pyrola: Demographic Dataset of _Pyrola japonica_ and _Pyrola...
In lefko3: Historical and Ahistorical Population Projection Matrix Analysis
pyrola R Documentation
Demographic Dataset of Pyrola japonica and Pyrola subaphylla
Populations, in Horizontal Format
Description
A dataset containing the states and fates of Pyrola japonica and
Pyrola subaphylla, family Ericaceae, from populations in the vicinity
of Mt. Bandai, Fukushima Prefecture, Japan, resulting from monitoring that
occurred annually between 2015 and 2020.
Usage
data(pyrola)
Format
A data frame with 454 individuals and 57 variables. Each row
corresponds to an unique individual, and each variable from
sprouted.2015 on refers to the state of the individual in a particular
year.
- species
String denoting which of the two species the individual
belongs to.
- population
Integer denoting whcih population the individual belongs
to. Synonymous with species in this dataset.
- id
A numeric variable giving a unique number to each
individual within each species. Note that numbers are reused among the two
species.
- sprouted.2015
A binomial indicating whether the individual had
living aboveground tissue observable in the 2015 census.
- lvs.num.2015
Number of leaves in 2015.
- lvs.lng.2015
Length of largest leaf in 2015.
- lvs.wdt.2015
Width of largest leaf in 2015.
- inf.num.2015
Number of inflorescences in 2015.
- inf.lng.tot.2015
Summed inflorescence length in 2015.
- flo.tot.2015
Number of flowers in 2015.
- frt.tot.2015
Number of fruits in 2015.
- sprouted.2016
A binomial indicating whether the individual had
living aboveground tissue observable in the 2016 census.
- lvs.num.2016
Number of leaves in 2016.
- lvs.lng.2016
Length of largest leaf in 2016.
- lvs.wdt.2016
Width of largest leaf in 2016.
- inf.num.2016
Number of inflorescences in 2016.
- inf.lng.tot.2016
Summed inflorescence length in 2016.
- flo.tot.2016
Number of flowers in 2016.
- frt.tot.2016
Number of fruits in 2016.
- sprouted.2017
A binomial indicating whether the individual had
living aboveground tissue observable in the 2017 census.
- lvs.num.2017
Number of leaves in 2017.
- lvs.lng.2017
Length of largest leaf in 2017.
- lvs.wdt.2017
Width of largest leaf in 2017.
- inf.num.2017
Number of inflorescences in 2017.
- inf.lng.tot.2017
Summed inflorescence length in 2017.
- flo.tot.2017
Number of flowers in 2017.
- frt.tot.2017
Number of fruits in 2017.
- sprouted.2018
A binomial indicating whether the individual had
living aboveground tissue observable in the 2018 census.
- lvs.num.2018
Number of leaves in 2018.
- lvs.lng.2018
Length of largest leaf in 2018.
- lvs.wdt.2018
Width of largest leaf in 2018.
- inf.num.2018
Number of inflorescences in 2018.
- inf.lng.tot.2018
Summed inflorescence length in 2018.
- flo.tot.2018
Number of flowers in 2018.
- frt.tot.2018
Number of fruits in 2018.
- sprouted.2019
A binomial indicating whether the individual had
living aboveground tissue observable in the 2019 census.
- lvs.num.2019
Number of leaves in 2019.
- lvs.lng.2019
Length of largest leaf in 2019.
- lvs.wdt.2019
Width of largest leaf in 2019.
- inf.num.2019
Number of inflorescences in 2019.
- inf.lng.tot.2019
Summed inflorescence length in 2019.
- flo.tot.2019
Number of flowers in 2019.
- frt.tot.2019
Number of fruits in 2019.
- sprouted.2020
A binomial indicating whether the individual had
living aboveground tissue observable in the 2020 census.
- lvs.num.2020
Number of leaves in 2020.
- lvs.lng.2020
Length of largest leaf in 2020.
- lvs.wdt.2020
Width of largest leaf in 2020.
- inf.num.2020
Number of inflorescences in 2020.
- inf.lng.tot.2020
Summed inflorescence length in 2020.
- flo.tot.2020
Number of flowers in 2020.
- frt.tot.2020
Number of fruits in 2020.
Source
Shefferson, R.P., K. Shutoh, and K. Suetsugu. In review.
