## test data directory
testdata <- system.file("testdata", package = "breedR")
load_res <- function(key, dir = testdata) {
fn <- paste0("res_", key, ".rds")
readRDS(file.path(dir, fn))
}
## Generate sample REML output files
## 10-variate model.
## large residual covariance matrix (10x10) which wraps lines
if (!file.exists(tf <- file.path(testdata, "airemlf90_log_4.txt"))) {
tdat <- data.frame(replicate(n = 10, rnorm(1e2)))
res <- remlf90(
cbind(X1, X2, X3, X4, X5, X6, X7, X8, X9, X10) ~ 1,
data = tdat,
method = "ai"
)
writeLines(res$reml$output, tf)
}
## Generate fitted multi-trait model
if (!file.exists(tf <- file.path(testdata, "res_mt.rds"))) {
dat <-
droplevels(
douglas[douglas$site == "s3",
names(douglas)[!grepl("H0[^4]|AN|BR|site",
names(douglas))]]
)
res_mt <-
remlf90(
fixed = cbind(H04, C13) ~ orig,
random = ~ block,
genetic = list(
model = 'add_animal',
pedigree = dat[, 1:3],
id = 'self'),
data = dat
)
saveRDS(res_mt, file = file.path(testdata, "res_mt.rds"))
}
## Generate fitted multitrait-competition model
if (!file.exists(tf <- file.path(testdata, "res_mtcp.rds"))) {
dat <-
droplevels(
douglas[douglas$site == "s3",
names(douglas)[!grepl("H0[^4]|AN|BR|site",
names(douglas))]]
)
res_mtcp <-
remlf90(
fixed = cbind(H04, C13) ~ orig,
genetic = list(
model = 'competition',
pedigree = dat[, 1:3],
id = 'self',
coord = dat[, c("x", "y")],
pec = FALSE
),
data = dat,
method = "em"
)
saveRDS(res_mtcp, file = file.path(testdata, "res_mtcp.rds"))
}
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