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library(lme4) | |
load("areaRep26_glmer.Rdata") | |
n <- nrow(areaRep26_glmer) | |
nsp <- length(unique(areaRep26_glmer$especie)) | |
## experimental design: each species appears in exactly 1 'sistema' | |
## each species appears once in each 'tempo' | |
with(areaRep26_glmer,table(especie,sistema)) | |
with(areaRep26_glmer,table(especie,tempo)) | |
summary(areaRep26_glmer) |
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simulate.formula <- function(object, nsim=1, seed=NULL, ...) { | |
## utility fun for generating new class | |
cfun <- function(cc) { | |
c(paste0("formula_lhs_", cc), "formula_lhs", class(object)) | |
} | |
if(length(object)==3) { ## two-sided formula | |
lhs <- object[[2L]] | |
.Basis <- try(eval(lhs, envir=environment(object), |
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EVCounts <- structure(list(name = c("ANUBIS", "ANUBIS", "ANUBIS", "ANUBIS", | |
"ANUBIS", "ANUBIS", "ANUBIS", "ANUBIS", "ANUBIS", "ANUBIS", "ANUBIS", | |
"ANUBIS", "ASHERA", "ASHERA", "ASHERA", "ASHERA", "ATHENA", "ATHENA", | |
"ATHENA", "ATHENA", "ATHENA", "ATHENA", "ATHENA", "ATUTAHI", | |
"ATUTAHI", "ATUTAHI", "BASTET", "BASTET", "BASTET", "BASTET", | |
"BASTET", "BASTET", "BAUBO", "BAUBO", "BAUBO", "BAUBO", "BRAN", | |
"BRAN", "BRAN", "BRAN", "BRAN", "CHAC", "CHAC", "CHAC", "CHAC", | |
"CHAC", "CHAC", "CHAC", "COEUS", "COEUS", "COEUS", "COEUS", "COEUS", | |
"DIONYSUS", "DIONYSUS", "DIONYSUS", "DIONYSUS", "DON", "DON", | |
"DON", "DON", "DON", "ERIS", "ERIS", "ERIS", "ERIS", "ERIS", |
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percentile | year | inc1 | inc2 | |
---|---|---|---|---|
p20p80 | 1980 | 31718.0283 | 29193.2179 | |
p20p80 | 1981 | 31735.9894 | 29279.6271 | |
p20p80 | 1982 | 30590.3481 | 28139.5886 | |
p20p80 | 1983 | 30775.1342 | 28381.5553 | |
p20p80 | 1984 | 32216.2634 | 29989.8252 | |
p20p80 | 1985 | 32851.6509 | 30679.849 | |
p20p80 | 1986 | 33408.1257 | 31126.8753 | |
p20p80 | 1987 | 34021.8476 | 31658.5276 | |
p20p80 | 1988 | 34504.1039 | 32200.9287 |
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## https://cran.r-project.org/web/packages/gnorm/vignettes/gnormUse.html | |
library(gnorm) | |
#' @param lwr lower (loose) bound | |
#' @param upr upper (loose) bound | |
#' @param tail_prob prob outside {lwr, upr} | |
#' @param ctr_prob probability of being in the middle 50\% of {lwr, upr} | |
get_gnorm <- function(lwr=-1, upr=1, tail_prob=2*pnorm(lwr), | |
ctr_prob=abs(diff(pnorm(c(-1,1)*lwr/2)))) { | |
## default tail_prob/ctr_prob assume lwr/upr symmetric around 0 ... | |
## start from Gaussian |
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library(readxl) | |
my_sum <- function(f) { | |
C <- contr.sum(length(levels(f))) | |
colnames(C) <- paste0(".sum_",levels(f)[-length(levels(f))]) | |
return(C) | |
} | |
dd <- read_excel("Truncated.compois.problem.xlsx") | |
dd$pop <- as.factor(dd$pop) |
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```{r} | |
dd <- read_excel("Truncated.compois.problem.xlsx") | |
dd <- transform(dd, pop = factor(pop), morph = factor(morph)) | |
m0 <- glmmTMB(mates ~ pop*morph, | |
family='truncated_compois', data=dd) | |
m1 <- update(m0, contrasts = list(pop = my_sum(dd$pop), morph = my_sum(dd$morph))) | |
tt <- purrr::map_dfr(list(treatment=m0,sum=m1), | |
tidy, effects = "fixed", .id = "contrasts", conf.int = TRUE) %>% | |
filter(term != "(Intercept)") %>% |
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##https://www.dataquest.io/blog/r-api-tutorial/ | |
## https://tonyelhabr.rbind.io/post/nested-json-to-tidy-data-frame-r/ | |
## https://api.covid19tracker.ca/docs/1.0/vaccine-age-groups | |
library(httr) | |
library(jsonlite) | |
library(tibble) | |
library(purrr) | |
library(ggplot2) | |
library(dplyr) | |
library(nlme) |
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library(tidyverse) | |
library(dotwhisker) | |
library(broom.mixed) | |
data <- read_csv("https://raw.githubusercontent.com/mgree013/Rethinking_Biodiversity_Streams/main/data.csv", | |
col_types = cols()) | |
## add centred/scaled vars | |
## might not help but can't hurt | |
data_s <- mutate(data, |
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library(lme4) | |
library(nlme) | |
set.seed(101) | |
## want to sample a *mostly* balanced design? | |
np <- nrow(Penicillin) | |
pu <- Penicillin[sample(np, size=round(np/2)),] | |
pu$dummy <- 1 | |
## WILL NOT WORK without a "grouped data" structure | |
## set up a dummy grouping variable for the top level (necessary) |