Fix rogue links

idem-lab · Jul 26, 2024 · 8f616df · 8f616df
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Showing 9 changed files with 38 additions and 29 deletions.
diff --git a/NEWS.md b/NEWS.md
@@ -9,9 +9,9 @@
   * `transmission_probability_matrix()` for creating new transmission probability
   matrices
 
-* there is now a print method for age group information in setting matrices - [#139](https://github.com/njtierney/conmat/issues/139)
+* there is now a print method for age group information in setting matrices - [#139](https://github.com/idem-lab/conmat/issues/139)
 
-* improved age break checking [#138](https://github.com/njtierney/conmat/issues/138)
+* improved age break checking [#138](https://github.com/idem-lab/conmat/issues/138)
 
 * extended `add_school_work_participation()`, `add_modelling_features()`, `fit_single_contact_model()`, `fit_setting_contacts()`, `estimate_setting_contacts()` to use different school and work demographics arguments. (#82 and #15, resolved by #153).
 
@@ -53,14 +53,14 @@
 
 * Added a `NEWS.md` file to track changes to the package.
 * Decouple prediction and estimation of models with `fit_setting_contacts` to 
-  fit models, and `predict_setting_contacts` to predict. Fixes [#7](https://github.com/njtierney/conmat/issues/7)
-* Implement parallelisation with `furrr`. Resolves [#31](https://github.com/njtierney/conmat/issues/31)
+  fit models, and `predict_setting_contacts` to predict. Fixes [#7](https://github.com/idem-lab/conmat/issues/7)
+* Implement parallelisation with `furrr`. Resolves [#31](https://github.com/idem-lab/conmat/issues/31)
 * Change argument of `fit_setting_contacts` from `survey_population` to just `population`
-* Reduce vignette size, closes [#28](https://github.com/njtierney/conmat/issues/28)
-* Add transmission probability data from Eyre et al., closes [#39](https://github.com/njtierney/conmat/issues/39)
-* Add household adjustment - [#41](https://github.com/njtierney/conmat/issues/41)
+* Reduce vignette size, closes [#28](https://github.com/idem-lab/conmat/issues/28)
+* Add transmission probability data from Eyre et al., closes [#39](https://github.com/idem-lab/conmat/issues/39)
+* Add household adjustment - [#41](https://github.com/idem-lab/conmat/issues/41)
 * Added setting weights, related to #44 (but no longer Eyre weights)
-* Added `apply_vaccination` to take in vaccination rates of ages and apply to contact matrices [#40](https://github.com/njtierney/conmat/issues/40)
+* Added `apply_vaccination` to take in vaccination rates of ages and apply to contact matrices [#40](https://github.com/idem-lab/conmat/issues/40)
 * Data from `get_polymod_population` has been revised as a result of the [socialmixr package](https://github.com/epiforecasts/socialmixr/blob/main/NEWS.md) being updated to version 0.2.0, where the world population data has been updated to 2017 by switching from the wpp2015 to wpp2017 package. We have explored the new data and found it to be very similar and should not introduce any errant errors. See the exploration [here](https://gist.github.com/njtierney/4862fa73abab97093d779fa7f2904d11).
 * Added new print methods for: `conmat_setting_prediction_matrix`, `conmat_prediction_matrix`, `ngm_setting_matrix`, `setting_contact_model`, `setting_vaccination_matrix`, and `setting_data`, see #116. Main change is that list objects don't return the entire list and output but a summary of the list contents and details on what that object contains.
 * Added a new S3 method for `conmat_population` to avoid fragile use of the `lower.age.limit` variable name. This resolves #77.
diff --git a/R/data_abs_employ_age_lga.R b/R/data_abs_employ_age_lga.R
@@ -16,7 +16,7 @@
 #'   \item{total}{sum of these totals...or thereabouts??}
 #' }
 #' @note still need to finalise these columns
-#' @source ABS.stat \url{https://stat.data.abs.gov.au/Index.aspx?} LABOUR >
-#'   Employment and Unemployment > Labour force status >
+#' @source ABS.stat \url{https://www.abs.gov.au/statistics} LABOUR >
+#'   Employment and Unemployment > Labour force, Australia >
 #'   Census 2016, G43 labour status by age and sex (LGA)
 "abs_employ_age_lga"
diff --git a/R/data_abs_household_lga.R b/R/data_abs_household_lga.R
@@ -16,6 +16,6 @@
 #'   \item{n_households}{number of households with that number of people}
 #' }
 #' @note still need to clean this
-#' @source  \url{https://stat.data.abs.gov.au/Index.aspx?Datasetcode=ABS_FAMILY_PROJ}
+#' @source  \url{https://www.abs.gov.au/statistics}
 #' (downloaded the CSV) PEOPLE > People and Communities > Household Composition > Census 2016, T23 Household Composition By Number Of Persons Usually Resident (LGA)
 "abs_household_lga"
diff --git a/README.Rmd b/README.Rmd
@@ -17,7 +17,7 @@ knitr::opts_chunk$set(
 
