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60 changes: 28 additions & 32 deletions docs/rtm_chl_analysis_perc_flow_pulse.html
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<meta name="author" content="Dave Bosworth" />

<meta name="date" content="2023-09-27" />
<meta name="date" content="2024-02-28" />

<title>NDFS Synthesis Manuscript: Chlorophyll analysis</title>

Expand Down Expand Up @@ -1584,7 +1584,7 @@ <h1 class="title toc-ignore">NDFS Synthesis Manuscript: Chlorophyll
<h3 class="subtitle">Explore relationship with daily average percent
flow pulse water</h3>
<h4 class="author">Dave Bosworth</h4>
<h4 class="date">September 27, 2023</h4>
<h4 class="date">February 28, 2024</h4>

</div>

Expand Down Expand Up @@ -1612,37 +1612,37 @@ <h1>Global code and functions</h1>
<pre><code>## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 4.2.3 (2023-03-15 ucrt)
## os Windows 10 x64 (build 19044)
## os Windows 10 x64 (build 19045)
## system x86_64, mingw32
## ui RTerm
## language (EN)
## collate English_United States.utf8
## ctype English_United States.utf8
## tz America/Los_Angeles
## date 2023-09-27
## date 2024-02-28
## pandoc 3.1.1 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
##
## ─ Packages ───────────────────────────────────────────────────────────────────
## package * version date (UTC) lib source
## bslib 0.4.2 2022-12-16 [1] CRAN (R 4.2.2)
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Expand All @@ -1653,8 +1653,8 @@ <h1>Global code and functions</h1>
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Expand All @@ -1664,37 +1664,37 @@ <h1>Global code and functions</h1>
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## yaml 2.3.7 2023-01-23 [1] CRAN (R 4.2.2)
Expand All @@ -1709,25 +1709,21 @@ <h1>Import Data</h1>
<pre class="r"><code># Define file path for processed data
fp_data &lt;- here(&quot;manuscript_synthesis/data/processed&quot;)

# Import daily average chlorophyll data
df_chla &lt;- readRDS(file.path(fp_data, &quot;chla_wt_daily_avg_2013-2019.rds&quot;)) %&gt;% select(-WaterTemp)

# Import daily average water quality data
df_wq &lt;- readRDS(file.path(fp_data, &quot;wq_daily_avg_2013-2019.rds&quot;))
# Import daily average percent flow pulse water data
df_pfp &lt;- readRDS(file.path(fp_data, &quot;perc_flow_pulse_daily_avg_2016-2019.rds&quot;))</code></pre>
</div>
<div id="prepare-data" class="section level1">
<h1>Prepare Data</h1>
<pre class="r"><code># Create a vector for the factor order of StationCode
sta_order &lt;- c(
&quot;LIS&quot;,
&quot;STTD&quot;,
&quot;LIB&quot;,
&quot;RYI&quot;,
&quot;RVB&quot;
)
sta_order &lt;- c(&quot;LIS&quot;, &quot;STTD&quot;, &quot;LIB&quot;, &quot;RYI&quot;, &quot;RVB&quot;)

# Prepare chlorophyll and percent flow pulse water data for exploration and analysis
df_chla_c &lt;- df_chla %&gt;%
df_chla_c &lt;- df_wq %&gt;%
select(StationCode, Date, Chla) %&gt;%
drop_na(Chla) %&gt;%
# Join flow data to chlorophyll data
left_join(df_pfp, by = join_by(StationCode, Date)) %&gt;%
# Remove all NA flow values
Expand All @@ -1738,7 +1734,7 @@ <h1>Prepare Data</h1>
# Apply factor order to StationCode
StationCode = factor(StationCode, levels = sta_order),
# Convert percent flow pulse water values to proportions so they scale
# correctly with scales::label_percent()
# correctly with scales::label_percent()
PercFlowPulseAvg = PercFlowPulseAvg / 100
) %&gt;%
arrange(StationCode, Date)</code></pre>
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81 changes: 39 additions & 42 deletions docs/rtm_chl_gam_categorical_initial.html
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40 changes: 21 additions & 19 deletions docs/rtm_chl_model_final.html
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Expand Up @@ -11,7 +11,7 @@

<meta name="author" content="Dave Bosworth" />

<meta name="date" content="2024-02-01" />
<meta name="date" content="2024-02-29" />

<title>NDFS Synthesis Manuscript: Chlorophyll analysis</title>

Expand Down Expand Up @@ -1583,7 +1583,7 @@ <h1 class="title toc-ignore">NDFS Synthesis Manuscript: Chlorophyll
analysis</h1>
<h3 class="subtitle">Final results from selected model</h3>
<h4 class="author">Dave Bosworth</h4>
<h4 class="date">February 01, 2024</h4>
<h4 class="date">February 29, 2024</h4>

