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README.Rmd

@@ -17,10 +17,10 @@ knitr::opts_chunk$set(
 
 # Dcifer: Genetic Distance Between Polyclonal Infections
 
-![](man/figures/aqua10f.png)<!-- -->
-
 Package `dcifer` (Distance for Complex Infections: Fast Estimation of Relatedness) calculates genetic distance between polyclonal infections by estimating relatedness from biallelic and multiallelic data @gerlovina2022dcifer. In addition to estimates, the package provides a likelihood function and statistical inference. Functions for reading and reformatting data, performing preparatory steps, and visualizing the results are also included. We will illustrate the analysis process using microhaplotype data from two health facilities in Maputo and Inhambane provinces of Mozambique @tessema2022sensitive.
 
+![](man/figures/aqua10f.png)<!-- -->
+
 You can install the released version of dcifer from [CRAN](https://CRAN.R-project.org) with:
 
 ``` r
@@ -314,5 +314,7 @@ text(mean(CI), yCI + 0.05*diff(llrng), "confidence interval", col = cols[3])
 text(res2$rhat - 0.025, yLR, "MLE", col = cols[3], srt = 90)
 par(pardef)
 ```
-
+<center>
+![](man/figures/logo.svg){width=18%} 
+</center>
 

README.md

@@ -3,8 +3,6 @@
 
 # Dcifer: Genetic Distance Between Polyclonal Infections
 
-![](man/figures/aqua10f.png)<!-- -->
-
 Package `dcifer` (Distance for Complex Infections: Fast Estimation of
 Relatedness) calculates genetic distance between polyclonal infections
 by estimating relatedness from biallelic and multiallelic data \[1\]. In
@@ -15,6 +13,8 @@ included. We will illustrate the analysis process using microhaplotype
 data from two health facilities in Maputo and Inhambane provinces of
 Mozambique \[2\].
 
+![](man/figures/aqua10f.png)<!-- -->
+
 You can install the released version of dcifer from
 [CRAN](https://CRAN.R-project.org) with:
 
@@ -419,6 +419,10 @@ text(res2$rhat - 0.025, yLR, "MLE", col = cols[3], srt = 90)
 par(pardef)
 ```
 
+<center>
+<img src="man/figures/logo.svg" style="width:18.0%" />
+</center>
+
 <div id="refs" class="references csl-bib-body">
 
 <div id="ref-gerlovina2022dcifer" class="csl-entry">

vignettes/vignetteDcifer.Rmd

@@ -1,5 +1,5 @@
 ---
-title: "Dcifer: Genetic Distance Between Polyclonal Infections"
+title: "Dcifer: Genetic Distance Between Polyclonal Infections "
 output: rmarkdown::pdf_document
 vignette: >
   %\VignetteIndexEntry{vignetteDcifer}