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/idem-lab/conmat/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/idem-lab/conmat/actions/workflows/R-CMD-check.yaml)
-[![Codecov test coverage](https://codecov.io/gh/idem-lab/conmat/branch/master/graph/badge.svg)](https://codecov.io/gh/idem-lab/conmat?branch=master)
+[![Codecov test coverage](https://codecov.io/gh/idem-lab/conmat/branch/master/graph/badge.svg)](https://app.codecov.io/gh/idem-lab/conmat?branch=master)
 <!-- badges: end -->
 
 The goal of conmat is to make it easy to generate synthetic contact matrices for a given age population.

diff --git a/README.md b/README.md
@@ -7,7 +7,7 @@
 
 [![R-CMD-check](https://github.com/idem-lab/conmat/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/idem-lab/conmat/actions/workflows/R-CMD-check.yaml)
 [![Codecov test
-coverage](https://codecov.io/gh/idem-lab/conmat/branch/master/graph/badge.svg)](https://codecov.io/gh/idem-lab/conmat?branch=master)
+coverage](https://codecov.io/gh/idem-lab/conmat/branch/master/graph/badge.svg)](https://app.codecov.io/gh/idem-lab/conmat?branch=master)
 <!-- badges: end -->
 
 The goal of conmat is to make it easy to generate synthetic contact
@@ -133,7 +133,8 @@ contact_model <- fit_single_contact_model(
   contact_data = polymod_contact_data,
   population = polymod_survey_data
 )
-#> Warning in bgam.fit(G, mf, chunk.size, gp, scale, gamma, method = method, : fitted rates numerically 0 occurred
+#> Warning in bgam.fit(G, mf, chunk.size, gp, scale, gamma, method = method, :
+#> algorithm did not converge
 ```
 
 This fits a generalised additive model (GAM), predicting the contact
@@ -152,9 +153,9 @@ contact_model
 #>     school_probability + work_probability + offset(log_contactable_population)
 #> 
 #> Estimated degrees of freedom:
-#> 1.76 4.07 4.67 6.95 7.57 4.90  total = 32.91 
+#> 1.00 4.20 3.60 8.58 7.74 4.80  total = 32.92 
 #> 
-#> fREML score: 24428.78     rank: 55/57
+#> fREML score: 24130.3     rank: 55/57
 ```
 
 We can use this contact model to then predict the contact rate in a new
@@ -208,16 +209,16 @@ synthetic_contact_fairfield
 #> # A tibble: 324 × 3
 #>    age_group_from age_group_to contacts
 #>    <fct>          <fct>           <dbl>
-#>  1 [0,5)          [0,5)         0.00285
-#>  2 [0,5)          [5,10)        0.00309
-#>  3 [0,5)          [10,15)       0.00329
-#>  4 [0,5)          [15,20)       0.00554
-#>  5 [0,5)          [20,25)       0.0132 
-#>  6 [0,5)          [25,30)       0.0263 
-#>  7 [0,5)          [30,35)       0.0358 
-#>  8 [0,5)          [35,40)       0.0374 
-#>  9 [0,5)          [40,45)       0.0353 
-#> 10 [0,5)          [45,50)       0.0322 
+#>  1 [0,5)          [0,5)         0.00124
+#>  2 [0,5)          [5,10)        0.00262
+#>  3 [0,5)          [10,15)       0.00354
+#>  4 [0,5)          [15,20)       0.00604
+#>  5 [0,5)          [20,25)       0.0143 
+#>  6 [0,5)          [25,30)       0.0279 
+#>  7 [0,5)          [30,35)       0.0366 
+#>  8 [0,5)          [35,40)       0.0370 
+#>  9 [0,5)          [40,45)       0.0345 
+#> 10 [0,5)          [45,50)       0.0313 
 #> # ℹ 314 more rows
 ```
 

diff --git a/man/abs_employ_age_lga.Rd b/man/abs_employ_age_lga.Rd
diff --git a/man/abs_household_lga.Rd b/man/abs_household_lga.Rd
diff --git a/man/conmat-package.Rd b/man/conmat-package.Rd
diff --git a/man/figures/README-plot-matrix-differents-1.png b/man/figures/README-plot-matrix-differents-1.png