diff --git a/articles/how-to-run-ITHIM.html b/articles/how-to-run-ITHIM.html index 649cdae9..140923e8 100644 --- a/articles/how-to-run-ITHIM.html +++ b/articles/how-to-run-ITHIM.html @@ -107,11 +107,11 @@

Cloning the Github repositoryhttps://github.com/ITHIM/ITHIM-R.git’

-

+

To change to the Bogota branch for which this guide was written, navigate to the ITHIM-R folder within the command window, then type:

‘git checkout bogota’

-

+

The Github repository has now been downloaded to your computer and the working branch has been set to the Bogota branch which is the branch this documentation refers to.

@@ -127,7 +127,7 @@

Installing the package in RStudio1.) If Git has been installed then the there should be a ‘Build’ tab in the top right hand corner of RStudio. Click on this tab and then on ‘Install’ in the panel below it.

-

+

This will install the ITHIM-R package but it will also most likely initially throw an error message ‘Exited with status 1’ stating that some other R packages that are needed for the ITHIM-R package have not @@ -135,7 +135,7 @@

Installing the package in RStudio -

+

Once all missing R packages have been installed, go back to the ‘Build’ tab and install the ITHIM-R package again. It should now install smoothly.

@@ -150,14 +150,14 @@

Installing the package in RStudio -

+

Finally, you will also have to install the ‘drpa’ package from Github (drpa) by first installing the ‘remotes’ package as explained above and then by typing

remotes::install_github(“meta-analyses/drpa”)

into the RStudio console.

-

+

@@ -176,7 +176,7 @@

Update input parameters
City specific files @@ -197,7 +198,7 @@
City specific files(example +

Travel survey (example trips dataset). A table of all trips taken by a group of people on a given day. It also includes people who take no trips. This data should come from an official travel survey for the city where possible.

@@ -211,9 +212,9 @@
City specific files(example injuries -dataset). A table of recorded road-traffic injury (fatality) events -in a city during one or more years.

+

Injury events (example +injuries dataset). A table of recorded road-traffic injury +(fatality) events in a city during one or more years.

  • One row per event
  • Minimal columns: victim mode @@ -226,10 +227,10 @@
    City specific files(example burden -dataset). This gives the burden of disease for different diseases. -If no city specific information exists, country level information can be -used.

    +

    Disease burden data (example +burden dataset). This gives the burden of disease for different +diseases. If no city specific information exists, country level +information can be used.

    • One row per disease/metric/age/gender combination
    • Minimal rows: Measure (death/YLL); @@ -240,7 +241,7 @@
      City specific files(example +

      Population of city (example population dataset). This information is used to scale the Burden of Disease data to the city’s population in question.

        @@ -255,10 +256,10 @@
        City specific files(example physical -activity dataset). This is used to represent the physical activity -levels in the city and should be taken from an official physical -activity survey of the city where possible.

        +

        Physical activity survey (example +physical activity dataset). This is used to represent the physical +activity levels in the city and should be taken from an official +physical activity survey of the city where possible.

        @@ -313,7 +314,7 @@

        Call multi_city_script.R

        Once these parameter values have been updated, click on ‘Source’ and the model should run.

        -

        +

        It produces pop-up windows showing the plots of the results giving the years of life lost for each scenario and required disease outcome.

        @@ -330,7 +331,7 @@

        Results -

        +

        The health effects of ITHIM are presented as years of life lost (YLLs) and number of attributable deaths. The background burden data for the study areas are estimated from the Global Burden of diff --git a/index.html b/index.html index 7f180a71..99c41e30 100644 --- a/index.html +++ b/index.html @@ -77,7 +77,7 @@

        Website for the package

        How to use the package

        -

        We have written a how-to guide that explains how to install the ITHIM-R package, how to run the model ITHIM-Global model using this package and how to produce summaries of the key results. Please read it here: how to run ITHIM?

        +

        We have written a how-to guide that explains how to install the ITHIM-R package, how to run the ITHIM-Global model using this package and how to produce summaries of the key results. Please read it here: how to run ITHIM?

