differences for PR #139

Author: actions-user

.DS_Store

@@ -248,13 +248,6 @@ contact_data <- socialmixr::contact_matrix(
   age.limits = c(0, 20, 40),
   symmetric = TRUE
 )
-```
-
-``` output
-Removing participants that have contacts without age information. To change this behaviour, set the 'missing.contact.age' option
-```
-
-``` r
 # prepare contact matrix
 contact_matrix <- t(contact_data$matrix)
 

compare-interventions.md

@@ -98,8 +98,16 @@ contact_data <- socialmixr::contact_matrix(
 )
 ```
 
-``` output
-Removing participants that have contacts without age information. To change this behaviour, set the 'missing.contact.age' option
+``` warning
+Warning: The `age.limits` argument of `contact_matrix()` is deprecated as of socialmixr
+1.0.0.
+ℹ Please use the `age_limits` argument instead.
+ℹ The deprecated feature was likely used in the socialmixr package.
+  Please report the issue at
+  <https://github.com/epiforecasts/socialmixr/issues>.
+This warning is displayed once per session.
+Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
+generated.
 ```
 
 ``` r
@@ -226,12 +234,11 @@ contact_data_zambia <- socialmixr::contact_matrix(
 )
 ```
 
-``` output
-Removing participants without age information. To change this behaviour, set the 'missing.participant.age' option
-```
-
-``` output
-Removing participants that have contacts without age information. To change this behaviour, set the 'missing.contact.age' option
+``` warning
+Warning: Survey contains multiple observations per participant (4531 rows, 3576 unique
+participants).
+• Results will aggregate across all observations.
+ℹ Use `filter` to select by "Building_id".
 ```
 
 ``` r
@@ -243,8 +250,8 @@ contact_data_zambia
 $matrix
          contact.age.group
 age.group   [0,20)      20+
-   [0,20) 3.650000 1.451168
-   20+    1.988136 2.461856
+   [0,20) 3.766393 1.427100
+   20+    1.955162 2.642584
 
 $demography
    age.group population proportion  year
@@ -255,8 +262,8 @@ $demography
 $participants
    age.group participants proportion
       <char>        <int>      <num>
-1:    [0,20)          180 0.08490566
-2:       20+         1940 0.91509434
+1:    [0,20)          244 0.08531469
+2:       20+         2616 0.91468531
 ```
 
 ``` r

config.yaml

@@ -93,7 +93,21 @@ contact_data <- socialmixr::contact_matrix(
   age.limits = c(0, 20, 40),
   symmetric = TRUE
 )
+```
+
+``` warning
+Warning: The `age.limits` argument of `contact_matrix()` is deprecated as of socialmixr
+1.0.0.
+ℹ Please use the `age_limits` argument instead.
+ℹ The deprecated feature was likely used in the socialmixr package.
+  Please report the issue at
+  <https://github.com/epiforecasts/socialmixr/issues>.
+This warning is displayed once per session.
+Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
+generated.
+```
 
+``` r
 # prepare contact matrix
 contact_matrix <- t(contact_data$matrix)
 