Vegetative dormancy and the evolution of mycoheterotrophy in sister
Pyrola species. Journal of Ecology.
Examples
data(pyrola)
pyrola$species <- as.factor(pyrola$species)
pyrola$population <- as.factor(pyrola$population)
jreg <- pyrola[which(pyrola$population == 1),]
stagevec_jp <- c("P1", "Sdl", "Dorm", "V0nr", "V1nr", "V2nr", "V3nr", "V4nr",
"V0r", "V1r", "V2r", "V3r", "V4r")
sizeavec_jp <- c(0, 0, 0, 0, 1, 2, 3, 7, 0, 1, 2, 3, 7)
sizeahbin_jp <- c(0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 3.5, 0.5, 0.5, 0.5, 0.5,
3.5)
repvec_jp <- c(0, 0, 0, 0, rep(0, 4), rep(1, 5))
propvec_jp <- c(1, rep(0, 12))
immvec_jp <- c(1, 1, rep(0, 11))
matvec_jp <- c(0, 0, rep(1, 11))
obsvec_jp <- c(0, 0, 0, rep(1, 10))
indata_jp <- c(0, 0, rep(1, 11))
comments_jp <- c("protocorm", "seedling", "dormant adult", "stump", "1lf nr",
"2lf nr", "3lf nr", "4+lf nr", "0lf r", "1lf r", "2lf r", "3lf r",
"4+lf r")
jp_frame <- sf_create(sizes = sizeavec_jp, stagenames = stagevec_jp,
binhalfwidth = sizeahbin_jp, repstatus = repvec_jp, obsstatus = obsvec_jp,
indataset = indata_jp, propstatus = propvec_jp, immstatus = immvec_jp,
matstatus = matvec_jp, comments = comments_jp)
jhfv <- verticalize3(data = jreg, noyears = 6, firstyear = 2015,
individcol = "id", blocksize = 8, sizeacol = "lvs.num.2015",
obsacol = "sprouted.2015", repstracol = "flo.tot.2015",
repstrbcol = "frt.tot.2015", fecacol = "flo.tot.2015",
fecbcol = "frt.tot.2015", NAas0 = TRUE, stagesize = "sizea",
stageassign = jp_frame)
surv_model <- glm(alive3 ~ sizea2 + as.factor(year2), data = jhfv, family = "binomial")
obs_data <- subset(jhfv, alive3 == 1)
obs_model <- glm(obsstatus3 ~ as.factor(year2), data = obs_data, family = "binomial")
size_data <- subset(obs_data, obsstatus3 == 1)
size_model <- glm(sizea3 ~ sizea2, data = size_data, family = "poisson")
reps_model <- glm(repstatus3 ~ sizea2, data = size_data, family = "binomial")
fec_data <- subset(jhfv, repstatus2 == 1)
fec_model <- MASS::glm.nb(fec2added ~ 1, data = fec_data)
mod_params <- create_pm(name_terms = TRUE)
mod_params$modelparams[4] <- "alive3"
mod_params$modelparams[5] <- "obsstatus3"
mod_params$modelparams[6] <- "sizea3"
mod_params$modelparams[9] <- "repstatus3"
mod_params$modelparams[11] <- "fec2added"
mod_params$modelparams[12] <- "sizea2"
mod_params$modelparams[18] <- "repstatus2"
jp_germ <- 0.90
jp_supp2 <- supplemental(stage3 = c("Sdl", "Dorm", "V0nr", "V1nr", "P1", "Sdl"),
stage2 = c("P1", "Sdl", "Sdl", "Sdl", "rep", "rep"),
eststage3 = c(NA, NA, NA, NA, NA, NA),
eststage2 = c(NA, NA, NA, NA, NA, NA),
givenrate = c(0.25, 0.35, 0.10, 0.10, NA, NA), # 0.345, 0.054
multiplier = c(NA, NA, NA, NA, jp_germ * 0.5, jp_germ * 0.5),
type = c(1, 1, 1, 1, 3, 3), stageframe = jp_frame, historical = FALSE)
jp_ahmpm <- flefko2(year = "all", stageframe = jp_frame, supplement = jp_supp2,
paramnames = mod_params, surv_model = surv_model, obs_model = obs_model,
size_model = size_model, repst_model = reps_model, fec_model = fec_model,
data = jhfv, err_check = TRUE)
lambda3(jp_ahmpm)
lefko3 documentation built on Sept. 11, 2024, 9:35 p.m.