        Citation

        @@ -118,8 +118,8 @@

        CO2 EmissionsHealth outcomes

        The health effects of ITHIM are presented as years of life lost (YLLs) and number of attributable deaths. Background burden data for study areas are estimated from Global Burden of Disease studies.

        -
        -Model Layout
        Model Layout
        +
        +

        Model Layout

        diff --git a/license.html b/license.html index c6b6d508..6d7f63e8 100644 --- a/license.html +++ b/license.html @@ -217,27 +217,27 @@

        17. Interpretation of Sectio

        How to Apply These Terms to Your New Programs

        If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms.

        To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively state the exclusion of warranty; and each file should have at least the “copyright” line and a pointer to where the full notice is found.

        -
        <one line to give the program's name and a brief idea of what it does.>
-Copyright (C) <year>  <name of author>
-
-This program is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program.  If not, see <http://www.gnu.org/licenses/>.
        +
        <one line to give the program's name and a brief idea of what it does.>
+Copyright (C) <year>  <name of author>
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.

        Also add information on how to contact you by electronic and paper mail.

        If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode:

        -
        <program>  Copyright (C) <year>  <name of author>
-This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'.
-This is free software, and you are welcome to redistribute it
-under certain conditions; type 'show c' for details.
        +
        <program>  Copyright (C) <year>  <name of author>
+This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'.
+This is free software, and you are welcome to redistribute it
+under certain conditions; type 'show c' for details.

        The hypothetical commands show w and show c should show the appropriate parts of the General Public License. Of course, your program’s commands might be different; for a GUI interface, you would use an “about box”.

        You should also get your employer (if you work as a programmer) or school, if any, to sign a “copyright disclaimer” for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see <http://www.gnu.org/licenses/>.

        The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read <http://www.gnu.org/philosophy/why-not-lgpl.html>.

        diff --git a/pkgdown.yml b/pkgdown.yml index 3d0bdb8a..eb88b250 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -1,9 +1,9 @@ -pandoc: 3.1.1 +pandoc: 2.19.2 pkgdown: 2.0.7 pkgdown_sha: ~ articles: how-to-run-ITHIM: how-to-run-ITHIM.html -last_built: 2023-11-22T14:39Z +last_built: 2023-11-23T07:45Z urls: reference: https://ithim.github.io/ITHIM-R/reference article: https://ithim.github.io/ITHIM-R/articles diff --git a/reference/distances_for_injury_function.html b/reference/distances_for_injury_function.html index 22eedcc9..0edd0119 100644 --- a/reference/distances_for_injury_function.html +++ b/reference/distances_for_injury_function.html @@ -108,11 +108,11 @@

        Details

      • A new list (injuries_list) is created containing all strike and casualty mode and age and sex combinations - together with strike and casualty mode distances (add_distance_columns.R) for the baseline and all scenarios. For + together with strike and casualty mode distances (add_distance_columns()) for the baseline and all scenarios. For the whw model, any strike mode and casualty pairs where strike mode equals casualty mode are removed as fatalities for these combinations have already been added to the nov matrix. Combinations which do not have a non-zero strike or casualty mode distance - are also removed. - This list will later be used in the injuries_function_2.R function + are also removed. This list will later be used in the injuries_function_2() function to predict fatality counts using the Poisson injury regression model.

      • The casualty and strike mode exponents used to account for the safety in number effect are added to both the injuries_for_model and injuries_list.

        • diff --git a/reference/gen_ap_rr.html b/reference/gen_ap_rr.html index 49724d51..fed80cb1 100644 --- a/reference/gen_ap_rr.html +++ b/reference/gen_ap_rr.html @@ -81,7 +81,7 @@

        Details

      • loop through the scenarios:

diff --git a/reference/get_all_distances.html b/reference/get_all_distances.html index ec6da4cc..718c47a3 100644 --- a/reference/get_all_distances.html +++ b/reference/get_all_distances.html @@ -76,7 +76,7 @@

Value

Details

This function performs the following steps: