Open sgoodreau opened 4 years ago
@sgoodreau @EmilyPo
I didn't have time to insert this into the document in a good place, but here's a start to the table - code below (and it's easy to change the rounding).
Two questions:
Code - I put it in the code chunk starting at 309
# Distances
distances <- rbind( geo.sep(net.precov, 'Pre-Covid'),
geo.sep(emptynet, 'Pure Isolation'),
geo.sep(net.essl, 'Essential Only'),
geo.sep(net.comb.1, 'Just One Friend'),
geo.sep(net.comb.2, 'Just One Friend Per HH'))
# Labels
net.order <- c('Pre-Covid', 'Pure Isolation',
'Essential Only', 'Just One Friend',
'Just One Friend Per HH')
rownames(distances) <-net.order
# Function to add percentages
add_percent <- function(x, r1, r2, n=200) {
xround <- round(x, r1)
percround <- round(100*x/n, r2)
return(paste0(xround, " (", percround, "%)"))
}
# Vector of largest components, in net.order order
largest.components <- c(largcomp.precov,
1,
largcomp.essl,
largcomp.comb.1,
largcomp.comb.2)
# Summary table
summary.table <- data.frame(Network=net.order,
`Largest Cluster`=
add_percent(largest.components,
r1=0, r2=1, n=200),
`vs Essential Network`=
round(largest.components/largcomp.essl, 1),
`3 Degrees of Separation`=
add_percent(distances[,1],
r1=1, r2=2, n=200),
`6 Degrees of Separation`=
add_percent(distances[,2],
r1=1, r2=2, n=200),
check.names=FALSE,
row.names=NULL)
Note: I used the kableExtra option "responsive" because "Tables with option responsive looks the same with others on a large screen. However, on a small screen like phone, they are horizontally scrollable. Please resize your window to see the result."
library(kableExtra)
knitr::kable(summary.table) %>%
kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"))
Note, if you run the code on the inverted table t(summary.table)
, it looks something like this:
@sgoodreau @EmilyPo I see that the 71% statistic is in the published version and also in SocDistNets.html. The weird thing is, when I knit SocDistNets.Rmd, this is what I see:
Is this happening to anyone else? If not, I won't worry about it! It's just weird - it's a fresh knit from a fresh clone - no cache. Is something changing the seed? It's kind of a big difference for just that.
That is odd…I’m getting that too when I re-knit. For it to be up online at 71% the change had to have happened when I was monkeying with the yaml (trying to get the google analytics tag in the html header without directly editing the html) - but I thought I only committed the html file that contains the google analytics tag in case we needed it again.
But I didn’t touch anything other part of the code??
On Apr 14, 2020, at 4:33 PM, JKB notifications@github.com wrote:
@sgoodreau https://github.com/sgoodreau @EmilyPo https://github.com/EmilyPo I see that the 71% statistic is in the published version and also in SocDistNets.html. The weird thing is, when I knit SocDistNets.Rmd, this is what I see:
https://user-images.githubusercontent.com/4825649/79283694-718fb580-7e6d-11ea-9c05-1900854e6340.png Is this happening to anyone else? If not, I won't worry about it! It's just weird - it's a fresh knit from a fresh clone - no cache. Is something changing the seed? It's kind of a big difference for just that.
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/statnet/COVID-JustOneFriend/issues/10#issuecomment-613731978, or unsubscribe https://github.com/notifications/unsubscribe-auth/AD6YCJGESIWFWATLPIDXDZ3RMTXFTANCNFSM4MGU62LA.
I actually think the change starts in the essential network.
What i’ve got locally:
What’s on the web:
Tried to go back and see the different commit versions, but couldn't find a difference in the rmd files other than the author list change Steve made earlier today...
On Apr 14, 2020, at 4:44 PM, Emily D Pollock emilypo@uw.edu wrote:
That is odd…I’m getting that too when I re-knit. For it to be up online at 71% the change had to have happened when I was monkeying with the yaml (trying to get the google analytics tag in the html header without directly editing the html) - but I thought I only committed the html file that contains the google analytics tag in case we needed it again.
But I didn’t touch anything other part of the code??
On Apr 14, 2020, at 4:33 PM, JKB <notifications@github.com mailto:notifications@github.com> wrote:
@sgoodreau https://github.com/sgoodreau @EmilyPo https://github.com/EmilyPo I see that the 71% statistic is in the published version and also in SocDistNets.html. The weird thing is, when I knit SocDistNets.Rmd, this is what I see:
https://user-images.githubusercontent.com/4825649/79283694-718fb580-7e6d-11ea-9c05-1900854e6340.png Is this happening to anyone else? If not, I won't worry about it! It's just weird - it's a fresh knit from a fresh clone - no cache. Is something changing the seed? It's kind of a big difference for just that.
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/statnet/COVID-JustOneFriend/issues/10#issuecomment-613731978, or unsubscribe https://github.com/notifications/unsubscribe-auth/AD6YCJGESIWFWATLPIDXDZ3RMTXFTANCNFSM4MGU62LA.
My guess is that the same seed produces different results on different systems. We do need to be careful about changing the numbers so much with each change, so perhaps it's best for me to be the only one who renders the final html from now on? Not super efficient, but if it leads to consistent numbers it seems worth it.
On 4/14/2020 4:56 PM, Emily Pollock wrote:
I actually think the change starts in the essential network.
What i’ve got locally:
What’s on the web:
On Apr 14, 2020, at 4:44 PM, Emily D Pollock emilypo@uw.edu wrote:
That is odd…I’m getting that too when I re-knit. For it to be up online at 71% the change had to have happened when I was monkeying with the yaml (trying to get the google analytics tag in the html header without directly editing the html) - but I thought I only committed the html file that contains the google analytics tag in case we needed it again.
But I didn’t touch anything other part of the code??
On Apr 14, 2020, at 4:33 PM, JKB <notifications@github.com mailto:notifications@github.com> wrote:
@sgoodreau https://github.com/sgoodreau @EmilyPo https://github.com/EmilyPo I see that the 71% statistic is in the published version and also in SocDistNets.html. The weird thing is, when I knit SocDistNets.Rmd, this is what I see:
https://user-images.githubusercontent.com/4825649/79283694-718fb580-7e6d-11ea-9c05-1900854e6340.png Is this happening to anyone else? If not, I won't worry about it! It's just weird - it's a fresh knit from a fresh clone - no cache. Is something changing the seed? It's kind of a big difference for just that.
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/statnet/COVID-JustOneFriend/issues/10#issuecomment-613731978, or unsubscribe https://github.com/notifications/unsubscribe-auth/AD6YCJGESIWFWATLPIDXDZ3RMTXFTANCNFSM4MGU62LA.
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/statnet/COVID-JustOneFriend/issues/10#issuecomment-613738360, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB66LAQPBBPWPW3RICUWQ5DRMTZ3DANCNFSM4MGU62LA.
--
Steven M. Goodreau / Professor / Dept. of Anthropology Physical address: Denny Hall M236 Mailing address: Campus Box 353100 / 4216 Memorial Way NE Univ. of Washington / Seattle WA 98195 1-206-685-3870 (phone) /1-206-543-3285 (fax) http://faculty.washington.edu/goodreau
And we will need to exploit the stochastic capacity we have to generate distributions :)
I’ll definitely leave the rendering to you, Steve, but I am surprised that setting the seed isn’t sufficient. I will poke around tomorrow, maybe explore seed sensitivity to get an interval for the stats.
seed setting is complicated in R. if you add any code in between, it changes the sequence, and subsequent calculations can change. i think the sol'n is to run the distributions, so we can justify our numbers...
Moving the discussion re: simulation uncertainty to #14
Needs to be in a tab though so only seen by the "What's Going On?" crowd, or else somehow very carefully worded to make sense to the others.