/
README.Rmd
106 lines (72 loc) · 4.27 KB
/
README.Rmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
---
output: github_document
bibliography: vignettes\\references.bib
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
devtools::load_all()
library(DemoKin)
library(knitr)
```
# DemoKin
:::::::::::::: {.columns}
::: {.column width="60%"}
`DemoKin` uses matrix demographic methods to compute expected (average) kin counts from demographic rates under a range of scenarios and assumptions. The package is an R-language implementation of Caswell [-@caswell_formal_2019; -@caswell_formal_2020; -@caswell_formal_2022], and Caswell and Song [-@caswell_formal_2021]. It draws on previous theoretical development by Goodman, Keyfitz and Pullum [-@goodman_family_1974].
:::
::: {.column width="40%"}
<img src="man/figures/DemoKin-Logo.png" align="right" width="200" />
:::
::::::::::::::
## Installation
Download the stable version [from CRAN](https://cran.r-project.org/web/packages/DemoKin/):
``` {r, eval=FALSE, include = T}
install.packages("DemoKin")
```
Or you can install the development version from GitHub:
``` {r, eval=FALSE}
# install.packages("devtools")
devtools::install_github("IvanWilli/DemoKin")
```
## Usage
Consider an average Swedish woman called 'Focal.' For this exercise, we assume a female closed population in which everyone experiences the Swedish 2015 mortality and fertility rates at each age throughout their life; i.e., the 'time-invariant' assumption in Caswell [-@caswell_formal_2019].
We then ask:
> What is the expected number of relatives of Focal over her life course?
Let's explore this using the Swedish data already included with `DemoKin`.
```{r, fig.height=6, fig.width=8, message=FALSE, warning=FALSE}
library(DemoKin)
swe_surv_2015 <- swe_px[,"2015"]
swe_asfr_2015 <- swe_asfr[,"2015"]
swe_2015 <- kin(p = swe_surv_2015, f = swe_asfr_2015, time_invariant = TRUE)
```
*p* is the survival probability by age from a life table and *f* are the age specific fertility ratios by age (see `?kin` for details).
Now, we can visualize the implied kin counts (i.e., the average number of living kin) of Focal at age 35 using a network or 'Keyfitz' kinship diagram with the function `plot_diagram`:
```{r, fig.height=6, dpi=1200,fig.width=8, message=FALSE, warning=FALSE}
# We need to reformat the data a little bit
kin_total <- swe_2015$kin_summary
# Keep only data for Focal's age 35
kin_total <- kin_total[kin_total$age_focal == 35 , c("kin", "count_living")]
names(kin_total) <- c("kin", "count")
plot_diagram(kin_total, rounding = 2)
```
Relatives are identified by a unique code:
```{r, fig.height=6, fig.width=8, echo=FALSE}
# kable(DemoKin::demokin_codes[,c("DemoKin", "Labels_2sex")])
kable(DemoKin::demokin_codes[,-c(2)])
```
## Vignette
For more details, including an extension to time-variant rates, deceased kin, and multi-state models in a one-sex framework, see the [Reference_OneSex](https://cran.r-project.org/web/packages/DemoKin/vignettes/Reference_OneSex.html) vignette; also accessible from DemoKin: `vignette("Reference_OneSex", package = "DemoKin")`. For two-sex models, see the [Reference_TwoSex](https://cran.r-project.org/web/packages/DemoKin/vignettes/Reference_TwoSex.html) vignette; also accessible from DemoKin: `vignette("Reference_TwoSex", package = "DemoKin")`.
If the vignette does not load, you may need to install the package as `devtools::install_github("IvanWilli/DemoKin", build_vignettes = T)`.
## Citation
Williams, Iván; Alburez-Gutierrez, Diego; Song, Xi; and Hal Caswell. (2021) DemoKin: An R package to implement demographic matrix kinship models. URL: https://github.com/IvanWilli/DemoKin.
## Acknowledgments
We thank Silvia Leek from the Max Planck Institute for Demographic Research for designing the DemoKin logo. The logo includes elements that have been taken or adapted [from this file](https://commons.wikimedia.org/wiki/File:Escudo_de_la_Orden_de_San_Jer%C3%B3nimo.svg), originally by Ansunando, [CC BY-SA 4.0](https://creativecommons.org/licenses/by-sa/4.0) via Wikimedia Commons. Sha Jiang provided useful comments for improving the package.
## Get involved!
`DemoKin` is under constant development.
If you're interested in contributing, please get in touch, create an issue, or submit a pull request.
We look forward to hearing from you!
## References