Merge pull request #3 from Global-Health-Engineering/dev

Correct documentation and bump version to 0.1.0

Author: seawaR

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: fungalgrowth
 Title: Fungal Growth Assay on Human Faeces
-Version: 0.0.0.9000
+Version: 0.1.0
 Authors@R: c(
     person("Jules", "Peter", , "jupeter@ethz.ch", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-1966-1197")),
@@ -22,6 +22,6 @@ Depends:
 LazyData: true
 Language: en-GB
 Config/Needs/website: rmarkdown
-Date: 2026-05-12
-URL: https://github.com/openwashdata/fungalgrowth
-BugReports: https://github.com/openwashdata/fungalgrowth/issues
+Date: 2026-05-15
+URL: https://github.com/Global-Health-Engineering/fungalgrowth
+BugReports: https://github.com/Global-Health-Engineering/fungalgrowth/issues

LICENSE

@@ -45,7 +45,7 @@ You can install the development version of fungalgrowth from
 
 ``` r
 # install.packages("devtools")
-devtools::install_github("openwashdata/fungalgrowth")
+devtools::install_github("global-health-engineering/fungalgrowth")
 ```
 
 ```{r}
@@ -230,7 +230,7 @@ ggplot(fungal_growth, aes(x = dpi, y = area_size, group = id_treatment)) +
 ## License
 
 Data are available as
-[CC-BY](https://github.com/openwashdata/%7B%7B%7Bpackagename%7D%7D%7D/blob/main/LICENSE.md).
+[CC-BY](https://github.com/Global-Health-Engineering/fungalgrowth/blob/main/LICENSE.md).
 
 ## Citation
 

README.Rmd

@@ -24,7 +24,7 @@ You can install the development version of fungalgrowth from
 
 ``` r
 # install.packages("devtools")
-devtools::install_github("openwashdata/fungalgrowth")
+devtools::install_github("global-health-engineering/fungalgrowth")
 ```
 
 ``` r
@@ -81,7 +81,7 @@ experiment_setup |>
   gt::as_raw_html()
 ```
 
-<div id="xdbvyxdswg" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
+<div id="qdrhsbrzmb" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
   &#10;  <table class="gt_table" data-quarto-disable-processing="false" data-quarto-bootstrap="false" style="-webkit-font-smoothing: antialiased; -moz-osx-font-smoothing: grayscale; font-family: system-ui, 'Segoe UI', Roboto, Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol', 'Noto Color Emoji'; display: table; border-collapse: collapse; line-height: normal; margin-left: auto; margin-right: auto; color: #333333; font-size: 16px; font-weight: normal; font-style: normal; background-color: #FFFFFF; width: auto; border-top-style: solid; border-top-width: 2px; border-top-color: #A8A8A8; border-right-style: none; border-right-width: 2px; border-right-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #A8A8A8; border-left-style: none; border-left-width: 2px; border-left-color: #D3D3D3;" bgcolor="#FFFFFF">
   <thead style="border-style: none;">
     <tr class="gt_col_headings" style="border-style: none; border-top-style: solid; border-top-width: 2px; border-top-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3;">
@@ -263,7 +263,7 @@ experiment_endpoint |>
   gt::as_raw_html()
 ```
 
-<div id="xwhedxugju" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
+<div id="rvfihomqfl" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
   &#10;  <table class="gt_table" data-quarto-disable-processing="false" data-quarto-bootstrap="false" style="-webkit-font-smoothing: antialiased; -moz-osx-font-smoothing: grayscale; font-family: system-ui, 'Segoe UI', Roboto, Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol', 'Noto Color Emoji'; display: table; border-collapse: collapse; line-height: normal; margin-left: auto; margin-right: auto; color: #333333; font-size: 16px; font-weight: normal; font-style: normal; background-color: #FFFFFF; width: auto; border-top-style: solid; border-top-width: 2px; border-top-color: #A8A8A8; border-right-style: none; border-right-width: 2px; border-right-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #A8A8A8; border-left-style: none; border-left-width: 2px; border-left-color: #D3D3D3;" bgcolor="#FFFFFF">
   <thead style="border-style: none;">
     <tr class="gt_col_headings" style="border-style: none; border-top-style: solid; border-top-width: 2px; border-top-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3;">
@@ -529,7 +529,7 @@ faecal_measurements |>
   gt::as_raw_html()
 ```
 
-<div id="bnlfmwlniz" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
+<div id="ppcjqsxaej" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
   &#10;  <table class="gt_table" data-quarto-disable-processing="false" data-quarto-bootstrap="false" style="-webkit-font-smoothing: antialiased; -moz-osx-font-smoothing: grayscale; font-family: system-ui, 'Segoe UI', Roboto, Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol', 'Noto Color Emoji'; display: table; border-collapse: collapse; line-height: normal; margin-left: auto; margin-right: auto; color: #333333; font-size: 16px; font-weight: normal; font-style: normal; background-color: #FFFFFF; width: auto; border-top-style: solid; border-top-width: 2px; border-top-color: #A8A8A8; border-right-style: none; border-right-width: 2px; border-right-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #A8A8A8; border-left-style: none; border-left-width: 2px; border-left-color: #D3D3D3;" bgcolor="#FFFFFF">
   <thead style="border-style: none;">
     <tr class="gt_col_headings" style="border-style: none; border-top-style: solid; border-top-width: 2px; border-top-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3;">
@@ -879,7 +879,7 @@ inoculum_species |>
   gt::as_raw_html()
 ```
 