</div>

Expand Down Expand Up @@ -1625,7 +1625,7 @@ <h1>Global code and functions</h1>
## collate English_United States.utf8
## ctype English_United States.utf8
## tz America/Los_Angeles
## date 2024-02-01
## date 2024-02-29
## pandoc 3.1.1 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
##
## ─ Packages ───────────────────────────────────────────────────────────────────
Expand All @@ -1635,27 +1635,27 @@ <h1>Global code and functions</h1>
## bslib 0.4.2 2022-12-16 [1] CRAN (R 4.2.2)
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## hms 1.1.3 2023-03-21 [1] CRAN (R 4.2.3)
Expand All @@ -1667,7 +1667,7 @@ <h1>Global code and functions</h1>
## knitr 1.42 2023-01-25 [1] CRAN (R 4.2.2)
## later 1.3.0 2021-08-18 [1] CRAN (R 4.2.1)
## lattice 0.21-8 2023-04-05 [1] CRAN (R 4.2.3)
## lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.2.1)
## lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.2.3)
## lubridate * 1.9.3 2023-09-27 [1] CRAN (R 4.2.3)
## magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.1)
## MASS * 7.3-58.2 2023-01-23 [2] CRAN (R 4.2.3)
Expand All @@ -1692,9 +1692,9 @@ <h1>Global code and functions</h1>
## purrr * 1.0.2 2023-08-10 [1] CRAN (R 4.2.3)
## R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.1)
## Rcpp 1.0.11 2023-07-06 [1] CRAN (R 4.2.3)
## readr * 2.1.4 2023-02-10 [1] CRAN (R 4.2.2)
## readr * 2.1.5 2024-01-10 [1] CRAN (R 4.2.3)
## remotes 2.4.2 2021-11-30 [1] CRAN (R 4.2.1)
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## rlang 1.1.3 2024-01-10 [1] CRAN (R 4.2.3)
## rmarkdown 2.21 2023-03-26 [1] CRAN (R 4.2.3)
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## rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.1)
Expand All @@ -1703,21 +1703,21 @@ <h1>Global code and functions</h1>
## scales * 1.2.1 2022-08-20 [1] CRAN (R 4.2.1)
## sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.1)
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## stringi 1.7.12 2023-01-11 [1] CRAN (R 4.2.2)
## stringr * 1.5.0 2022-12-02 [1] CRAN (R 4.2.2)
## stringi 1.8.3 2023-12-11 [1] CRAN (R 4.2.3)
## stringr * 1.5.1 2023-11-14 [1] CRAN (R 4.2.3)
## survival * 3.5-5 2023-03-12 [1] CRAN (R 4.2.3)
## TH.data * 1.1-2 2023-04-17 [1] CRAN (R 4.2.3)
## tibble * 3.2.1 2023-03-20 [1] CRAN (R 4.2.3)
## tidyr * 1.3.0 2023-01-24 [1] CRAN (R 4.2.2)
## tidyr * 1.3.1 2024-01-24 [1] CRAN (R 4.2.3)
## tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.2.1)
## tidyverse * 2.0.0 2023-02-22 [1] CRAN (R 4.2.2)
## timechange 0.2.0 2023-01-11 [1] CRAN (R 4.2.2)
## timechange 0.3.0 2024-01-18 [1] CRAN (R 4.2.3)
## tzdb 0.4.0 2023-05-12 [1] CRAN (R 4.2.3)
## urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.2.1)
## usethis 2.1.6 2022-05-25 [1] CRAN (R 4.2.1)
## utf8 1.2.3 2023-01-31 [1] CRAN (R 4.2.2)
## vctrs 0.6.3 2023-06-14 [1] CRAN (R 4.2.3)
## withr 2.5.1 2023-09-26 [1] CRAN (R 4.2.3)
## vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.2.3)
## withr 3.0.0 2024-01-16 [1] CRAN (R 4.2.3)
## xfun 0.39 2023-04-20 [1] CRAN (R 4.2.3)
## xtable 1.8-4 2019-04-21 [1] CRAN (R 4.2.1)
## yaml 2.3.7 2023-01-23 [1] CRAN (R 4.2.2)
Expand All @@ -1733,8 +1733,8 @@ <h1>Import Data</h1>
<pre class="r"><code># Define file path for processed data
fp_data &lt;- here(&quot;manuscript_synthesis/data/processed&quot;)

# Import weekly average chlorophyll data
df_chla &lt;- readRDS(file.path(fp_data, &quot;chla_wt_week_avg_2013-2019.rds&quot;)) %&gt;% select(-WaterTemp)
# Import weekly average water quality data
df_wq &lt;- readRDS(file.path(fp_data, &quot;wq_week_avg_2013-2019.rds&quot;))

# Import weekly average flow data
df_flow &lt;- readRDS(file.path(fp_data, &quot;flow_week_avg_2013-2019.rds&quot;))</code></pre>
Expand All @@ -1748,7 +1748,9 @@ <h1>Prepare Data</h1>
df_flow_c &lt;- df_flow %&gt;% mutate(StationCode = if_else(StationCode == &quot;LIS&quot;, &quot;STTD&quot;, StationCode))

# Prepare chlorophyll and flow data for analysis
df_chla_c &lt;- df_chla %&gt;%
df_chla_c &lt;- df_wq %&gt;%
select(StationCode, Year, Week, Chla) %&gt;%
drop_na(Chla) %&gt;%
# Filter to only include representative stations for 4 habitat types (RD22,
# STTD, LIB, RVB) and only include years 2015-2019
filter(
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