra)==0){
Ultra=1
}#set default value for Ultra
}
}

cat("Please enter value of the ultrasonograpy\n")
Ultra_value= scan(n=2)
if(length(Ultra_value)==0|length(Ultra_value)==1){
cat("Please enter value of the ultrasonograpy\n")
Ultra_value= scan(n=2)
if(length(Ultra_value)==0|length(Ultra_value)==1){
cat("If you have your value of the ultrasonograpy information,Please enter value of the ultrasonograpy
\nIf you do not have your Ultra_value information, please find your value of ultrasonograpy and come back later :)")

}
}
Ultra_value=log(Ultra_value)

###################################### call files #################################
# call the parameter estimates file
# call the percentile calculator file
#source("parameter_estimates_0724.R")
PE=c(1.00E+08,1.00E+08,-104831172.1,52832547.06,-1117646.629,9710.174862,-986.2224919,-22740.22177,30810.69263,5300984.981,1043187.94,90.71708885,-232.1046216,-6.113439813,90.71708885,533.0426195,-0.570223621,-0.069058537,-232.1046216,-0.570223621,0.478146091,-0.001591362,-6.113439813,-0.069058537,-0.001591362,0.000249136,2.43E+09,3.10E+09,3.57E+09,37331415.62,-5176104.585,235496.0824,-3519.758932,5345.554067,-4225.676036,7551.077517,-5176104.585,719113.1796,-32774.93074,490.6145911,-751.0820969,606.2291852,-1087.483294,235496.0824,-32774.93074,1496.223004,-22.42995406,34.60672354,-28.51832122,51.41272781,-3519.758932,490.6145911,-22.42995406,0.33669342,-0.523297205,0.439948057,-0.797879667,5345.554067,-751.0820969,34.60672354,-0.523297205,0.852776564,-0.830920531,1.642089091,-4225.676036,606.2291852,-28.51832122,0.439948057,-0.830920531,1.246450706,-3.414284564,7551.077517,-1087.483294,51.41272781,-0.797879667,1.642089091,-3.414284564,14.12057172,
1.00E+08,2.00E+08,-45321028.17,46904870.36,-940673.9393,8191.222712,-4455.40148,-15136.90373,21622.16068,4812665.195,872067.0296,1874.399257,-174.124097,-6.794793239,1874.399257,502.3529193,0.032034413,-0.08511131,-174.124097,0.032034413,0.413031129,-0.001180691,-6.794793239,-0.08511131,-0.001180691,0.000247237,2421500000,3.09E+09,3.56E+09,32686265.67,-4541702.117,207108.7475,-3103.082675,4704.286973,-3647.482623,6203.077201,-4541702.117,632297.1927,-28883.52011,433.413054,-662.2484929,524.1688115,-894.9974204,207108.7475,-28883.52011,1321.526265,-19.85863685,30.57761525,-24.70380626,42.39593086,-3103.082675,433.413054,-19.85863685,0.298804355,-0.463420784,0.381874436,-0.659332578,4704.286973,-662.2484929,30.57761525,-0.463420784,0.753174645,-0.718173125,1.35104125,-3647.482623,524.1688115,-24.70380626,0.381874436,-0.718173125,1.0487327,-2.719678552,6203.077201,-894.9974204,42.39593086,-0.659332578,1.35104125,-2.719678552,10.50024808,
1.00E+08,3.00E+08,-33556658.67,44797501.17,-836868.7882,6602.770836,-2876.644283,-14630.53979,25638.14201,4739164.833,861052.8146,2189.4129,-168.7752992,-7.111943862,2189.4129,484.8366867,-0.064749515,-0.084252075,-168.7752992,-0.064749515,0.400957009,-0.000859266,-7.111943862,-0.084252075,-0.000859266,0.000256888,2421500000,3.09E+09,3.56E+09,31882574.93,-4429735.345,201991.745,-3026.279967,4587.249979,-3558.498552,6071.978393,-4429735.345,616664.4728,-28167.68253,422.6502224,-645.7006896,511.2800611,-875.8089089,201991.745,-28167.68253,1288.687598,-19.36409576,29.81062737,-24.09203536,41.4750142,-3026.279967,422.6502224,-19.36409576,0.291345805,-0.451758532,0.372358523,-0.644842802,4587.249979,-645.7006896,29.81062737,-0.451758532,0.733956132,-0.699715635,1.319362462,-3558.498552,511.2800611,-24.09203536,0.372358523,-0.699715635,1.020896157,-2.65116028,6071.978393,-875.8089089,41.4750142,-0.644842802,1.319362462,-2.65116028,10.2469788,
