Marc Jacobs MJacobs1985
MJacobs1985
/ m_dnorm
Created
December 3, 2021 11:27
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| par(mfrow = c(2, 2)) | |
| Book<- read_excel("X:/StatisticsPlatform/Website/ELearning/Workshops/Bayesian Analysis/Data/Book1.xlsx") | |
| d<-Book%>%dplyr::select(ADF,ADG,BW_start) | |
| d<-d[complete.cases(d), ] | |
| summary(d$ADG) | |
| summary(d$ADF) | |
| cov(d$ADG, d$ADF) | |
| pairs(d) | |
| m_dnorm <- ulam( | |
| alist( |
MJacobs1985
/ PSIS
Created
December 3, 2021 11:17
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| rethinking::compare( m11.5 , m11.6 , func=PSIS ) | |
| k <- PSIS( m11.6 , pointwise=TRUE )$k | |
| xyplot(as.factor(bl)~ADG | Country, data=d, | |
| xlab="log ADG" , | |
| ylab="total blocks" , | |
| col=rangi2 , lwd=2 , | |
| ylim=c(0,75) , cex=1+normalize(k) ) |
MJacobs1985
/ m11.5 _ m11.6
Last active
December 3, 2021 11:18
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Book<- read_excel("X:/StatisticsPlatform/Website/ELearning/Workshops/Bayesian Analysis/Data/Book1.xlsx") | |
| d<-Book%>%dplyr::select(block,ADG,BW_start,Country) | |
| d$bl<-d$block | |
| table(d$Country, d$bl) | |
| d$block<-NULL | |
| d<-d[complete.cases(d), ] | |
| d$Country<-as.factor(d$Country) | |
| dim(d) | |
| head(d) | |
| fit<-glm(bl~ ADG + BW_start + Country, |
MJacobs1985
/ m11.4
Created
December 2, 2021 21:46
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| m11.4 <- ulam( | |
| alist( | |
| Included2017 ~ dbinom( 1 , p ) , | |
| logit(p) <- a + b*ADG +c*BW_start + d[Country] , | |
| a ~ dnorm( 2 , 1 ), | |
| b ~ dnorm( 0.5 , 1 ), | |
| c ~ dnorm( 0.5 , 1 ), | |
| d[Country] ~ dnorm( 3 , 1 ) | |
| ) , data=d, chains=4, cores=4) | |
| show(m11.4) |
MJacobs1985
/ m11.3
Last active
December 2, 2021 21:46
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| d<-Book%>%dplyr::select(Included2017,ADG,BW_start,Country) | |
| table(d$Country, d$Included2017) | |
| d$Included2017<-as.factor(d$Included2017) | |
| levels(d$Included2017)<-list("1"="Yes", "0"="No") | |
| fit<-glm(Included2017~ ADG + BW_start + Country, | |
| data=d, | |
| family="binomial",x=TRUE, y=TRUE) | |
| summary(fit) | |
| d$Included2017<-as.numeric(d$Included2017)-1 | |
| d<-d[complete.cases(d), ] |
MJacobs1985
/ m11.2
Created
December 2, 2021 21:31
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| d<-Book%>%dplyr::select(Included2017, ADG,ADF,BW_start) | |
| d<-d[complete.cases(d), ] | |
| d$Included2017<-as.factor(d$Included2017) | |
| levels(d$Included2017)<-list("1"="Yes", "0"="No") | |
| fit<-glm(Included2017~ADF*ADG + BW_start, | |
| data=d, | |
| family="binomial",x=TRUE, y=TRUE) | |
| d$Included2017<-as.numeric(d$Included2017-1) | |
| m11.2 <- quap( |
MJacobs1985
/ m8.6
Created
December 2, 2021 14:48
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| m8.6 <- ulam( | |
| alist( | |
| ADG ~ dnorm( mu , sigma ) , | |
| mu <- a + b*ADF + c*BW_start + d*ADF*BW_start , | |
| a ~ dnorm( 0.5 , 0.25 ) , | |
| b ~ dnorm( 0 , 0.25 ) , | |
| c ~ dnorm( 0 , 0.25 ) , | |
| d ~ dnorm( 0 , 0.25 ) , | |
| sigma ~ dexp( 1 ) | |
| ) , data=d, chains=4, cores=4) |
MJacobs1985
/ m8.5
Created
December 2, 2021 14:17
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| d<-Book%>%dplyr::select(ADG,ADF,BW_start) | |
| d<-d[complete.cases(d), ] | |
| fit<-lm(ADG~ADF*BW_start, data=d) | |
| m8.5 <- quap( | |
| alist( | |
| ADG ~ dnorm( mu , sigma ) , | |
| mu <- a + b*ADF + c*BW_start + d*ADF*BW_start , | |
| a ~ dnorm( 0.5 , 0.25 ) , | |
| b ~ dnorm( 0 , 0.25 ) , | |
| c ~ dnorm( 0 , 0.25 ) , |
MJacobs1985
/ m5.9 _ m5.10
Last active
December 2, 2021 13:07
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| d<-Book%>%dplyr::select(ADG,ADF,Country, Challenge) | |
| d$Country<-as.factor(d$Country);levels(d$Country) | |
| d$Challenge<-as.factor(d$Challenge);levels(d$Challenge) | |
| d$Country_id <- as.integer(d$Country ) | |
| d$Challenge_id <- as.integer(d$Challenge ) | |
| m5.9 <- quap( | |
| alist( | |
| ADG ~ dnorm( mu , sigma ), | |
| mu <- a[Country_id], | |
| a[Country_id] ~ dnorm(0 , 0.5 ), |
MJacobs1985
/ m5.3B
Created
December 2, 2021 13:01
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| m5.3_B <- quap( | |
| alist( | |
| ADG ~ dnorm(mu , sigma ) , | |
| mu <- a + b*ADF + bB*B + bI*I + bS*S + bUK*UK, | |
| a ~ dnorm (-2, 3 ) , | |
| b ~ dnorm (1 , 2 ) , | |
| bB ~ dnorm (0 , 2 ) , | |
| bI ~ dnorm (-10 , 3 ) , | |
| bS ~ dnorm (4 , 2 ) , | |
| bUK ~ dnorm (-1 , 2 ) , |