contact-matrices.md

@@ -1,19 +1,19 @@
 "file" "checksum" "built" "date"
-"CODE_OF_CONDUCT.md" "549f00b0992a7743c2bc16ea6ce3db57" "site/built/CODE_OF_CONDUCT.md" "2026-01-09"
-"LICENSE.md" "14377518ee654005a18cf28549eb30e3" "site/built/LICENSE.md" "2026-01-09"
-"config.yaml" "a0c04c1d43ce0640c3ea333b140e89c8" "site/built/config.yaml" "2026-01-09"
-"index.md" "32bc80d6f4816435cc0e01540cb2a513" "site/built/index.md" "2026-01-09"
-"links.md" "8184cf4149eafbf03ce8da8ff0778c14" "site/built/links.md" "2026-01-09"
-"episodes/contact-matrices.Rmd" "9e9d596cf25f68a50522b15a234472ac" "site/built/contact-matrices.md" "2026-01-09"
-"episodes/simulating-transmission.Rmd" "539a63b7a617e7a40ad1c5dd9650d96f" "site/built/simulating-transmission.md" "2026-01-09"
-"episodes/model-choices.Rmd" "aa195e66455fb6a97b4930fd08c08001" "site/built/model-choices.md" "2026-01-09"
-"episodes/modelling-interventions.Rmd" "8b9d77d31ac2672f4278b780e3d943db" "site/built/modelling-interventions.md" "2026-01-09"
-"episodes/compare-interventions.Rmd" "2ef6697bbad9bcfb843ab9d50469123b" "site/built/compare-interventions.md" "2026-01-09"
-"episodes/vaccine-comparisons.Rmd" "bb9110b17b2b5cdc915df3f17eae15df" "site/built/vaccine-comparisons.md" "2026-01-09"
-"episodes/disease-burden.Rmd" "9deead362349c98be8f1d9380a7b975a" "site/built/disease-burden.md" "2026-01-09"
-"instructors/instructor-notes.md" "ca3834a1b0f9e70c4702aa7a367a6bb5" "site/built/instructor-notes.md" "2026-01-09"
-"learners/BF_measles.Rmd" "5725a25d664730bbce3736a3243c2182" "site/built/BF_measles.md" "2026-01-09"
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-"renv/profiles/lesson-requirements/renv.lock" "3a4dd221fcee1f60beb9e679efeae403" "site/built/renv.lock" "2026-01-09"
+"CODE_OF_CONDUCT.md" "549f00b0992a7743c2bc16ea6ce3db57" "site/built/CODE_OF_CONDUCT.md" "2026-02-03"
+"LICENSE.md" "14377518ee654005a18cf28549eb30e3" "site/built/LICENSE.md" "2026-02-03"
+"config.yaml" "a0c04c1d43ce0640c3ea333b140e89c8" "site/built/config.yaml" "2026-02-03"
+"index.md" "32bc80d6f4816435cc0e01540cb2a513" "site/built/index.md" "2026-02-03"
+"links.md" "8184cf4149eafbf03ce8da8ff0778c14" "site/built/links.md" "2026-02-03"
+"episodes/contact-matrices.Rmd" "9e9d596cf25f68a50522b15a234472ac" "site/built/contact-matrices.md" "2026-02-03"
+"episodes/simulating-transmission.Rmd" "539a63b7a617e7a40ad1c5dd9650d96f" "site/built/simulating-transmission.md" "2026-02-03"
+"episodes/model-choices.Rmd" "aa195e66455fb6a97b4930fd08c08001" "site/built/model-choices.md" "2026-02-03"
+"episodes/modelling-interventions.Rmd" "8b9d77d31ac2672f4278b780e3d943db" "site/built/modelling-interventions.md" "2026-02-03"
+"episodes/compare-interventions.Rmd" "2ef6697bbad9bcfb843ab9d50469123b" "site/built/compare-interventions.md" "2026-02-03"
+"episodes/vaccine-comparisons.Rmd" "bb9110b17b2b5cdc915df3f17eae15df" "site/built/vaccine-comparisons.md" "2026-02-03"
+"episodes/disease-burden.Rmd" "9deead362349c98be8f1d9380a7b975a" "site/built/disease-burden.md" "2026-02-03"
+"instructors/instructor-notes.md" "ca3834a1b0f9e70c4702aa7a367a6bb5" "site/built/instructor-notes.md" "2026-02-03"
+"learners/BF_measles.Rmd" "5725a25d664730bbce3736a3243c2182" "site/built/BF_measles.md" "2026-02-03"
+"learners/reference.md" "9e836f1ec999f95f55135cdd2c78d2e6" "site/built/reference.md" "2026-02-03"
+"learners/setup.md" "be1de7ec41f52f14d00bcb74e87b5046" "site/built/setup.md" "2026-02-03"
+"profiles/learner-profiles.md" "31b503c4b5bd1f0960ada730eca4a25e" "site/built/learner-profiles.md" "2026-02-03"
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disease-burden.md

@@ -94,7 +94,21 @@ cm_results <- socialmixr::contact_matrix(
   age.limits = c(0, 15, 65),
   symmetric = TRUE
 )
+```
+
+``` warning
+Warning: The `age.limits` argument of `contact_matrix()` is deprecated as of socialmixr
+1.0.0.
+ℹ Please use the `age_limits` argument instead.
+ℹ The deprecated feature was likely used in the socialmixr package.
+  Please report the issue at
+  <https://github.com/epiforecasts/socialmixr/issues>.
+This warning is displayed once per session.
+Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
+generated.
+```
 
+``` r
 # transpose contact matrix
 cm_matrix <- t(cm_results$matrix)