1.00E+08,4.00E+08,-42767832.95,46624948.18,-935869.6642,8223.960266,-4926.740737,-15743.2358,26750.04826,4701901.438,846909.8099,2204.179552,-164.6384475,-7.012953825,2204.179552,482.6073892,0.042474051,-0.083766991,-164.6384475,0.042474051,0.397063598,-0.00086551,-7.012953825,-0.083766991,-0.00086551,0.000252982,2421500000,3.09E+09,3.56E+09,31382469.86,-4360256.995,198823.8624,-2978.821883,4515.358048,-3502.92028,5977.757939,-4360256.995,606993.2327,-27725.96121,416.0228339,-635.5822664,503.2951555,-862.2172986,198823.8624,-27725.96121,1268.480382,-19.06048362,29.34352983,-23.71580376,40.83131098,-2978.821883,416.0228339,-19.06048362,0.286778157,-0.444680716,0.366544022,-0.634834022,4515.358048,-635.5822664,29.34352983,-0.444680716,0.722465967,-0.688797859,1.298887027,-3502.92028,503.2951555,-23.71580376,0.366544022,-0.688797859,1.005015554,-2.610100735,5977.757939,-862.2172986,40.83131098,-0.634834022,1.298887027,-2.610100735,10.08883146,
1.00E+08,5.00E+08,99990074.28,37612613.88,-1137934.011,13140.27116,-6944.704847,-13126.89878,11438.78296,2585962.726,272976.7997,-1422.143549,-80.57183691,-0.539409258,-1422.143549,110.9100383,-0.138524017,-0.007279714,-80.57183691,-0.138524017,0.116981589,-0.000555212,-0.539409258,-0.007279714,-0.000555212,4.43E-05,2.43E+09,3.10E+09,3.57E+09,8931752.736,-1237994.25,56307.37604,-841.3473599,1275.692794,-1001.624367,1768.424292,-1237994.25,171935.8066,-7833.907248,117.2353695,-179.1838343,143.6770705,-254.7466792,56307.37604,-7833.907248,357.5200395,-5.358138332,8.253556996,-6.757977622,12.04620619,-841.3473599,117.2353695,-5.358138332,0.080408391,-0.124770356,0.104241046,-0.186980834,1275.692794,-179.1838343,8.253556996,-0.124770356,0.20299601,-0.196680022,0.385101573,-1001.624367,143.6770705,-6.757977622,0.104241046,-0.196680022,0.2939981,-0.800056738,1768.424292,-254.7466792,12.04620619,-0.186980834,0.385101573,-0.800056738,3.290066354,
1.00E+08,6.00E+08,57166129.78,30690132.72,-951940.3449,11697.15268,-16873.9999,14098.24089,-21654.89385,2143978.951,286989.7662,-1139.952347,-99.70132897,-1.603176671,-1139.952347,116.1832168,0.634464491,-0.028068097,-99.70132897,0.634464491,0.105399188,-0.00048411,-1.603176671,-0.028068097,-0.00048411,4.72E-05,2.43E+09,3.10E+09,3.56E+09,6812160.269,-942818.0332,42828.65389,-639.2917731,965.9252891,-765.4361403,1293.229941,-942818.0332,130739.2004,-5948.964938,88.92870037,-135.3973421,109.4836494,-185.5820317,42828.65389,-5948.964938,271.1149413,-4.058425933,6.225419864,-5.136338653,8.744399203,-639.2917731,88.92870037,-4.058425933,0.060828821,-0.093965595,0.079047907,-0.135292031,965.9252891,-135.3973421,6.225419864,-0.093965595,0.151920304,-0.147621417,0.273549213,-765.4361403,109.4836494,-5.136338653,0.079047907,-0.147621417,0.220678956,-0.559085847,1293.229941,-185.5820317,8.744399203,-0.135292031,0.273549213,-0.559085847,2.068382735,
1.00E+08,7.00E+08,-448704043.7,86508264.37,-3156017.032,40894.82195,-40517.94623,5597.88637,-15895.71101,2240533.361,734772.239,-8591.125476,-272.546173,1.87285219,-8591.125476,192.1930952,2.811021777,-0.035243316,-272.546173,2.811021777,0.174604131,-0.001713797,1.87285219,-0.035243316,-0.001713797,3.71E-05,2.44E+09,3.10E+09,3.57E+09,7709224.709,-1061576.256,47983.66956,-712.7090357,1087.976099,-846.6003949,1449.558521,-1061576.256,146469.279,-6631.517845,98.64131524,-151.7337785,120.4199718,-206.9553258,47983.66956,-6631.517845,300.708224,-4.47904442,6.941462641,-5.618147136,9.701784468,-712.7090357,98.64131524,-4.47904442,0.066798237,-0.10425161,0.085990107,-0.149345736,1087.976099,-151.7337785,6.941462641,-0.10425161,0.170407929,-0.161998504,0.306075211,-846.6003949,120.4199718,-5.618147136,0.085990107,-0.161998504,0.232452453,-0.604347148,1449.558521,-206.9553258,9.701784468,-0.149345736,0.306075211,-0.604347148,2.372234158,
