#' from https://stackoverflow.com/questions/18509527/first-letter-to-upper-case
#' @export
firstup <- function(x) {
substr(x, 1, 1) <- toupper(substr(x, 1, 1))
x
}
#' Successively print population matrices for inclusion in an appendix
#'
#' @param data.list
#' @param parent.method
#' @param years
#' @param first.year
#'
#' @export
printPopulationMatrices <- function(data.list, parent.method, years, first.year, second.year) {
for (i in 1:length(data.list)) {
dat <- eval(parse(text=data.list[i]))
cat("\\subsection{", dat$N.Stages.wo.break, "}", sep="")
for (j in 1:length(parent.methods)){
cat("\\subsubsection{Parent assignment method: ", parent.methods[j], "}", sep="")
cat('\n')
# PLANTS WITH FRUIT
temp <- xtable(
dat[[1]][[j]]$trans01 %>% filter(Repro > 0),
digits=0,
caption=paste(
"Plants that produced fruit in fecundity-year ",
first.year,
".",
sep=""
)
)
names(temp) <- c(
"PlantID",
paste("Stage,",first.year),
paste("Reproduction,",first.year),
paste("Stage,",second.year),
paste("Reproduction,",second.year)
)
print(
temp,
include.rownames=F, caption.placement = "top"
)
# CLONE TRANSITION COUNTS
print(
xtable(
dat[[1]][[j]]$clone_transition_counts,
digits=0,
caption=c(
paste(
"Clone production counts (",
years,
" data) using the \`\`",
parent.methods[j],
"\'\' parent assignment method. Columns represent the stages parent plants were in during fecundity-year $z$ and the rows represent the stages of clonal offspring produced in fecundity-year $z+1$.",
sep=""
),
paste(
"Clone production counts (",
years,
" data) using the \`\`",
parent.methods[j],
"\'\' parent assignment method.",
sep=""
)
)
),
caption.placement = "top"
)
# GROWTH, STATIS, RETROGRESSION, SURVIVAL
print(
xtable(
dat[[1]][[j]]$transition.counts,
digits=0,
caption=c(
paste(
"Growth, stasis, retrogression, and survival counts (",
years,
" data) using the \`\`",
parent.methods[j],
"\'\' parent assignment method. Columns represent the stages plants were in during fecundity-year $z$ and the rows represent the stages the plants transitioned to in fecundity-year $z+1$.",
sep=""
),
paste(
"Growth, stasis, retrogression, and survival counts (",
years,
" data) using the \`\`",
parent.methods[j],
"\'\' parent assignment method.",
sep=""
)
)
),
caption.placement = "top"
)
# NUMBER OF INDIVIDUALS PER STAGE
print(
xtable(
dat[[1]][[j]]$n_per_stage %>% filter(stage!="Seed"),
digits=0,
caption=paste(
"Number of individuals per stage in ",
first.year,
" using the \`\`",
parent.methods[j],
"\'\' parent assignment method.",
sep=""
)
),
include.rownames=F, caption.placement = "top"
)
cat("\\clearpage")
}
}
}
#' Successively print LTRE population matrices for inclusion in an appendix
#'
#' @param data.list
#' @param parent.method
#' @param years
#' @param first.year
#' @param LTRE_variable
#'
#' @importFrom tools toTitleCase
#' @export
printLTREPopulationMatrices <- function(data.list, parent.method, years, first.year, second.year, LTRE_variable, LTRE_variable_section_heading) {
for (i in 1:length(data.list)) {
dat <- eval(parse(text=data.list[i]))
cat("\\subsubsection{", LTRE_variable_section_heading, "}", sep="")
for (j in 1:length(parent.methods)){
cat('\n')
# PLANTS WITH FRUIT
if (
(
dat[[4]][[j]]$trans01 %>%
filter(Repro > 0) %$%
dim(.)[1]
) > 0
) {
temp <- xtable(
dat[[4]][[j]]$trans01 %>% filter(Repro > 0),
digits=0,
caption=paste(
"Plants ",
LTRE_variable,
" during the study that produced fruit in fecundity-year ",
first.year,
".",
sep=""
)
)
names(temp) <- c(
"PlantID",
paste("Stage,",first.year),
paste("Reproduction,",first.year),
paste("Stage,",second.year),
paste("Reproduction,",second.year)
)
print(
temp,
include.rownames=F, caption.placement = "top"
)
}
# CLONE TRANSITION COUNTS
print(
xtable(
dat[[4]][[j]]$clone_transition_counts,
digits=0,
caption=c(
paste(
"Clone production counts using the \`\`",
parent.methods[j],
"\'\' parent assignment method for the ",
years,
" data for plants ",
LTRE_variable,
" during the study. Columns represent the stages parent plants were in during fecundity-year $z$ and the rows represent the stages of clonal offspring produced in fecundity-year $z+1$.",
sep=""
),
paste(
"Clone production counts using the \`\`",
parent.methods[j],
"\'\' parent assignment method for the ",
years,
" data for plants ",
LTRE_variable,
" at some point during the study.",
sep=""
)
)
),
caption.placement = "top"
)
# GROWTH, STATIS, RETROGRESSION, SURVIVAL
print(
xtable(
dat[[4]][[j]]$transition.counts,
digits=0,
caption=c(
paste(
"Growth, stasis, retrogression, and survival counts using the \`\`",
parent.methods[j],
"\'\' parent assignment method for the ",
years,
" data for plants ",
LTRE_variable,
" during the study. Columns represent the stages plants were in during fecundity-year $z$ and the rows represent the stages the plants transitioned to in fecundity-year $z+1$.",
sep=""
),
paste(
"Growth, stasis, retrogression, and survival counts using the \`\`",
parent.methods[j],
"\'\' parent assignment method for the ",
years,
" data for plants ",
LTRE_variable,
" at some point during the study.",
sep=""
)
)
),
caption.placement = "top"
)
# NUMBER OF INDIVIDUALS PER STAGE
print(
xtable(
dat[[4]][[j]]$n_per_stage %>% filter(stage!="Seed"),
digits=0,
caption=paste(
"Number of individuals per stage in ",
first.year,
" for plants ",
LTRE_variable,
" at some point during the study, using the \`\`",
parent.methods[j],
"\'\' parent assignment method.",
sep=""
)
),
include.rownames=F, caption.placement = "top"
)
cat("\\clearpage")
}
}
}
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