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| pyrola | R Documentation |
Demographic Dataset of Pyrola japonica and Pyrola subaphylla Populations, in Horizontal Format
Description
A dataset containing the states and fates of Pyrola japonica and Pyrola subaphylla, family Ericaceae, from populations in the vicinity of Mt. Bandai, Fukushima Prefecture, Japan, resulting from monitoring that occurred annually between 2015 and 2020.
Usage
data(pyrola)
Format
A data frame with 454 individuals and 57 variables. Each row
corresponds to an unique individual, and each variable from
sprouted.2015 on refers to the state of the individual in a particular
year.
- species
String denoting which of the two species the individual belongs to.
- population
Integer denoting whcih population the individual belongs to. Synonymous with species in this dataset.
- id
A numeric variable giving a unique number to each individual within each species. Note that numbers are reused among the two species.
- sprouted.2015
A binomial indicating whether the individual had living aboveground tissue observable in the 2015 census.
- lvs.num.2015
Number of leaves in 2015.
- lvs.lng.2015
Length of largest leaf in 2015.
- lvs.wdt.2015
Width of largest leaf in 2015.
- inf.num.2015
Number of inflorescences in 2015.
- inf.lng.tot.2015
Summed inflorescence length in 2015.
- flo.tot.2015
Number of flowers in 2015.
- frt.tot.2015
Number of fruits in 2015.
- sprouted.2016
A binomial indicating whether the individual had living aboveground tissue observable in the 2016 census.
- lvs.num.2016
Number of leaves in 2016.
- lvs.lng.2016
Length of largest leaf in 2016.
- lvs.wdt.2016
Width of largest leaf in 2016.
- inf.num.2016
Number of inflorescences in 2016.
- inf.lng.tot.2016
Summed inflorescence length in 2016.
- flo.tot.2016
Number of flowers in 2016.
- frt.tot.2016
Number of fruits in 2016.
- sprouted.2017
A binomial indicating whether the individual had living aboveground tissue observable in the 2017 census.
- lvs.num.2017
Number of leaves in 2017.
- lvs.lng.2017
Length of largest leaf in 2017.
- lvs.wdt.2017
Width of largest leaf in 2017.
- inf.num.2017
Number of inflorescences in 2017.
- inf.lng.tot.2017
Summed inflorescence length in 2017.
- flo.tot.2017
Number of flowers in 2017.
- frt.tot.2017
Number of fruits in 2017.
- sprouted.2018
A binomial indicating whether the individual had living aboveground tissue observable in the 2018 census.
- lvs.num.2018
Number of leaves in 2018.
- lvs.lng.2018
Length of largest leaf in 2018.
- lvs.wdt.2018
Width of largest leaf in 2018.
- inf.num.2018
Number of inflorescences in 2018.
- inf.lng.tot.2018
Summed inflorescence length in 2018.
- flo.tot.2018
Number of flowers in 2018.
- frt.tot.2018
Number of fruits in 2018.
- sprouted.2019
A binomial indicating whether the individual had living aboveground tissue observable in the 2019 census.
- lvs.num.2019
Number of leaves in 2019.
- lvs.lng.2019
Length of largest leaf in 2019.
- lvs.wdt.2019
Width of largest leaf in 2019.
- inf.num.2019
Number of inflorescences in 2019.
- inf.lng.tot.2019
Summed inflorescence length in 2019.
- flo.tot.2019
Number of flowers in 2019.
- frt.tot.2019
Number of fruits in 2019.
- sprouted.2020
A binomial indicating whether the individual had living aboveground tissue observable in the 2020 census.
- lvs.num.2020
Number of leaves in 2020.
- lvs.lng.2020
Length of largest leaf in 2020.
- lvs.wdt.2020
Width of largest leaf in 2020.
- inf.num.2020
Number of inflorescences in 2020.
- inf.lng.tot.2020
Summed inflorescence length in 2020.
- flo.tot.2020
Number of flowers in 2020.
- frt.tot.2020
Number of fruits in 2020.
Source
Shefferson, R.P., K. Shutoh, and K. Suetsugu. In review. Vegetative dormancy and the evolution of mycoheterotrophy in sister Pyrola species. Journal of Ecology.