1.00E+08,8.00E+08,181214946.6,30678205.32,-908796.146,10478.32739,-12438.07875,8741.318298,-9826.96908,1642937.994,196369.5828,-461.402583,-63.37046165,-1.105933466,-461.402583,53.51293871,0.048529185,-0.006355286,-63.37046165,0.048529185,0.062093815,1.23E-05,-1.105933466,-0.006355286,1.23E-05,2.60E-05,2.43E+09,3.10E+09,3.56E+09,4065891.601,-562643.8283,25555.9695,-381.4351517,576.2947549,-458.191086,784.0547735,-562643.8283,78008.89278,-3549.152067,53.04958281,-80.76039305,65.50488505,-112.4360857,25555.9695,-3549.152067,161.7239694,-2.420634276,3.712431982,-3.071743499,5.294414575,-381.4351517,53.04958281,-2.420634276,0.036276582,-0.056024264,0.047255527,-0.081866018,576.2947549,-80.76039305,3.712431982,-0.056024264,0.090522053,-0.088098974,0.16499255,-458.191086,65.50488505,-3.071743499,0.047255527,-0.088098974,0.131710032,-0.336573407,784.0547735,-112.4360857,5.294414575,-0.081866018,0.16499255,-0.336573407,1.255639031,
1.00E+08,9.00E+08,-445468849.1,87881051.58,-3287694.246,43305.65478,-45358.52584,11928.5673,-34510.74253,2008759.784,480522.9977,-4076.863537,-168.0284335,0.681118142,-4076.863537,113.4403025,1.488070349,-0.017418587,-168.0284335,1.488070349,0.11749098,-0.000962669,0.681118142,-0.017418587,-0.000962669,2.41E-05,2.44E+09,3.10E+09,3.57E+09,5963409.689,-821830.2351,37172.79075,-552.4597649,845.9217293,-663.9197412,1144.060236,-821830.2351,113483.2014,-5141.724941,76.52844718,-118.0937759,94.54523516,-163.5247734,37172.79075,-5141.724941,233.3264762,-3.477629223,5.407378136,-4.41570681,7.674071304,-552.4597649,76.52844718,-3.477629223,0.051898174,-0.081275879,0.067651039,-0.118249011,845.9217293,-118.0937759,5.407378136,-0.081275879,0.133420297,-0.128175231,0.243902901,-663.9197412,94.54523516,-4.41570681,0.067651039,-0.128175231,0.185979796,-0.487138549,1144.060236,-163.5247734,7.674071304,-0.118249011,0.243902901,-0.487138549,1.928103826,
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2.00E+08,1.00E+08,-126692711.4,57470328.84,-1389266.721,14243.68083,-7430.290173,-22501.93838,61897.64163,5951807.886,734754.0877,1588.830664,-100.0805535,-6.076868379,1588.830664,817.8305409,-0.643550723,-0.211560704,-100.0805535,-0.643550723,0.557658741,-0.005599274,-6.076868379,-0.211560704,-0.005599274,0.000360433,2.41E+09,3.06E+09,3539500000,49876616.73,-7003097.043,322307.0132,-4868.722695,7584.685276,-5868.15727,9255.632813,-7003097.043,985227.5098,-45423.42389,687.2239854,-1079.381487,852.3620404,-1352.023887,322307.0132,-45423.42389,2097.680855,-31.78338607,50.32526081,-40.56735958,64.78151084,-4868.722695,687.2239854,-31.78338607,0.482221262,-0.769412633,0.632756624,-1.018196266,7584.685276,-1079.381487,50.32526081,-0.769412633,1.292064723,-1.235912315,2.198487193,-5868.15727,852.3620404,-40.56735958,0.632756624,-1.235912315,1.784251751,-4.403493837,9255.632813,-1352.023887,64.78151084,-1.018196266,2.198487193,-4.403493837,16.26463643,
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3.00E+08,8.00E+08,112105296.4,39854020.08,-1312206.419,16300.58209,-19731.59054,10141.81428,-11253.68896,1960323.873,238951.8409,-498.9235984,-75.35540216,-1.264189807,-498.9235984,70.61198599,-0.209135509,-0.011016069,-75.35540216,-0.209135509,0.078648185,-0.000144267,-1.264189807,-0.011016069,-0.000144267,3.38E-05,2.43E+09,3.07E+09,3.56E+09,5947889.86,-821731.1113,37276.19073,-555.8413711,841.6085754,-603.685563,932.5968402,-821731.1113,113749.7415,-5168.939542,77.19300085,-117.8284627,86.34152212,-134.0822688,37276.19073,-5168.939542,235.2609134,-3.51845012,5.413303403,-4.051951392,6.333221545,-555.8413711,77.19300085,-3.51845012,0.052689282,-0.08167265,0.062398702,-0.098262301,841.6085754,-117.8284627,5.413303403,-0.08167265,0.133019295,-0.118323391,0.206124951,-603.685563,86.34152212,-4.051951392,0.062398702,-0.118323391,0.161167936,-0.397949406,932.5968402,-134.0822688,6.333221545,-0.098262301,0.206124951,-0.397949406,1.566925308,
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)
PE= matrix(PE,nrow=40,byrow = T)
index= (Race-1)*10+Ultra;
info= PE[index,]/1e8
fcoef=info[3:9]; sigma=info[10];Sigmab= matrix(info[11:26],4,4);Zeta=info[27:29];varfixed= matrix(info[30:78],7,7)