-<div id="waaqcldybd" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
+<div id="diqvvaexwn" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
   &#10;  <table class="gt_table" data-quarto-disable-processing="false" data-quarto-bootstrap="false" style="-webkit-font-smoothing: antialiased; -moz-osx-font-smoothing: grayscale; font-family: system-ui, 'Segoe UI', Roboto, Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol', 'Noto Color Emoji'; display: table; border-collapse: collapse; line-height: normal; margin-left: auto; margin-right: auto; color: #333333; font-size: 16px; font-weight: normal; font-style: normal; background-color: #FFFFFF; width: auto; border-top-style: solid; border-top-width: 2px; border-top-color: #A8A8A8; border-right-style: none; border-right-width: 2px; border-right-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #A8A8A8; border-left-style: none; border-left-width: 2px; border-left-color: #D3D3D3;" bgcolor="#FFFFFF">
   <thead style="border-style: none;">
     <tr class="gt_col_headings" style="border-style: none; border-top-style: solid; border-top-width: 2px; border-top-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3;">
@@ -1003,7 +1003,7 @@ fungal_growth |>
   gt::as_raw_html()
 ```
 
-<div id="wczgtwzymr" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
+<div id="entnskzoya" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
   &#10;  <table class="gt_table" data-quarto-disable-processing="false" data-quarto-bootstrap="false" style="-webkit-font-smoothing: antialiased; -moz-osx-font-smoothing: grayscale; font-family: system-ui, 'Segoe UI', Roboto, Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol', 'Noto Color Emoji'; display: table; border-collapse: collapse; line-height: normal; margin-left: auto; margin-right: auto; color: #333333; font-size: 16px; font-weight: normal; font-style: normal; background-color: #FFFFFF; width: auto; border-top-style: solid; border-top-width: 2px; border-top-color: #A8A8A8; border-right-style: none; border-right-width: 2px; border-right-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #A8A8A8; border-left-style: none; border-left-width: 2px; border-left-color: #D3D3D3;" bgcolor="#FFFFFF">
   <thead style="border-style: none;">
     <tr class="gt_col_headings" style="border-style: none; border-top-style: solid; border-top-width: 2px; border-top-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; border-left-style: none; border-left-width: 1px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 1px; border-right-color: #D3D3D3;">
@@ -1273,8 +1273,12 @@ NA
 
 <td style="text-align:left;">
 
-Coded description of fungal growth at this timepoint; numeric score
-recorded during observation.
+Mycelium health score assessed on a 0-5 scale by a single unblinded
+operator: 0: no visible mycelium, 1: sparse/dying mycelium, 2: patchy
+growth with signs of decline, 3: healthy mycelium covering but with
+clear visible substrate , 4: dense, vigorous mycelium some substrate
+visible, 5: dense mycelium mat without any visible material below the
+mycelium.
 </td>
 
 </tr>
@@ -1306,7 +1310,7 @@ ggplot(fungal_growth, aes(x = dpi, y = area_size, group = id_treatment)) +
 ## License
 
 Data are available as
-[CC-BY](https://github.com/openwashdata/%7B%7B%7Bpackagename%7D%7D%7D/blob/main/LICENSE.md).
+[CC-BY](https://github.com/Global-Health-Engineering/fungalgrowth/blob/main/LICENSE.md).
 
 ## Citation
 
@@ -1318,7 +1322,7 @@ citation("fungalgrowth")
 #> 
 #>   Peter J, Clavijo Daza A (2026). _fungalgrowth: Fungal Growth Assay on
 #>   Human Faeces_. R package version 0.0.0.9000,
-#>   <https://github.com/openwashdata/fungalgrowth>.
+#>   <https://github.com/Global-Health-Engineering/fungalgrowth>.
 #> 
 #> A BibTeX entry for LaTeX users is
 #> 
@@ -1327,6 +1331,6 @@ citation("fungalgrowth")
 #>     author = {Jules Peter and Adriana {Clavijo Daza}},
 #>     year = {2026},
 #>     note = {R package version 0.0.0.9000},
-#>     url = {https://github.com/openwashdata/fungalgrowth},
+#>     url = {https://github.com/Global-Health-Engineering/fungalgrowth},
 #>   }
 ```

README.md

@@ -1,16 +1,16 @@
 
-url: https://github.com/openwashdata/fungalgrowth
+url: https://github.com/Global-Health-Engineering/fungalgrowth
 template:
   bootstrap: 5
   includes:
     in_header: |
-      <script defer data-domain="openwashdata.github.io" src="https://plausible.io/js/script.js"></script>
+      <script defer data-domain="global-health-engineering.github.io" src="https://plausible.io/js/script.js"></script>
 
 home:
   links:
     - icon: github
       text: GitHub repository
-      href: https://github.com/openwashdata/fungalgrowth
+      href: https://github.com/Global-Health-Engineering/fungalgrowth
   sidebar:
     structure: [links, citation, authors, dev]