Examples
data(pyrola)
pyrola$species <- as.factor(pyrola$species)
pyrola$population <- as.factor(pyrola$population)
jreg <- pyrola[which(pyrola$population == 1),]
stagevec_jp <- c("P1", "Sdl", "Dorm", "V0nr", "V1nr", "V2nr", "V3nr", "V4nr",
"V0r", "V1r", "V2r", "V3r", "V4r")
sizeavec_jp <- c(0, 0, 0, 0, 1, 2, 3, 7, 0, 1, 2, 3, 7)
sizeahbin_jp <- c(0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 3.5, 0.5, 0.5, 0.5, 0.5,
3.5)
repvec_jp <- c(0, 0, 0, 0, rep(0, 4), rep(1, 5))
propvec_jp <- c(1, rep(0, 12))
immvec_jp <- c(1, 1, rep(0, 11))
matvec_jp <- c(0, 0, rep(1, 11))
obsvec_jp <- c(0, 0, 0, rep(1, 10))
indata_jp <- c(0, 0, rep(1, 11))
comments_jp <- c("protocorm", "seedling", "dormant adult", "stump", "1lf nr",
"2lf nr", "3lf nr", "4+lf nr", "0lf r", "1lf r", "2lf r", "3lf r",
"4+lf r")
jp_frame <- sf_create(sizes = sizeavec_jp, stagenames = stagevec_jp,
binhalfwidth = sizeahbin_jp, repstatus = repvec_jp, obsstatus = obsvec_jp,
indataset = indata_jp, propstatus = propvec_jp, immstatus = immvec_jp,
matstatus = matvec_jp, comments = comments_jp)
jhfv <- verticalize3(data = jreg, noyears = 6, firstyear = 2015,
individcol = "id", blocksize = 8, sizeacol = "lvs.num.2015",
obsacol = "sprouted.2015", repstracol = "flo.tot.2015",
repstrbcol = "frt.tot.2015", fecacol = "flo.tot.2015",
fecbcol = "frt.tot.2015", NAas0 = TRUE, stagesize = "sizea",
stageassign = jp_frame)
surv_model <- glm(alive3 ~ sizea2 + as.factor(year2), data = jhfv, family = "binomial")
obs_data <- subset(jhfv, alive3 == 1)
obs_model <- glm(obsstatus3 ~ as.factor(year2), data = obs_data, family = "binomial")
size_data <- subset(obs_data, obsstatus3 == 1)
size_model <- glm(sizea3 ~ sizea2, data = size_data, family = "poisson")
reps_model <- glm(repstatus3 ~ sizea2, data = size_data, family = "binomial")
fec_data <- subset(jhfv, repstatus2 == 1)
fec_model <- MASS::glm.nb(fec2added ~ 1, data = fec_data)
mod_params <- create_pm(name_terms = TRUE)
mod_params$modelparams[4] <- "alive3"
mod_params$modelparams[5] <- "obsstatus3"
mod_params$modelparams[6] <- "sizea3"
mod_params$modelparams[9] <- "repstatus3"
mod_params$modelparams[11] <- "fec2added"
mod_params$modelparams[12] <- "sizea2"
mod_params$modelparams[18] <- "repstatus2"
jp_germ <- 0.90
jp_supp2 <- supplemental(stage3 = c("Sdl", "Dorm", "V0nr", "V1nr", "P1", "Sdl"),
stage2 = c("P1", "Sdl", "Sdl", "Sdl", "rep", "rep"),
eststage3 = c(NA, NA, NA, NA, NA, NA),
eststage2 = c(NA, NA, NA, NA, NA, NA),
givenrate = c(0.25, 0.35, 0.10, 0.10, NA, NA), # 0.345, 0.054
multiplier = c(NA, NA, NA, NA, jp_germ * 0.5, jp_germ * 0.5),
type = c(1, 1, 1, 1, 3, 3), stageframe = jp_frame, historical = FALSE)
jp_ahmpm <- flefko2(year = "all", stageframe = jp_frame, supplement = jp_supp2,
paramnames = mod_params, surv_model = surv_model, obs_model = obs_model,
size_model = size_model, repst_model = reps_model, fec_model = fec_model,
data = jhfv, err_check = TRUE)
lambda3(jp_ahmpm)
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