 

################# Velocity calculator

i = GA[1]
j = GA[2]

int <- 1
t1 <- i
t2 <- i**2
t3 <- i**3
tt1 <- (i - Zeta[1])**3 * (i > Zeta[1])
tt2 <- (i - Zeta[2])**3 * (i > Zeta[2])
tt3 <- (i - Zeta[3])**3 * (i > Zeta[3])

Fxxi = cbind(int, t1, t2, t3, tt1, tt2, tt3)
Rxxi = cbind(int, t1, t2, t3)

int <- 1
t1 <- j
t2 <- j**2
t3 <- j**3
tt1 <- (j - Zeta[1])**3 * (j > Zeta[1])
tt2 <- (j - Zeta[2])**3 * (j > Zeta[2])
tt3 <- (j - Zeta[3])**3 * (j > Zeta[3])

Fxxj = cbind(int, t1, t2, t3, tt1, tt2, tt3)
Rxxj = cbind(int, t1, t2, t3)

dFxx = Fxxj - Fxxi
dRxx = Rxxj - Rxxi

mean <- dFxx%*%fcoef
var <- 2*sigma**2 + dRxx%*%Sigmab%*%t(dRxx) + dFxx%*%varfixed%*%t(dFxx)
std <- sqrt(var)

percentile = pnorm(Ultra_value[2]-Ultra_value[1], mean = mean, sd = std, lower.tail = TRUE, log.p = FALSE)
# please compute percentile instead of median

###################################### Ourputs #####################################
options(digits=3)
cat("percentile is ", 100*percentile,"% ", "(",race_index[Race],", ",ultra_index[Ultra],":",
exp(Ultra_value)[1]," ",exp(Ultra_value)[2],", ","GA:",GA[1]," ",GA[2],")",sep="")

 

###################################### Run Function #################################
#setwd("C:/Fetal Calculator")
#source("FetalGrowth_Calculator_velocity_0730.R")
#if you wan to quit the program, type in any character inputs twice

Back to Calculating percentiles for distance and velocity based on the NICHD Fetal Growth Standard

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